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<a href="PrecursorIonSelection_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: Alexandra Zerck $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: $</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="l00035"></a><span class="lineno"> 35</span> </div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#ifndef OPENMS_ANALYSIS_TARGETED_PRECURSORIONSELECTION_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_TARGETED_PRECURSORIONSELECTION_H</span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="PSLPFormulation_8h.html">OpenMS/ANALYSIS/TARGETED/PSLPFormulation.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <set></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> {</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keyword">class </span>PrecursorIonSelectionPreprocessing;</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keyword">class </span>PSProteinInference;</div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html"> 53</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a> :</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></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">public</span>:</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a name="l00075"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7"> 75</a></span>  <span class="keyword">enum</span> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7">Type</a></div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  {</div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7aafb6828f5a8b8b40648e96ce2e5f435b"> 77</a></span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7aafb6828f5a8b8b40648e96ce2e5f435b">IPS</a>,</div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a241370a8eee3fc0070dce7c2cc8da0b6"> 78</a></span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a241370a8eee3fc0070dce7c2cc8da0b6">ILP_IPS</a>,</div>
<div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a38aefbb94f63c43b1c8047151c83ca64"> 79</a></span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a38aefbb94f63c43b1c8047151c83ca64">SPS</a>,</div>
<div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7aa58d945ae9279992a5a9a1e908b770cb"> 80</a></span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7aa58d945ae9279992a5a9a1e908b770cb">UPSHIFT</a>,</div>
<div class="line"><a name="l00081"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a3ad159e1881c0b9db5274d155c9faf28"> 81</a></span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a3ad159e1881c0b9db5274d155c9faf28">DOWNSHIFT</a>,</div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7afd8b47cd00ea3ad6c3c275e1ffcce606"> 82</a></span>  DEX</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  };</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a>();</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a> & source);</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  ~<a class="code" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a>();</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> & getMaxScore() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keywordtype">void</span> setMaxScore(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> & max_score);</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> </div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore.html"> 94</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore.html">TotalScoreMore</a> :</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  std::binary_function<Feature, Feature, bool></div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  {</div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore.html#a97d404a322701f8ce1b604179b08a492"> 97</a></span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore.html#a97d404a322701f8ce1b604179b08a492">operator()</a>(<a class="code" href="classOpenMS_1_1Feature.html">Feature</a> <span class="keyword">const</span> & left, <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> <span class="keyword">const</span> & right)<span class="keyword"> const</span></div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keywordflow">return</span> (<a class="code" href="classdouble.html">DoubleReal</a>)left.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(<span class="stringliteral">"msms_score"</span>) > (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)right.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(<span class="stringliteral">"msms_score"</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> </div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  };</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> </div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PrecursorIonSelection_1_1SeqTotalScoreMore.html"> 105</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1PrecursorIonSelection_1_1SeqTotalScoreMore.html">SeqTotalScoreMore</a> :</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  std::binary_function<Feature, Feature, bool></div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  {</div>
<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PrecursorIonSelection_1_1SeqTotalScoreMore.html#a97d404a322701f8ce1b604179b08a492"> 108</a></span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1PrecursorIonSelection_1_1SeqTotalScoreMore.html#a97d404a322701f8ce1b604179b08a492">operator()</a>(<a class="code" href="classOpenMS_1_1Feature.html">Feature</a> <span class="keyword">const</span> & left, <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> <span class="keyword">const</span> & right)<span class="keyword"> const</span></div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordflow">if</span> (left.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>() < right.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>()) <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (left.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>() > right.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>()) <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordflow">else</span> <span class="keywordflow">return</span> (<a class="code" href="classdouble.html">DoubleReal</a>)left.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(<span class="stringliteral">"msms_score"</span>) > (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)right.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(<span class="stringliteral">"msms_score"</span>);</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  }</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="l00116"></a><span class="lineno"> 116</span> </div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> </div>
<div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a2c348a002bfdedc62091f660a1dc2ad3"> 121</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a2c348a002bfdedc62091f660a1dc2ad3">sortByTotalScore</a>(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features)</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>  <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<>::Iterator</a> beg = features.begin();</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<>::Iterator</a> end = features.end();</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  std::sort(beg, end, <a class="code" href="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore.html">TotalScoreMore</a>());</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  }</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keywordtype">void</span> getNextPrecursors(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & next_features, <a class="code" href="classunsigned_01int.html">UInt</a> number);</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keywordtype">void</span> getNextPrecursorsSeq(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & next_features, <a class="code" href="classunsigned_01int.html">UInt</a> number, <a class="code" href="classdouble.html">DoubleReal</a> & rt);</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordtype">void</span> getNextPrecursors(std::vector<Int> & solution_indices, std::vector<PSLPFormulation::IndexTriple> & variable_indices, std::set<Int> & measured_variables,</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & new_features, <a class="code" href="classunsigned_01int.html">UInt</a> step_size, <a class="code" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a> & ilp);</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> <span class="comment">// /**</span></div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> <span class="comment">// @brief Change scoring of features using peptide identifications only from spectra of the last</span></div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span> <span class="comment">// iteration</span></div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span> <span class="comment">//</span></div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> <span class="comment">// @param features FeatureMap with all possible precursors</span></div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span> <span class="comment">// @param new_pep_ids Peptide identifications</span></div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> <span class="comment">// @param preprocessed_db Information from preprocessed database</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> <span class="comment">//</span></div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> <span class="comment">// */</span></div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> <span class="comment">// void rescoreIncremental(FeatureMap<>& features,std::vector<PeptideIdentification>& new_pep_ids,</span></div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> <span class="comment">// std::vector<ProteinIdentification>& prot_ids,</span></div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> <span class="comment">// PrecursorIonSelectionPreprocessing& preprocessed_db);</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> </div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keywordtype">void</span> rescore(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features, std::vector<PeptideIdentification> & new_pep_ids,</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  std::vector<ProteinIdentification> & prot_ids,</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> & preprocessed_db, <span class="keywordtype">bool</span> check_meta_values = <span class="keyword">true</span>);</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span> </div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="keywordtype">void</span> simulateRun(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features, std::vector<PeptideIdentification> & pep_ids,</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  std::vector<ProteinIdentification> & prot_ids,</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> & preprocessed_db,</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> path, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<></a> & experiment, <a class="code" href="classOpenMS_1_1String.html">String</a> precursor_path = <span class="stringliteral">""</span>);</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> </div>
<div class="line"><a name="l00183"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a2b206fdbe8649b90b854129f37fc594a"> 183</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a2b206fdbe8649b90b854129f37fc594a">setLPSolver</a>(<a class="code" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> solver)</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  {</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  solver_ = solver;</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  std::cout << <span class="stringliteral">" LPSolver set to "</span> << solver_ << std::endl;</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> </div>
<div class="line"><a name="l00189"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#ac945a0966726a3a644d194b81c28d960"> 189</a></span>  <a class="code" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#ac945a0966726a3a644d194b81c28d960">getLPSolver</a>()</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>  <span class="keywordflow">return</span> solver_;</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  }</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span> </div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <span class="keywordtype">void</span> reset();</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span> </div>
<div class="line"><a name="l00196"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#add0a01651d44ed438fd2d9202013c2b4"> 196</a></span>  <span class="keyword">const</span> std::map<String, std::set<String> > & <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#add0a01651d44ed438fd2d9202013c2b4">getPeptideProteinCounter</a>()</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  {</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <span class="keywordflow">return</span> prot_id_counter_;</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> </div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="keywordtype">void</span> simulateILPBasedIPSRun_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<></a> & experiment,</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  std::vector<PeptideIdentification> & pep_ids,</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  std::vector<ProteinIdentification> & prot_ids,</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> & preprocessed_db,</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> output_path, <a class="code" href="classOpenMS_1_1String.html">String</a> precursor_path = <span class="stringliteral">""</span>);</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span> </div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="keywordtype">void</span> simulateRun_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features, std::vector<PeptideIdentification> & pep_ids,</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  std::vector<ProteinIdentification> & prot_ids,</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> & preprocessed_db, <a class="code" href="classOpenMS_1_1String.html">String</a> path, <a class="code" href="classOpenMS_1_1String.html">String</a> precursor_path = <span class="stringliteral">""</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>  <span class="keywordtype">void</span> shiftDown_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features, <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> & preprocessed_db, <a class="code" href="classOpenMS_1_1String.html">String</a> protein_acc);</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span> </div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <span class="keywordtype">void</span> shiftUp_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features, <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> & preprocessed_db, <a class="code" href="classOpenMS_1_1String.html">String</a> protein_acc);</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="keywordtype">void</span> rescore_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features, std::vector<PeptideIdentification> & new_pep_ids,</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> & preprocessed_db, <a class="code" href="classOpenMS_1_1PSProteinInference.html">PSProteinInference</a> & protein_inference);</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="keywordtype">void</span> checkForRequiredUserParams_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & features);</div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span> </div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <a class="code" href="classunsigned_01int.html">UInt</a> filterProtIds_(std::vector<ProteinIdentification> & prot_ids);</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span> </div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  std::vector<PeptideIdentification> filterPeptideIds_(std::vector<PeptideIdentification> & pep_ids);</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="keywordtype">void</span> convertPeptideIdScores_(std::vector<PeptideIdentification> & pep_ids);</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span> </div>
<div class="line"><a name="l00241"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a1d33655f6c9055337571b352a0f8c688"> 241</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a1d33655f6c9055337571b352a0f8c688">min_pep_ids_</a>;</div>
<div class="line"><a name="l00243"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a350439a140c1f53c49e6a414063bec95"> 243</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a350439a140c1f53c49e6a414063bec95">max_score_</a>;</div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#ae96b07c06ceff094f476fd92cbe89e10"> 245</a></span>  <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7">Type</a> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#ae96b07c06ceff094f476fd92cbe89e10">type_</a>;</div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#ae7c765448d55eedc24f212e92602a8ec"> 247</a></span>  std::map<String, std::set<String> > <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#ae7c765448d55eedc24f212e92602a8ec">prot_id_counter_</a>;</div>
<div class="line"><a name="l00249"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a0d138c04b4994b24723c3d3fc7d76209"> 249</a></span>  std::vector<Size> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a0d138c04b4994b24723c3d3fc7d76209">fraction_counter_</a>;</div>
<div class="line"><a name="l00251"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#aa0d44a6be23374eb5d1f099ef8b4ca82"> 251</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#aa0d44a6be23374eb5d1f099ef8b4ca82">mz_tolerance_</a>;</div>
<div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a05ce08b9b0435cc41cb9f2528c313237"> 253</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a05ce08b9b0435cc41cb9f2528c313237">mz_tolerance_unit_</a>;</div>
<div class="line"><a name="l00255"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a78c0d505b8706df48e8cf696e21035ee"> 255</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a78c0d505b8706df48e8cf696e21035ee">max_iteration_</a>;</div>
<div class="line"><a name="l00256"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#a3ff6e92379e0c12cecff4f086c60b0b7"> 256</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#a3ff6e92379e0c12cecff4f086c60b0b7">x_variable_number_</a>;</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span> </div>
<div class="line"><a name="l00258"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PrecursorIonSelection.html#afb8f1202d548f01394d85fbeb51f9adf"> 258</a></span>  <a class="code" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> <a class="code" href="classOpenMS_1_1PrecursorIonSelection.html#afb8f1202d548f01394d85fbeb51f9adf">solver_</a>;</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>  };</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> </div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span> <span class="preprocessor">#endif // #ifndef OPENMS_ANALYSIS_ID_PRECURSORIONSELECTION_H</span></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_aae35ae2dfad88d673b03c787aafca83d"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">OpenMS::MetaInfoInterface::getMetaValue</a></div><div class="ttdeci">const DataValue & getMetaValue(const String &name) const </div><div class="ttdoc">returns the value corresponding to a string </div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a1d1cfd8ffb84e947f82999c682b666a7aafb6828f5a8b8b40648e96ce2e5f435b"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7aafb6828f5a8b8b40648e96ce2e5f435b">OpenMS::PrecursorIonSelection::IPS</a></div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a2b206fdbe8649b90b854129f37fc594a"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a2b206fdbe8649b90b854129f37fc594a">OpenMS::PrecursorIonSelection::setLPSolver</a></div><div class="ttdeci">void setLPSolver(LPWrapper::SOLVER solver)</div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:183</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_ac945a0966726a3a644d194b81c28d960"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#ac945a0966726a3a644d194b81c28d960">OpenMS::PrecursorIonSelection::getLPSolver</a></div><div class="ttdeci">LPWrapper::SOLVER getLPSolver()</div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:189</div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a3ff6e92379e0c12cecff4f086c60b0b7"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a3ff6e92379e0c12cecff4f086c60b0b7">OpenMS::PrecursorIonSelection::x_variable_number_</a></div><div class="ttdeci">Size x_variable_number_</div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:256</div></div>
<div class="ttc" id="classOpenMS_1_1LPWrapper_html_ab659f8690ca779b8c3d73fe524a39a00"><div class="ttname"><a href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">OpenMS::LPWrapper::SOLVER</a></div><div class="ttdeci">SOLVER</div><div class="ttdef"><b>Definition:</b> LPWrapper.h:124</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_ae96b07c06ceff094f476fd92cbe89e10"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#ae96b07c06ceff094f476fd92cbe89e10">OpenMS::PrecursorIonSelection::type_</a></div><div class="ttdeci">Type type_</div><div class="ttdoc">precursor ion selection strategy </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:245</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap<></a></div></div>
<div class="ttc" id="structOpenMS_1_1PrecursorIonSelection_1_1SeqTotalScoreMore_html"><div class="ttname"><a href="structOpenMS_1_1PrecursorIonSelection_1_1SeqTotalScoreMore.html">OpenMS::PrecursorIonSelection::SeqTotalScoreMore</a></div><div class="ttdoc">Compare by score. </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a1d1cfd8ffb84e947f82999c682b666a7a241370a8eee3fc0070dce7c2cc8da0b6"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a241370a8eee3fc0070dce7c2cc8da0b6">OpenMS::PrecursorIonSelection::ILP_IPS</a></div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a1d1cfd8ffb84e947f82999c682b666a7aa58d945ae9279992a5a9a1e908b770cb"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7aa58d945ae9279992a5a9a1e908b770cb">OpenMS::PrecursorIonSelection::UPSHIFT</a></div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:80</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ab4e0f356f837ce58e57695da114adce3"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">OpenMS::Peak2D::getRT</a></div><div class="ttdeci">CoordinateType getRT() const </div><div class="ttdoc">Returns the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:203</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a1d1cfd8ffb84e947f82999c682b666a7a38aefbb94f63c43b1c8047151c83ca64"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a38aefbb94f63c43b1c8047151c83ca64">OpenMS::PrecursorIonSelection::SPS</a></div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a350439a140c1f53c49e6a414063bec95"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a350439a140c1f53c49e6a414063bec95">OpenMS::PrecursorIonSelection::max_score_</a></div><div class="ttdeci">DoubleReal max_score_</div><div class="ttdoc">maximal score in the FeatureMap </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:243</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a2c348a002bfdedc62091f660a1dc2ad3"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a2c348a002bfdedc62091f660a1dc2ad3">OpenMS::PrecursorIonSelection::sortByTotalScore</a></div><div class="ttdeci">void sortByTotalScore(FeatureMap<> &features)</div><div class="ttdoc">Sort features by total score. </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:121</div></div>
<div class="ttc" id="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore_html_a97d404a322701f8ce1b604179b08a492"><div class="ttname"><a href="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore.html#a97d404a322701f8ce1b604179b08a492">OpenMS::PrecursorIonSelection::TotalScoreMore::operator()</a></div><div class="ttdeci">bool operator()(Feature const &left, Feature const &right) const </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:97</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelectionPreprocessing_html"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">OpenMS::PrecursorIonSelectionPreprocessing</a></div><div class="ttdoc">This class implements the database preprocessing needing for precursor ion selection. </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelectionPreprocessing.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a1d1cfd8ffb84e947f82999c682b666a7"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7">OpenMS::PrecursorIonSelection::Type</a></div><div class="ttdeci">Type</div><div class="ttdoc">Precursor ion selection type (iterative, static, upshift, downshift, dynamic exclusion). </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:75</div></div>
<div class="ttc" id="structOpenMS_1_1PrecursorIonSelection_1_1SeqTotalScoreMore_html_a97d404a322701f8ce1b604179b08a492"><div class="ttname"><a href="structOpenMS_1_1PrecursorIonSelection_1_1SeqTotalScoreMore.html#a97d404a322701f8ce1b604179b08a492">OpenMS::PrecursorIonSelection::SeqTotalScoreMore::operator()</a></div><div class="ttdeci">bool operator()(Feature const &left, Feature const &right) const </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html"><div class="ttname"><a href="classOpenMS_1_1Feature.html">OpenMS::Feature</a></div><div class="ttdoc">An LC-MS feature. </div><div class="ttdef"><b>Definition:</b> Feature.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a05ce08b9b0435cc41cb9f2528c313237"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a05ce08b9b0435cc41cb9f2528c313237">OpenMS::PrecursorIonSelection::mz_tolerance_unit_</a></div><div class="ttdeci">String mz_tolerance_unit_</div><div class="ttdoc">precursor ion error tolerance unit (ppm or Da) </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:253</div></div>
<div class="ttc" id="classOpenMS_1_1PSProteinInference_html"><div class="ttname"><a href="classOpenMS_1_1PSProteinInference.html">OpenMS::PSProteinInference</a></div><div class="ttdoc">This class implements protein inference for the precursor ion selection strategies. </div><div class="ttdef"><b>Definition:</b> PSProteinInference.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_add0a01651d44ed438fd2d9202013c2b4"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#add0a01651d44ed438fd2d9202013c2b4">OpenMS::PrecursorIonSelection::getPeptideProteinCounter</a></div><div class="ttdeci">const std::map< String, std::set< String > > & getPeptideProteinCounter()</div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:196</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a0d138c04b4994b24723c3d3fc7d76209"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a0d138c04b4994b24723c3d3fc7d76209">OpenMS::PrecursorIonSelection::fraction_counter_</a></div><div class="ttdeci">std::vector< Size > fraction_counter_</div><div class="ttdoc">stores the number of selected precursors per fraction </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:249</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a1d33655f6c9055337571b352a0f8c688"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a1d33655f6c9055337571b352a0f8c688">OpenMS::PrecursorIonSelection::min_pep_ids_</a></div><div class="ttdeci">UInt min_pep_ids_</div><div class="ttdoc">minimal number of peptides identified for a protein to be declared identified </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:241</div></div>
<div class="ttc" id="PeptideIdentification_8h_html"><div class="ttname"><a href="PeptideIdentification_8h.html">PeptideIdentification.h</a></div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore_html"><div class="ttname"><a href="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore.html">OpenMS::PrecursorIonSelection::TotalScoreMore</a></div><div class="ttdoc">Compare by score. </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a78c0d505b8706df48e8cf696e21035ee"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a78c0d505b8706df48e8cf696e21035ee">OpenMS::PrecursorIonSelection::max_iteration_</a></div><div class="ttdeci">UInt max_iteration_</div><div class="ttdoc">maximal number of iterations </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:255</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_aa0d44a6be23374eb5d1f099ef8b4ca82"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#aa0d44a6be23374eb5d1f099ef8b4ca82">OpenMS::PrecursorIonSelection::mz_tolerance_</a></div><div class="ttdeci">DoubleReal mz_tolerance_</div><div class="ttdoc">precursor ion error tolerance </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:251</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_afb8f1202d548f01394d85fbeb51f9adf"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#afb8f1202d548f01394d85fbeb51f9adf">OpenMS::PrecursorIonSelection::solver_</a></div><div class="ttdeci">LPWrapper::SOLVER solver_</div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:258</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_ae7c765448d55eedc24f212e92602a8ec"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#ae7c765448d55eedc24f212e92602a8ec">OpenMS::PrecursorIonSelection::prot_id_counter_</a></div><div class="ttdeci">std::map< String, std::set< String > > prot_id_counter_</div><div class="ttdoc">stores the peptide sequences for all protein identifications </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:247</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html_a1d1cfd8ffb84e947f82999c682b666a7a3ad159e1881c0b9db5274d155c9faf28"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a3ad159e1881c0b9db5274d155c9faf28">OpenMS::PrecursorIonSelection::DOWNSHIFT</a></div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:81</div></div>
<div class="ttc" id="classOpenMS_1_1PrecursorIonSelection_html"><div class="ttname"><a href="classOpenMS_1_1PrecursorIonSelection.html">OpenMS::PrecursorIonSelection</a></div><div class="ttdoc">This class implements different precursor ion selection strategies. </div><div class="ttdef"><b>Definition:</b> PrecursorIonSelection.h:53</div></div>
<div class="ttc" id="PSLPFormulation_8h_html"><div class="ttname"><a href="PSLPFormulation_8h.html">PSLPFormulation.h</a></div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="group__Concept_html_gace75bfb1aba684e874dffee13738bd15"><div class="ttname"><a href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">OpenMS::DoubleReal</a></div><div class="ttdeci">double DoubleReal</div><div class="ttdoc">Double-precision real type. </div><div class="ttdef"><b>Definition:</b> Types.h:118</div></div>
<div class="ttc" id="classOpenMS_1_1PSLPFormulation_html"><div class="ttname"><a href="classOpenMS_1_1PSLPFormulation.html">OpenMS::PSLPFormulation</a></div><div class="ttdoc">Implements ILP formulation of precursor selection problems. </div><div class="ttdef"><b>Definition:</b> PSLPFormulation.h:51</div></div>
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