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<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_9f700962877a340cb515a8f4e78fa50c.html">TRANSFORMATIONS</a></li><li class="navelem"><a class="el" href="dir_37e9c1b52d0b253b62f883ccdf65930c.html">FEATUREFINDER</a></li><li class="navelem"><a class="el" href="dir_85426f95c54d3036067585334ac23a8c.html">SUPERHIRN</a></li> </ul>
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<div class="title">MS2Fragment.h</div> </div>
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<a href="MS2Fragment_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_MS2FRAGMENT_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_MS2FRAGMENT_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="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</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"><a class="line" href="classOpenMS_1_1MS2Fragment.html"> 59</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a></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="l00064"></a><span class="lineno"> 64</span>  <span class="comment">// declaration of the private members:</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> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="comment">// declaration of the public members:</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">// AMRT tag</span></div>
<div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#ac5b7a45b97e2838a2f716fec5b5debe0"> 72</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#ac5b7a45b97e2838a2f716fec5b5debe0">precursorMZ</a>;</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#ac4c908426d75fa4b3d4b0730ec640d7a"> 73</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#ac4c908426d75fa4b3d4b0730ec640d7a">precursorCHRG</a>;</div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#af6d5ab3629ea17ec17a1733f29f8a0d9"> 74</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#af6d5ab3629ea17ec17a1733f29f8a0d9">TR</a>;</div>
<div class="line"><a name="l00075"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a3536194dd1e8de94daf7e3a0ab288a48"> 75</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a3536194dd1e8de94daf7e3a0ab288a48">scan</a>;</div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a14f94e529dff0b8bfba8e16fbe9755d6"> 76</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a14f94e529dff0b8bfba8e16fbe9755d6">z</a>;</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a586cc81cc21e09854e9a1c0b55117c7b"> 78</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a586cc81cc21e09854e9a1c0b55117c7b">fragmentMZ</a>;</div>
<div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a9c3ea56b27e2166a26b7174605d2c6bd"> 79</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a9c3ea56b27e2166a26b7174605d2c6bd">intensityArea</a>;</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="comment">// scan and TR ranges:</span></div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#aae2cc135047973e28bd78a7f2d0fa4fc"> 82</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#aae2cc135047973e28bd78a7f2d0fa4fc">scanStart</a>;</div>
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a014fb5708d57185015ca24a5813c594d"> 83</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a014fb5708d57185015ca24a5813c594d">scanEnd</a>;</div>
<div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a4b463620f6b640d3fcfbde846db2e0fd"> 84</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a4b463620f6b640d3fcfbde846db2e0fd">trStart</a>;</div>
<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a390ce6b825a2580badce7d0103ea1e83"> 85</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a390ce6b825a2580badce7d0103ea1e83">trEnd</a>;</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> </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a6ffde16bc29cbbf7060d3e7c6e3725f7"> 90</a></span>  <span class="keyword">static</span> <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a6ffde16bc29cbbf7060d3e7c6e3725f7">OutlierAttribute</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 destructor</span></div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  ~<a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a>();</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">// constructor for the object MS2Fragment:</span></div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a>(<span class="keywordtype">double</span> iPrecursorMZ, <span class="keywordtype">int</span> iPrecursorCHRG, <span class="keywordtype">double</span> iTR, <span class="keywordtype">int</span> iScan, <span class="keywordtype">int</span> iZ, <span class="keywordtype">double</span> iFragmentMZ, <span class="keywordtype">double</span> iIntensityArea,</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordtype">int</span> iScanStart, <span class="keywordtype">int</span> iScanEnd, <span class="keywordtype">double</span> iTrStart, <span class="keywordtype">double</span> iTrEnd);</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a>(<span class="keywordtype">double</span> iPrecursorMZ, <span class="keywordtype">int</span> iPrecursorCHRG, <span class="keywordtype">double</span> iTR, <span class="keywordtype">int</span> iScan, <span class="keywordtype">int</span> iZ, <span class="keywordtype">double</span> iFragmentMZ, <span class="keywordtype">double</span> iIntensityArea);</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </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"><a class="line" href="classOpenMS_1_1MS2Fragment.html#aa72c3184cb52aa0af84b9c1c0154acf1"> 102</a></span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html#aa72c3184cb52aa0af84b9c1c0154acf1">MS2Fragment</a>() {}</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="comment">// class copy constructor</span></div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> &);</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="comment">// class copy constructor</span></div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> *);</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>  <span class="comment">// show info of the MS2 fragment</span></div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordtype">void</span> show_info();</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">// get the attribute of the fragment</span></div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="comment">// according to which outliers are removed</span></div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordtype">double</span> getOutlierDetectionAttribute();</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> </div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="comment">// overload operators:</span></div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> &);</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keywordtype">bool</span> operator==(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> &);</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> & operator<=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> &);</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> & operator>=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> &);</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> & operator<(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> &);</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> & operator>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html">MS2Fragment</a> &);</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span> </div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="comment">// start here all the get / set</span></div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="comment">// function to access the</span></div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="comment">// variables of the class</span></div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="comment">// get hte averaged precurso mass:</span></div>
<div class="line"><a name="l00133"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#af454969bce509d6ccbead8d122e3275f"> 133</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#af454969bce509d6ccbead8d122e3275f">getPrecursorMZ</a>(){ <span class="keywordflow">return</span> precursorMZ; }</div>
<div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a0e7de5e2eb348bfde5a920a8db3652a6"> 134</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a0e7de5e2eb348bfde5a920a8db3652a6">setPrecursorMZ</a>(<span class="keywordtype">double</span> iMZ){ precursorMZ = iMZ; }</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="comment">// get hte averaged precurso chrg:</span></div>
<div class="line"><a name="l00136"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a5fea4977a4d998e56a963728b3a8343a"> 136</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a5fea4977a4d998e56a963728b3a8343a">getPrecursorCHRG</a>(){ <span class="keywordflow">return</span> precursorCHRG; }</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="comment">// retention time:</span></div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a1f42ac65106ca909c7f6ec30a4dcb914"> 138</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a1f42ac65106ca909c7f6ec30a4dcb914">getTR</a>(){<span class="keywordflow">return</span> TR; }</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="comment">// start TR:</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#ad2059c92b90989921be291156cae6d66"> 140</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#ad2059c92b90989921be291156cae6d66">getStartTR</a>(){<span class="keywordflow">return</span> trStart; }</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="comment">// end TR:</span></div>
<div class="line"><a name="l00142"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#ad275baa611d6c9bf0e1f1275e407a33d"> 142</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#ad275baa611d6c9bf0e1f1275e407a33d">getEndTR</a>(){<span class="keywordflow">return</span> trEnd; }</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="comment">// get the Fragment MZ:</span></div>
<div class="line"><a name="l00144"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#af9e2769173902e66ef15b698f86d0948"> 144</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#af9e2769173902e66ef15b698f86d0948">getFragmentMz</a>(){<span class="keywordflow">return</span> fragmentMZ; }</div>
<div class="line"><a name="l00145"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a77c725f43226c4eb63a4921b2a7e9721"> 145</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a77c725f43226c4eb63a4921b2a7e9721">setFragmentMz</a>(<span class="keywordtype">double</span> iMz){fragmentMZ = iMz; }</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="comment">// get teh charge state:</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a28718522979732337ece5f39132d7cb8"> 147</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a28718522979732337ece5f39132d7cb8">getCHRG</a>(){<span class="keywordflow">return</span> z; }</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="comment">// get the apex scan:</span></div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a4f4c019219138d6bcc2cc5bbd576a772"> 149</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a4f4c019219138d6bcc2cc5bbd576a772">getApexScan</a>(){<span class="keywordflow">return</span> scan; }</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="comment">// get the apex scan:</span></div>
<div class="line"><a name="l00151"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a40ff9a78a344d0b49f95fca034205a99"> 151</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a40ff9a78a344d0b49f95fca034205a99">getStartScan</a>(){<span class="keywordflow">return</span> scanStart; }</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="comment">// get the apex scan:</span></div>
<div class="line"><a name="l00153"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a637c645784fce9d2fbde29e4162f7f75"> 153</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a637c645784fce9d2fbde29e4162f7f75">getEndScan</a>(){<span class="keywordflow">return</span> scanEnd; }</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="comment">// get the integrated peak area:</span></div>
<div class="line"><a name="l00156"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a665740e914da82b584063fa0f88b1e4b"> 156</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a665740e914da82b584063fa0f88b1e4b">getFragmentPeakArea</a>(){<span class="keywordflow">return</span> intensityArea; }</div>
<div class="line"><a name="l00157"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2Fragment.html#a51f42ff1c23d4f6d2943ecf399cc0a32"> 157</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MS2Fragment.html#a51f42ff1c23d4f6d2943ecf399cc0a32">setFragmentPeakArea</a>(<span class="keywordtype">double</span> iIntens){intensityArea = iIntens; }</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> </div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  };</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> </div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span> } <span class="comment">// ns</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="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MS2FRAGMENT_H</span></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a51f42ff1c23d4f6d2943ecf399cc0a32"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a51f42ff1c23d4f6d2943ecf399cc0a32">OpenMS::MS2Fragment::setFragmentPeakArea</a></div><div class="ttdeci">void setFragmentPeakArea(double iIntens)</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:157</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_1MS2Fragment_html_af9e2769173902e66ef15b698f86d0948"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#af9e2769173902e66ef15b698f86d0948">OpenMS::MS2Fragment::getFragmentMz</a></div><div class="ttdeci">double getFragmentMz()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a14f94e529dff0b8bfba8e16fbe9755d6"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a14f94e529dff0b8bfba8e16fbe9755d6">OpenMS::MS2Fragment::z</a></div><div class="ttdeci">int z</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_ad275baa611d6c9bf0e1f1275e407a33d"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#ad275baa611d6c9bf0e1f1275e407a33d">OpenMS::MS2Fragment::getEndTR</a></div><div class="ttdeci">double getEndTR()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:142</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a637c645784fce9d2fbde29e4162f7f75"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a637c645784fce9d2fbde29e4162f7f75">OpenMS::MS2Fragment::getEndScan</a></div><div class="ttdeci">int getEndScan()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:153</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_aa72c3184cb52aa0af84b9c1c0154acf1"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#aa72c3184cb52aa0af84b9c1c0154acf1">OpenMS::MS2Fragment::MS2Fragment</a></div><div class="ttdeci">MS2Fragment()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:102</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a390ce6b825a2580badce7d0103ea1e83"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a390ce6b825a2580badce7d0103ea1e83">OpenMS::MS2Fragment::trEnd</a></div><div class="ttdeci">double trEnd</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:85</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a665740e914da82b584063fa0f88b1e4b"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a665740e914da82b584063fa0f88b1e4b">OpenMS::MS2Fragment::getFragmentPeakArea</a></div><div class="ttdeci">double getFragmentPeakArea()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:156</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a5fea4977a4d998e56a963728b3a8343a"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a5fea4977a4d998e56a963728b3a8343a">OpenMS::MS2Fragment::getPrecursorCHRG</a></div><div class="ttdeci">int getPrecursorCHRG()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:136</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a4f4c019219138d6bcc2cc5bbd576a772"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a4f4c019219138d6bcc2cc5bbd576a772">OpenMS::MS2Fragment::getApexScan</a></div><div class="ttdeci">int getApexScan()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:149</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a6ffde16bc29cbbf7060d3e7c6e3725f7"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a6ffde16bc29cbbf7060d3e7c6e3725f7">OpenMS::MS2Fragment::OutlierAttribute</a></div><div class="ttdeci">static int OutlierAttribute</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a77c725f43226c4eb63a4921b2a7e9721"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a77c725f43226c4eb63a4921b2a7e9721">OpenMS::MS2Fragment::setFragmentMz</a></div><div class="ttdeci">void setFragmentMz(double iMz)</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:145</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a9c3ea56b27e2166a26b7174605d2c6bd"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a9c3ea56b27e2166a26b7174605d2c6bd">OpenMS::MS2Fragment::intensityArea</a></div><div class="ttdeci">double intensityArea</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_ac5b7a45b97e2838a2f716fec5b5debe0"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#ac5b7a45b97e2838a2f716fec5b5debe0">OpenMS::MS2Fragment::precursorMZ</a></div><div class="ttdeci">double precursorMZ</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a3536194dd1e8de94daf7e3a0ab288a48"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a3536194dd1e8de94daf7e3a0ab288a48">OpenMS::MS2Fragment::scan</a></div><div class="ttdeci">int scan</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a586cc81cc21e09854e9a1c0b55117c7b"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a586cc81cc21e09854e9a1c0b55117c7b">OpenMS::MS2Fragment::fragmentMZ</a></div><div class="ttdeci">double fragmentMZ</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a40ff9a78a344d0b49f95fca034205a99"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a40ff9a78a344d0b49f95fca034205a99">OpenMS::MS2Fragment::getStartScan</a></div><div class="ttdeci">int getStartScan()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:151</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a014fb5708d57185015ca24a5813c594d"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a014fb5708d57185015ca24a5813c594d">OpenMS::MS2Fragment::scanEnd</a></div><div class="ttdeci">int scanEnd</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:83</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a1f42ac65106ca909c7f6ec30a4dcb914"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a1f42ac65106ca909c7f6ec30a4dcb914">OpenMS::MS2Fragment::getTR</a></div><div class="ttdeci">double getTR()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:138</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_aae2cc135047973e28bd78a7f2d0fa4fc"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#aae2cc135047973e28bd78a7f2d0fa4fc">OpenMS::MS2Fragment::scanStart</a></div><div class="ttdeci">int scanStart</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:82</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_ac4c908426d75fa4b3d4b0730ec640d7a"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#ac4c908426d75fa4b3d4b0730ec640d7a">OpenMS::MS2Fragment::precursorCHRG</a></div><div class="ttdeci">int precursorCHRG</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_ad2059c92b90989921be291156cae6d66"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#ad2059c92b90989921be291156cae6d66">OpenMS::MS2Fragment::getStartTR</a></div><div class="ttdeci">double getStartTR()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:140</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_af454969bce509d6ccbead8d122e3275f"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#af454969bce509d6ccbead8d122e3275f">OpenMS::MS2Fragment::getPrecursorMZ</a></div><div class="ttdeci">double getPrecursorMZ()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:133</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a28718522979732337ece5f39132d7cb8"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a28718522979732337ece5f39132d7cb8">OpenMS::MS2Fragment::getCHRG</a></div><div class="ttdeci">int getCHRG()</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:147</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_af6d5ab3629ea17ec17a1733f29f8a0d9"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#af6d5ab3629ea17ec17a1733f29f8a0d9">OpenMS::MS2Fragment::TR</a></div><div class="ttdeci">double TR</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:74</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_1MS2Fragment_html_a4b463620f6b640d3fcfbde846db2e0fd"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a4b463620f6b640d3fcfbde846db2e0fd">OpenMS::MS2Fragment::trStart</a></div><div class="ttdeci">double trStart</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1MS2Fragment_html_a0e7de5e2eb348bfde5a920a8db3652a6"><div class="ttname"><a href="classOpenMS_1_1MS2Fragment.html#a0e7de5e2eb348bfde5a920a8db3652a6">OpenMS::MS2Fragment::setPrecursorMZ</a></div><div class="ttdeci">void setPrecursorMZ(double iMZ)</div><div class="ttdef"><b>Definition:</b> MS2Fragment.h:134</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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