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<a href="LCMS_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_LCMS_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_LCMS_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 <string></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">#include <map></span></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> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> {</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div>
<div class="line"><a name="l00055"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html"> 55</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</a></div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  {</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="comment">// declaration of the private members:</span></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> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="comment">// name of the spectra:</span></div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a70117048428b9c3ccf886c8ef770656e"> 64</a></span>  std::string <a class="code" href="classOpenMS_1_1LCMS.html#a70117048428b9c3ccf886c8ef770656e">spec_name</a>;</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="comment">// vector of object feature:</span></div>
<div class="line"><a name="l00067"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#aaa50dfe26a64481418eba7b4e4c41d88"> 67</a></span>  std::vector<SHFeature> <a class="code" href="classOpenMS_1_1LCMS.html#aaa50dfe26a64481418eba7b4e4c41d88">feature_list</a>;</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="comment">// a unique specrum id to identify a spectrum:</span></div>
<div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a049052f4f63f906d3e5884bbf4cc6ef0"> 70</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCMS.html#a049052f4f63f906d3e5884bbf4cc6ef0">spectrum_id</a>;</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="comment">// MASTER RUN ID:</span></div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a9817411f20f7f8f2b1143ddd1af71f6f"> 73</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCMS.html#a9817411f20f7f8f2b1143ddd1af71f6f">MASTER_ID</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="comment">// the LC-MS raw data names and their IDs</span></div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#aa9a3ceeb8749addce3de62f4b0ca612e"> 76</a></span>  std::map<int, std::string> <a class="code" href="classOpenMS_1_1LCMS.html#aa9a3ceeb8749addce3de62f4b0ca612e">raw_spec_names</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"> 78</span>  <span class="comment">// alignment error:</span></div>
<div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a7d7ac4e8df8fa9177f7184c42f3aa7cd"> 79</a></span>  std::map<double, std::pair<double, double> > <a class="code" href="classOpenMS_1_1LCMS.html#a7d7ac4e8df8fa9177f7184c42f3aa7cd">ALIGNMENT_ERROR</a>;</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="comment">// declaration of the public members:</span></div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#aba74e58aaedfcbe9016fe489a47238f0"> 86</a></span>  <span class="keyword">static</span> <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCMS.html#aba74e58aaedfcbe9016fe489a47238f0">MINIMAL_PEP_PROPHET_THERSHOLD</a>;</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> <span class="comment">// static double PEP_PROPHET_THERSHOLD;</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_1LCMS.html">LCMS</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_1LCMS.html">LCMS</a>(std::string);</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</a>();</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="comment">// copy constructor</span></div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</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">// copy constructor</span></div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</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">// show the content of the spectra</span></div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordtype">void</span> show_info();</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> </div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="comment">// copy constructor:</span></div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LCMS.html">LCMS</a> &);</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="comment">// sort the features according their parent mass:</span></div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="keywordtype">void</span> order_by_mass();</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="comment">// function to compare the feature mass:</span></div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordtype">float</span> compare_feature_mass(<span class="keyword">const</span> <span class="keywordtype">void</span> *, <span class="keyword">const</span> <span class="keywordtype">void</span> *);</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> </div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="comment">// this structure provides the function to compare</span></div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="comment">// in the sorting algorithm:</span></div>
<div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="structOpenMS_1_1LCMS_1_1OPERATOR__MZ.html"> 115</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1LCMS_1_1OPERATOR__MZ.html">OPERATOR_MZ</a></div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  {</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="comment">// provide the compare function for sort:</span></div>
<div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="structOpenMS_1_1LCMS_1_1OPERATOR__MZ.html#ad27555d4794d405fef85395fa09387b3"> 118</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1LCMS_1_1OPERATOR__MZ.html#ad27555d4794d405fef85395fa09387b3">operator()</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</a> A, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</a> B)<span class="keyword"> const</span></div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="comment">// check if they have same mass</span></div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordflow">if</span> (A.<a class="code" href="classOpenMS_1_1SHFeature.html#acf9cc8b997b6cb4566cadf85c1c527d4">MONO_MZ</a> == B.<a class="code" href="classOpenMS_1_1SHFeature.html#acf9cc8b997b6cb4566cadf85c1c527d4">MONO_MZ</a>)</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  {</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keywordflow">return</span> A.<a class="code" href="classOpenMS_1_1SHFeature.html#af6d5ab3629ea17ec17a1733f29f8a0d9">TR</a> < B.<a class="code" href="classOpenMS_1_1SHFeature.html#af6d5ab3629ea17ec17a1733f29f8a0d9">TR</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>  <span class="keywordflow">else</span></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>  <span class="keywordflow">return</span> A.<a class="code" href="classOpenMS_1_1SHFeature.html#acf9cc8b997b6cb4566cadf85c1c527d4">MONO_MZ</a> < B.<a class="code" href="classOpenMS_1_1SHFeature.html#acf9cc8b997b6cb4566cadf85c1c527d4">MONO_MZ</a>;</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  }</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  }</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </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> </div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="comment">// this structure provides the function to compare</span></div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="comment">// in the sorting algorithm:</span></div>
<div class="line"><a name="l00135"></a><span class="lineno"><a class="line" href="structOpenMS_1_1LCMS_1_1OPERATOR__FeatureCompare.html"> 135</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1LCMS_1_1OPERATOR__FeatureCompare.html">OPERATOR_FeatureCompare</a></div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  {</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="comment">// provide the compare function for sort:</span></div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="structOpenMS_1_1LCMS_1_1OPERATOR__FeatureCompare.html#ad27555d4794d405fef85395fa09387b3"> 138</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1LCMS_1_1OPERATOR__FeatureCompare.html#ad27555d4794d405fef85395fa09387b3">operator()</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</a> A, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</a> B)<span class="keyword"> const</span></div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="comment">// check if they have same mass</span></div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keywordflow">if</span> (A.<a class="code" href="classOpenMS_1_1SHFeature.html#a4b490cc4b4c5b509e03b5e4743724cdb">feature_ID</a> == B.<a class="code" href="classOpenMS_1_1SHFeature.html#a4b490cc4b4c5b509e03b5e4743724cdb">feature_ID</a>)</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  {</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  }</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  {</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordflow">return</span> <span class="keyword">false</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> </div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  };</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>  <span class="comment">// tag the feature with the spectrum id:</span></div>
<div class="line"><a name="l00154"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a2615876a9806c412d4d258537994a860"> 154</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#a2615876a9806c412d4d258537994a860">tag_peaks_with_spectrum_ID</a>()</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  {</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  std::vector<SHFeature>::iterator p = feature_list.begin();</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="keywordflow">while</span> (p != feature_list.end())</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>  (*p).set_spectrum_ID(get_spectrum_ID());</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  p++;</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>  }</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">// count the number of common peaks of a given number of LC-MS:</span></div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordtype">int</span> get_nb_common_peaks(<span class="keywordtype">int</span>);</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="comment">// start here all the get / set</span></div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="comment">// function to access the</span></div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="comment">// variables of the class</span></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>  <span class="comment">// get the whole feature list:</span></div>
<div class="line"><a name="l00173"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a18b9e84a938c4d197eea7bf6d56e5f91"> 173</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#a18b9e84a938c4d197eea7bf6d56e5f91">clear_feature_list</a>()</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  { <span class="keywordflow">return</span> feature_list.clear(); }</div>
<div class="line"><a name="l00175"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#ae49ef4258713ae66236ef4f955753255"> 175</a></span>  std::vector<SHFeature> <a class="code" href="classOpenMS_1_1LCMS.html#ae49ef4258713ae66236ef4f955753255">get_feature_list</a>()</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  { <span class="keywordflow">return</span> feature_list; }</div>
<div class="line"><a name="l00177"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a4269cf98ed173ae2cec9cfd156b74dee"> 177</a></span>  std::vector<SHFeature> * <a class="code" href="classOpenMS_1_1LCMS.html#a4269cf98ed173ae2cec9cfd156b74dee">get_feature_list_reference</a>()</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  { <span class="keywordflow">return</span> &feature_list; }</div>
<div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#ae7b27617696a8b097d00bbb3c5b1aa70"> 179</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1LCMS.html#ae7b27617696a8b097d00bbb3c5b1aa70">check_feature_list_empty</a>()</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  { <span class="keywordflow">return</span> feature_list.empty(); }</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="comment">// access end /start of list:</span></div>
<div class="line"><a name="l00183"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a8130b14a036e42230641337965ac02bd"> 183</a></span>  std::vector<SHFeature>::iterator <a class="code" href="classOpenMS_1_1LCMS.html#a8130b14a036e42230641337965ac02bd">get_feature_list_begin</a>()</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  { <span class="keywordflow">return</span> feature_list.begin(); }</div>
<div class="line"><a name="l00185"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a5a2d53d9393b2dd85b047f5cf262b4f4"> 185</a></span>  std::vector<SHFeature>::iterator <a class="code" href="classOpenMS_1_1LCMS.html#a5a2d53d9393b2dd85b047f5cf262b4f4">get_feature_list_end</a>()</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  { <span class="keywordflow">return</span> feature_list.end(); }</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> </div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="comment">// add a new feature to the list:</span></div>
<div class="line"><a name="l00189"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#ad54ee79a5a849bfe2b24d22fafdfa139"> 189</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#ad54ee79a5a849bfe2b24d22fafdfa139">add_feature</a>(<a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</a> * IN)</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  {</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> </div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="keywordflow">if</span> (IN-><a class="code" href="classOpenMS_1_1SHFeature.html#a9859dad25e54a0f0c6754fbf8697dcea">get_feature_ID</a>() == -1)</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>  IN-><a class="code" href="classOpenMS_1_1SHFeature.html#ab89d41ecea95fdfe48a60fb13470610a">set_feature_ID</a>((<span class="keywordtype">int</span>) feature_list.size());</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  }</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  feature_list.push_back(*IN);</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  IN = <a class="code" href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>;</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  }</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span> </div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="comment">// remove a feature from the LC/MS run by ID:</span></div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keywordtype">void</span> remove_feature_by_ID(<a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</a> *);</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="keywordtype">void</span> remove_feature_by_ID(<span class="keywordtype">int</span>);</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <span class="comment">// remove a feature from teh LC/MS run:</span></div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keywordtype">void</span> remove_feature(<a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</a> *);</div>
<div class="line"><a name="l00205"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#ae607d69f3e7ad0243eba857adfe5eab4"> 205</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#ae607d69f3e7ad0243eba857adfe5eab4">remove_feature</a>(<span class="keywordtype">int</span> i)</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  {</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="keywordflow">if</span> (i < <span class="keywordtype">int</span>(feature_list.size()))</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  {</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  feature_list.erase(feature_list.begin() + i);</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  }</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  }</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> </div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  <span class="comment">// remove a feature by iterator and return the iterator to the next element</span></div>
<div class="line"><a name="l00214"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a0e13e305681f6be0b5f944b348b991b5"> 214</a></span>  std::vector<SHFeature>::iterator <a class="code" href="classOpenMS_1_1LCMS.html#a0e13e305681f6be0b5f944b348b991b5">remove_feature_from_list</a>(std::vector<SHFeature>::iterator IN)</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  { <span class="keywordflow">return</span> feature_list.erase(IN); }</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span> </div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="comment">// get number of feature added:</span></div>
<div class="line"><a name="l00218"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a37fe7e2ab6407008caf5066c8059d07a"> 218</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCMS.html#a37fe7e2ab6407008caf5066c8059d07a">get_nb_features</a>()</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  { <span class="keywordflow">return</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>) feature_list.size(); }</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span> </div>
<div class="line"><a name="l00221"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a5b9dcf6bcbadffbcd4717c378d28332a"> 221</a></span>  std::string <a class="code" href="classOpenMS_1_1LCMS.html#a5b9dcf6bcbadffbcd4717c378d28332a">get_spec_name</a>()</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  { <span class="keywordflow">return</span> spec_name; }</div>
<div class="line"><a name="l00223"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#ac8140cda9f8c984fdd4ac852b349015e"> 223</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#ac8140cda9f8c984fdd4ac852b349015e">set_spec_name</a>(std::string IN)</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  { spec_name = IN; }</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span> </div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <span class="comment">// set / get spectrum id:</span></div>
<div class="line"><a name="l00227"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a30d75220b3fb99ea3b48f7f8098105e8"> 227</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCMS.html#a30d75220b3fb99ea3b48f7f8098105e8">get_spectrum_ID</a>()</div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  { <span class="keywordflow">return</span> spectrum_id; }</div>
<div class="line"><a name="l00229"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#ae7a1a66bf017082d76cf96c65310faf3"> 229</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#ae7a1a66bf017082d76cf96c65310faf3">set_spectrum_ID</a>(<span class="keywordtype">int</span> IN)</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  { spectrum_id = IN; }</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span> </div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="comment">// set the id of all features</span></div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <span class="keywordtype">void</span> setFeatureLCMSID();</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span> </div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="comment">// search the list of feature for the one with input ID:</span></div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <a class="code" href="classOpenMS_1_1SHFeature.html">SHFeature</a> * find_feature_by_ID(<span class="keywordtype">int</span>);</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span> </div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="comment">// access the raw data names:</span></div>
<div class="line"><a name="l00239"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a0594367083652d030fc378ca10e3f759"> 239</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#a0594367083652d030fc378ca10e3f759">remove_raw_spec_name</a>(<span class="keywordtype">int</span> ID)</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  { raw_spec_names.erase(ID); }</div>
<div class="line"><a name="l00241"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a6ac2db2287b5133555895597d19408a6"> 241</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#a6ac2db2287b5133555895597d19408a6">add_raw_spec_name</a>(<span class="keywordtype">int</span> ID, std::string name)</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  { raw_spec_names.insert(make_pair(ID, name)); }</div>
<div class="line"><a name="l00243"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#ac4ab0746d6c0228e36102f7d688b3a81"> 243</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1LCMS.html#ac4ab0746d6c0228e36102f7d688b3a81">check_raw_spec_name_empty</a>()</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  { <span class="keywordflow">return</span> raw_spec_names.empty(); }</div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a22d16dc75350a30c9ea7522543728406"> 245</a></span>  std::map<int, std::string>::iterator <a class="code" href="classOpenMS_1_1LCMS.html#a22d16dc75350a30c9ea7522543728406">get_raw_spec_name_start</a>()</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  { <span class="keywordflow">return</span> raw_spec_names.begin(); }</div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#ad0cfbfed1b3126635dfcc16368be113f"> 247</a></span>  std::map<int, std::string>::iterator <a class="code" href="classOpenMS_1_1LCMS.html#ad0cfbfed1b3126635dfcc16368be113f">get_raw_spec_name_end</a>()</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  { <span class="keywordflow">return</span> raw_spec_names.end(); }</div>
<div class="line"><a name="l00249"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a073655c23df39c4dc538b4e23a655d91"> 249</a></span>  std::map<int, std::string> <a class="code" href="classOpenMS_1_1LCMS.html#a073655c23df39c4dc538b4e23a655d91">get_raw_spec_name_map</a>()</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  { <span class="keywordflow">return</span> raw_spec_names; }</div>
<div class="line"><a name="l00251"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a309a40b5c8ea9bdf2140cf193543ff44"> 251</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCMS.html#a309a40b5c8ea9bdf2140cf193543ff44">get_nb_raw_specs</a>()</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  { <span class="keywordflow">return</span> (<span class="keywordtype">int</span>) raw_spec_names.size(); }</div>
<div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a57071f9a75b2acfe03539c18a1a97ba1"> 253</a></span>  std::string <a class="code" href="classOpenMS_1_1LCMS.html#a57071f9a75b2acfe03539c18a1a97ba1">get_raw_spec_name</a>(<span class="keywordtype">int</span> ID)</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  {</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  std::map<int, std::string>::iterator p = raw_spec_names.find(ID);</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keywordflow">if</span> (p == raw_spec_names.end())</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  {</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <span class="keywordflow">return</span> <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  }</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <span class="keywordflow">return</span> (*p).second;</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  }</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span> </div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="comment">// compare the LC/MS runs names</span></div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="keywordtype">bool</span> check_LCMS_name(std::string);</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span> </div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="comment">// check if this LC/MS ID is present in the raw LC/MS runs</span></div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keywordtype">bool</span> find_LC_MS_by_ID(<span class="keywordtype">int</span>);</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span> </div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="comment">// add the raw spectrum map:</span></div>
<div class="line"><a name="l00270"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#af262b2edcfb4150cc0e6a8c164950854"> 270</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#af262b2edcfb4150cc0e6a8c164950854">add_raw_spec_name_map</a>(std::map<int, std::string> IN)</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  {</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  std::map<int, std::string>::iterator p = IN.begin();</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="keywordflow">while</span> (p != IN.end())</div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  {</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  <span class="keywordtype">int</span> ID = (*p).first;</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  std::map<int, std::string>::iterator <a class="code" href="namespaceOpenMS_1_1Constants.html#a480d6423b1e9ca40c69c5a83458b49b0">F</a> = raw_spec_names.find(ID);</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="keywordflow">if</span> (F != raw_spec_names.end())</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  {</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  ID += (int) raw_spec_names.size();</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  }</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  raw_spec_names.insert(make_pair(ID, (*p).second));</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  p++;</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  }</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  }</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span> </div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="comment">// counts the number of ms features, which contain MS2 info:</span></div>
<div class="line"><a name="l00287"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a54e5e1ec2a920217fe46d1ba752c2ae5"> 287</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCMS.html#a54e5e1ec2a920217fe46d1ba752c2ae5">get_nb_identified_features</a>()</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  {</div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  <span class="keywordtype">int</span> count = 0;</div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  std::vector<SHFeature>::iterator P = get_feature_list_begin();</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <span class="keywordflow">while</span> (P != get_feature_list_end())</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  {</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="keywordflow">if</span> ((*P).get_MS2_info())</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  count++;</div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  P++;</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  }</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="keywordflow">return</span> count;</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  }</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span> </div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <span class="comment">// counts the number of ms features, which contain MS2 info (no thresholding)</span></div>
<div class="line"><a name="l00301"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#aacec49d7ffbee606a2dc750acd6d3967"> 301</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCMS.html#aacec49d7ffbee606a2dc750acd6d3967">get_nb_identified_features</a>(<span class="keywordtype">double</span> PepProb_T)</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  {</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  <span class="keywordtype">int</span> count = 0;</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  std::vector<SHFeature>::iterator P = get_feature_list_begin();</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <span class="keywordflow">while</span> (P != get_feature_list_end())</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  {</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <span class="keywordflow">if</span> ((*P).get_MS2_info(PepProb_T))</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  count++;</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  P++;</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  }</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keywordflow">return</span> count;</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  }</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span> </div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  <span class="comment">// access the alignment error:</span></div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  <span class="comment">// save an error:</span></div>
<div class="line"><a name="l00317"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a7185157195b5d65d84fcebe23ca38f82"> 317</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#a7185157195b5d65d84fcebe23ca38f82">add_alignment_error</a>(<span class="keywordtype">double</span> TR, <span class="keywordtype">double</span> ERROR_UP, <span class="keywordtype">double</span> ERROR_DOWN)</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  {</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  std::pair<double, double> tmp(ERROR_UP, ERROR_DOWN);</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  ALIGNMENT_ERROR.insert(std::pair<<span class="keywordtype">double</span>, std::pair<double, double> >(TR, tmp));</div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  }</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span> </div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  <span class="comment">// get alignment error at specific TR:</span></div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keywordtype">void</span> get_alignment_error(<span class="keywordtype">double</span>, <span class="keywordtype">double</span> *, <span class="keywordtype">double</span> *);</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span> </div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="comment">// access MASTER run ID:</span></div>
<div class="line"><a name="l00327"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#ad439ff344eee2c26ba2bd79d0c0f5ed9"> 327</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCMS.html#ad439ff344eee2c26ba2bd79d0c0f5ed9">set_MASTER_ID</a>(<span class="keywordtype">int</span> IN)</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  { MASTER_ID = IN; }</div>
<div class="line"><a name="l00329"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCMS.html#a2332cb7b192f2b3196169f873afb2842"> 329</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCMS.html#a2332cb7b192f2b3196169f873afb2842">get_MASTER_ID</a>()</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  { <span class="keywordflow">return</span> MASTER_ID; }</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  };</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span> </div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span> }</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span> </div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span> <span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCMS_H</span></div>
<div class="ttc" id="structOpenMS_1_1LCMS_1_1OPERATOR__MZ_html"><div class="ttname"><a href="structOpenMS_1_1LCMS_1_1OPERATOR__MZ.html">OpenMS::LCMS::OPERATOR_MZ</a></div><div class="ttdef"><b>Definition:</b> LCMS.h:115</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a30d75220b3fb99ea3b48f7f8098105e8"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a30d75220b3fb99ea3b48f7f8098105e8">OpenMS::LCMS::get_spectrum_ID</a></div><div class="ttdeci">int get_spectrum_ID()</div><div class="ttdef"><b>Definition:</b> LCMS.h:227</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_ae7b27617696a8b097d00bbb3c5b1aa70"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#ae7b27617696a8b097d00bbb3c5b1aa70">OpenMS::LCMS::check_feature_list_empty</a></div><div class="ttdeci">bool check_feature_list_empty()</div><div class="ttdef"><b>Definition:</b> LCMS.h:179</div></div>
<div class="ttc" id="structOpenMS_1_1LCMS_1_1OPERATOR__FeatureCompare_html"><div class="ttname"><a href="structOpenMS_1_1LCMS_1_1OPERATOR__FeatureCompare.html">OpenMS::LCMS::OPERATOR_FeatureCompare</a></div><div class="ttdef"><b>Definition:</b> LCMS.h:135</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_ae607d69f3e7ad0243eba857adfe5eab4"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#ae607d69f3e7ad0243eba857adfe5eab4">OpenMS::LCMS::remove_feature</a></div><div class="ttdeci">void remove_feature(int i)</div><div class="ttdef"><b>Definition:</b> LCMS.h:205</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_ae7a1a66bf017082d76cf96c65310faf3"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#ae7a1a66bf017082d76cf96c65310faf3">OpenMS::LCMS::set_spectrum_ID</a></div><div class="ttdeci">void set_spectrum_ID(int IN)</div><div class="ttdef"><b>Definition:</b> LCMS.h:229</div></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a480d6423b1e9ca40c69c5a83458b49b0"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a480d6423b1e9ca40c69c5a83458b49b0">OpenMS::Constants::F</a></div><div class="ttdeci">const double F</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a6ac2db2287b5133555895597d19408a6"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a6ac2db2287b5133555895597d19408a6">OpenMS::LCMS::add_raw_spec_name</a></div><div class="ttdeci">void add_raw_spec_name(int ID, std::string name)</div><div class="ttdef"><b>Definition:</b> LCMS.h:241</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_aacec49d7ffbee606a2dc750acd6d3967"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#aacec49d7ffbee606a2dc750acd6d3967">OpenMS::LCMS::get_nb_identified_features</a></div><div class="ttdeci">int get_nb_identified_features(double PepProb_T)</div><div class="ttdef"><b>Definition:</b> LCMS.h:301</div></div>
<div class="ttc" id="IsotopeWaveletParallelFor_8h_html_a070d2ce7b6bb7e5c05602aa8c308d0c4"><div class="ttname"><a href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a></div><div class="ttdeci">#define NULL</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletParallelFor.h:41</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a309a40b5c8ea9bdf2140cf193543ff44"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a309a40b5c8ea9bdf2140cf193543ff44">OpenMS::LCMS::get_nb_raw_specs</a></div><div class="ttdeci">int get_nb_raw_specs()</div><div class="ttdef"><b>Definition:</b> LCMS.h:251</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a0594367083652d030fc378ca10e3f759"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a0594367083652d030fc378ca10e3f759">OpenMS::LCMS::remove_raw_spec_name</a></div><div class="ttdeci">void remove_raw_spec_name(int ID)</div><div class="ttdef"><b>Definition:</b> LCMS.h:239</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a7185157195b5d65d84fcebe23ca38f82"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a7185157195b5d65d84fcebe23ca38f82">OpenMS::LCMS::add_alignment_error</a></div><div class="ttdeci">void add_alignment_error(double TR, double ERROR_UP, double ERROR_DOWN)</div><div class="ttdef"><b>Definition:</b> LCMS.h:317</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a8130b14a036e42230641337965ac02bd"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a8130b14a036e42230641337965ac02bd">OpenMS::LCMS::get_feature_list_begin</a></div><div class="ttdeci">std::vector< SHFeature >::iterator get_feature_list_begin()</div><div class="ttdef"><b>Definition:</b> LCMS.h:183</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_ad439ff344eee2c26ba2bd79d0c0f5ed9"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#ad439ff344eee2c26ba2bd79d0c0f5ed9">OpenMS::LCMS::set_MASTER_ID</a></div><div class="ttdeci">void set_MASTER_ID(int IN)</div><div class="ttdef"><b>Definition:</b> LCMS.h:327</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_aaa50dfe26a64481418eba7b4e4c41d88"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#aaa50dfe26a64481418eba7b4e4c41d88">OpenMS::LCMS::feature_list</a></div><div class="ttdeci">std::vector< SHFeature > feature_list</div><div class="ttdef"><b>Definition:</b> LCMS.h:67</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_1SHFeature_html_a4b490cc4b4c5b509e03b5e4743724cdb"><div class="ttname"><a href="classOpenMS_1_1SHFeature.html#a4b490cc4b4c5b509e03b5e4743724cdb">OpenMS::SHFeature::feature_ID</a></div><div class="ttdeci">int feature_ID</div><div class="ttdef"><b>Definition:</b> SHFeature.h:125</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a5b9dcf6bcbadffbcd4717c378d28332a"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a5b9dcf6bcbadffbcd4717c378d28332a">OpenMS::LCMS::get_spec_name</a></div><div class="ttdeci">std::string get_spec_name()</div><div class="ttdef"><b>Definition:</b> LCMS.h:221</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a37fe7e2ab6407008caf5066c8059d07a"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a37fe7e2ab6407008caf5066c8059d07a">OpenMS::LCMS::get_nb_features</a></div><div class="ttdeci">unsigned int get_nb_features()</div><div class="ttdef"><b>Definition:</b> LCMS.h:218</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_aa9a3ceeb8749addce3de62f4b0ca612e"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#aa9a3ceeb8749addce3de62f4b0ca612e">OpenMS::LCMS::raw_spec_names</a></div><div class="ttdeci">std::map< int, std::string > raw_spec_names</div><div class="ttdef"><b>Definition:</b> LCMS.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a2332cb7b192f2b3196169f873afb2842"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a2332cb7b192f2b3196169f873afb2842">OpenMS::LCMS::get_MASTER_ID</a></div><div class="ttdeci">int get_MASTER_ID()</div><div class="ttdef"><b>Definition:</b> LCMS.h:329</div></div>
<div class="ttc" id="classOpenMS_1_1SHFeature_html_acf9cc8b997b6cb4566cadf85c1c527d4"><div class="ttname"><a href="classOpenMS_1_1SHFeature.html#acf9cc8b997b6cb4566cadf85c1c527d4">OpenMS::SHFeature::MONO_MZ</a></div><div class="ttdeci">double MONO_MZ</div><div class="ttdef"><b>Definition:</b> SHFeature.h:121</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_ad0cfbfed1b3126635dfcc16368be113f"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#ad0cfbfed1b3126635dfcc16368be113f">OpenMS::LCMS::get_raw_spec_name_end</a></div><div class="ttdeci">std::map< int, std::string >::iterator get_raw_spec_name_end()</div><div class="ttdef"><b>Definition:</b> LCMS.h:247</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_ac4ab0746d6c0228e36102f7d688b3a81"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#ac4ab0746d6c0228e36102f7d688b3a81">OpenMS::LCMS::check_raw_spec_name_empty</a></div><div class="ttdeci">bool check_raw_spec_name_empty()</div><div class="ttdef"><b>Definition:</b> LCMS.h:243</div></div>
<div class="ttc" id="classOpenMS_1_1SHFeature_html_ab89d41ecea95fdfe48a60fb13470610a"><div class="ttname"><a href="classOpenMS_1_1SHFeature.html#ab89d41ecea95fdfe48a60fb13470610a">OpenMS::SHFeature::set_feature_ID</a></div><div class="ttdeci">void set_feature_ID(int IN)</div><div class="ttdef"><b>Definition:</b> SHFeature.h:353</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a70117048428b9c3ccf886c8ef770656e"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a70117048428b9c3ccf886c8ef770656e">OpenMS::LCMS::spec_name</a></div><div class="ttdeci">std::string spec_name</div><div class="ttdef"><b>Definition:</b> LCMS.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a18b9e84a938c4d197eea7bf6d56e5f91"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a18b9e84a938c4d197eea7bf6d56e5f91">OpenMS::LCMS::clear_feature_list</a></div><div class="ttdeci">void clear_feature_list()</div><div class="ttdef"><b>Definition:</b> LCMS.h:173</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_ae49ef4258713ae66236ef4f955753255"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#ae49ef4258713ae66236ef4f955753255">OpenMS::LCMS::get_feature_list</a></div><div class="ttdeci">std::vector< SHFeature > get_feature_list()</div><div class="ttdef"><b>Definition:</b> LCMS.h:175</div></div>
<div class="ttc" id="classOpenMS_1_1SHFeature_html_af6d5ab3629ea17ec17a1733f29f8a0d9"><div class="ttname"><a href="classOpenMS_1_1SHFeature.html#af6d5ab3629ea17ec17a1733f29f8a0d9">OpenMS::SHFeature::TR</a></div><div class="ttdeci">double TR</div><div class="ttdef"><b>Definition:</b> SHFeature.h:120</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a049052f4f63f906d3e5884bbf4cc6ef0"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a049052f4f63f906d3e5884bbf4cc6ef0">OpenMS::LCMS::spectrum_id</a></div><div class="ttdeci">int spectrum_id</div><div class="ttdef"><b>Definition:</b> LCMS.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a2615876a9806c412d4d258537994a860"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a2615876a9806c412d4d258537994a860">OpenMS::LCMS::tag_peaks_with_spectrum_ID</a></div><div class="ttdeci">void tag_peaks_with_spectrum_ID()</div><div class="ttdef"><b>Definition:</b> LCMS.h:154</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a0e13e305681f6be0b5f944b348b991b5"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a0e13e305681f6be0b5f944b348b991b5">OpenMS::LCMS::remove_feature_from_list</a></div><div class="ttdeci">std::vector< SHFeature >::iterator remove_feature_from_list(std::vector< SHFeature >::iterator IN)</div><div class="ttdef"><b>Definition:</b> LCMS.h:214</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_ac8140cda9f8c984fdd4ac852b349015e"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#ac8140cda9f8c984fdd4ac852b349015e">OpenMS::LCMS::set_spec_name</a></div><div class="ttdeci">void set_spec_name(std::string IN)</div><div class="ttdef"><b>Definition:</b> LCMS.h:223</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a5a2d53d9393b2dd85b047f5cf262b4f4"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a5a2d53d9393b2dd85b047f5cf262b4f4">OpenMS::LCMS::get_feature_list_end</a></div><div class="ttdeci">std::vector< SHFeature >::iterator get_feature_list_end()</div><div class="ttdef"><b>Definition:</b> LCMS.h:185</div></div>
<div class="ttc" id="classOpenMS_1_1SHFeature_html_a9859dad25e54a0f0c6754fbf8697dcea"><div class="ttname"><a href="classOpenMS_1_1SHFeature.html#a9859dad25e54a0f0c6754fbf8697dcea">OpenMS::SHFeature::get_feature_ID</a></div><div class="ttdeci">int get_feature_ID()</div><div class="ttdef"><b>Definition:</b> SHFeature.h:355</div></div>
<div class="ttc" id="structOpenMS_1_1LCMS_1_1OPERATOR__FeatureCompare_html_ad27555d4794d405fef85395fa09387b3"><div class="ttname"><a href="structOpenMS_1_1LCMS_1_1OPERATOR__FeatureCompare.html#ad27555d4794d405fef85395fa09387b3">OpenMS::LCMS::OPERATOR_FeatureCompare::operator()</a></div><div class="ttdeci">bool operator()(const SHFeature A, const SHFeature B) const </div><div class="ttdef"><b>Definition:</b> LCMS.h:138</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a073655c23df39c4dc538b4e23a655d91"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a073655c23df39c4dc538b4e23a655d91">OpenMS::LCMS::get_raw_spec_name_map</a></div><div class="ttdeci">std::map< int, std::string > get_raw_spec_name_map()</div><div class="ttdef"><b>Definition:</b> LCMS.h:249</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_ad54ee79a5a849bfe2b24d22fafdfa139"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#ad54ee79a5a849bfe2b24d22fafdfa139">OpenMS::LCMS::add_feature</a></div><div class="ttdeci">void add_feature(SHFeature *IN)</div><div class="ttdef"><b>Definition:</b> LCMS.h:189</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a4269cf98ed173ae2cec9cfd156b74dee"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a4269cf98ed173ae2cec9cfd156b74dee">OpenMS::LCMS::get_feature_list_reference</a></div><div class="ttdeci">std::vector< SHFeature > * get_feature_list_reference()</div><div class="ttdef"><b>Definition:</b> LCMS.h:177</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a57071f9a75b2acfe03539c18a1a97ba1"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a57071f9a75b2acfe03539c18a1a97ba1">OpenMS::LCMS::get_raw_spec_name</a></div><div class="ttdeci">std::string get_raw_spec_name(int ID)</div><div class="ttdef"><b>Definition:</b> LCMS.h:253</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a9817411f20f7f8f2b1143ddd1af71f6f"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a9817411f20f7f8f2b1143ddd1af71f6f">OpenMS::LCMS::MASTER_ID</a></div><div class="ttdeci">int MASTER_ID</div><div class="ttdef"><b>Definition:</b> LCMS.h:73</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_1LCMS_html_a54e5e1ec2a920217fe46d1ba752c2ae5"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a54e5e1ec2a920217fe46d1ba752c2ae5">OpenMS::LCMS::get_nb_identified_features</a></div><div class="ttdeci">int get_nb_identified_features()</div><div class="ttdef"><b>Definition:</b> LCMS.h:287</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_af262b2edcfb4150cc0e6a8c164950854"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#af262b2edcfb4150cc0e6a8c164950854">OpenMS::LCMS::add_raw_spec_name_map</a></div><div class="ttdeci">void add_raw_spec_name_map(std::map< int, std::string > IN)</div><div class="ttdef"><b>Definition:</b> LCMS.h:270</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_aba74e58aaedfcbe9016fe489a47238f0"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#aba74e58aaedfcbe9016fe489a47238f0">OpenMS::LCMS::MINIMAL_PEP_PROPHET_THERSHOLD</a></div><div class="ttdeci">static double MINIMAL_PEP_PROPHET_THERSHOLD</div><div class="ttdef"><b>Definition:</b> LCMS.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a22d16dc75350a30c9ea7522543728406"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a22d16dc75350a30c9ea7522543728406">OpenMS::LCMS::get_raw_spec_name_start</a></div><div class="ttdeci">std::map< int, std::string >::iterator get_raw_spec_name_start()</div><div class="ttdef"><b>Definition:</b> LCMS.h:245</div></div>
<div class="ttc" id="structOpenMS_1_1LCMS_1_1OPERATOR__MZ_html_ad27555d4794d405fef85395fa09387b3"><div class="ttname"><a href="structOpenMS_1_1LCMS_1_1OPERATOR__MZ.html#ad27555d4794d405fef85395fa09387b3">OpenMS::LCMS::OPERATOR_MZ::operator()</a></div><div class="ttdeci">bool operator()(const SHFeature A, const SHFeature B) const </div><div class="ttdef"><b>Definition:</b> LCMS.h:118</div></div>
<div class="ttc" id="classOpenMS_1_1LCMS_html_a7d7ac4e8df8fa9177f7184c42f3aa7cd"><div class="ttname"><a href="classOpenMS_1_1LCMS.html#a7d7ac4e8df8fa9177f7184c42f3aa7cd">OpenMS::LCMS::ALIGNMENT_ERROR</a></div><div class="ttdeci">std::map< double, std::pair< double, double > > ALIGNMENT_ERROR</div><div class="ttdef"><b>Definition:</b> LCMS.h:79</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 11:19:16 using doxygen 1.8.5</font></TD>
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