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<a href="IonizationSimulation_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">// $Maintainer: Chris Bielow$</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Stephan Aiche, Chris Bielow$</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> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_SIMULATION_IONIZATIONSIMULATION_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_SIMULATION_IONIZATIONSIMULATION_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="Adduct_8h.html">OpenMS/DATASTRUCTURES/Adduct.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="SimTypes_8h.html">OpenMS/SIMULATION/SimTypes.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="ConsensusMap_8h.html">OpenMS/KERNEL/ConsensusMap.h</a>></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="comment">// STL includes</span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <set></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> {</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html"> 64</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1IonizationSimulation.html">IonizationSimulation</a> :</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>,</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  {</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#a84655a74f51157d0db787c89bdfcef46"> 71</a></span>  <span class="keyword">typedef</span> <span class="keyword">enum</span></div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  {</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#a84655a74f51157d0db787c89bdfcef46af44dbf64796c3c09b804546061c39258"> 73</a></span>  <a class="code" href="classOpenMS_1_1IonizationSimulation.html#a84655a74f51157d0db787c89bdfcef46af44dbf64796c3c09b804546061c39258">MALDI</a>,</div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#a84655a74f51157d0db787c89bdfcef46a4ce1f413b646020308281e301ce1e4ec"> 74</a></span>  ESI</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  } IonizationType;</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <a class="code" href="classOpenMS_1_1IonizationSimulation.html">IonizationSimulation</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> &);</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <a class="code" href="classOpenMS_1_1IonizationSimulation.html">IonizationSimulation</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IonizationSimulation.html">IonizationSimulation</a> & source);</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1IonizationSimulation.html">IonizationSimulation</a>();</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <a class="code" href="classOpenMS_1_1IonizationSimulation.html">IonizationSimulation</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IonizationSimulation.html">IonizationSimulation</a> & source);</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keywordtype">void</span> ionize(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapSim</a> & features, <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & charge_consensus, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment);</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <a class="code" href="classOpenMS_1_1IonizationSimulation.html">IonizationSimulation</a>();</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keyword">class </span>CompareCmpByEF_;</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> </div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordtype">void</span> ionizeEsi_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapSim</a> &, <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & charge_consensus);</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keywordtype">void</span> ionizeMaldi_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapSim</a> &, <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & charge_consensus);</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> isFeatureValid_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> & feature);</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordtype">void</span> setFeatureProperties_(<a class="code" href="classOpenMS_1_1Feature.html">Feature</a> & f,</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> & adduct_mass,</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & adduct_formula,</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keyword">const</span> <a class="code" href="namespaceOpenMS.html#aeeb197e95f7bd1ada2cca075468bab8f">SimChargeType</a> charge,</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keyword">const</span> <a class="code" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> new_intensity,</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> parent_index);</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordtype">void</span> setDefaultParams_();</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <a class="code" href="classunsigned_01int.html">UInt</a> countIonizedResidues_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> &) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> </div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> </div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="comment">// Members //</span></div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span> </div>
<div class="line"><a name="l00145"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#a1ab0fe0248799c192b1084a377d5a978"> 145</a></span>  <a class="code" href="classOpenMS_1_1IonizationSimulation.html#a84655a74f51157d0db787c89bdfcef46">IonizationType</a> <a class="code" href="classOpenMS_1_1IonizationSimulation.html#a1ab0fe0248799c192b1084a377d5a978">ionization_type_</a>;</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="comment">/*</span></div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> <span class="comment"> @brief List of residues that are counted as basic during execution of countBasicResidues_</span></div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> <span class="comment">*/</span></div>
<div class="line"><a name="l00150"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#abe20ef41cf84a2353c11b006dc638201"> 150</a></span>  std::set<String> <a class="code" href="classOpenMS_1_1IonizationSimulation.html#abe20ef41cf84a2353c11b006dc638201">basic_residues_</a>;</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div>
<div class="line"><a name="l00155"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#ae504db913e79d0f53604b13022d1b6d3"> 155</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1IonizationSimulation.html#ae504db913e79d0f53604b13022d1b6d3">esi_probability_</a>;</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="comment">// important: leave that as vector<double> because gsl expects 'double' and not 'DoubleReal' (which might be something different)</span></div>
<div class="line"><a name="l00161"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#a59ee927a14ddb37ade8cf9b28f0404b3"> 161</a></span>  std::vector<double> <a class="code" href="classOpenMS_1_1IonizationSimulation.html#a59ee927a14ddb37ade8cf9b28f0404b3">esi_impurity_probabilities_</a>;</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="l00167"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#a9157248c2b0cf08dc059d90d5200f06f"> 167</a></span>  <a class="code" href="classOpenMS_1_1Adduct.html#ac491cec851c0e0300106ac3bc8bfa460">Adduct::AdductsType</a> <a class="code" href="classOpenMS_1_1IonizationSimulation.html#a9157248c2b0cf08dc059d90d5200f06f">esi_adducts_</a>;</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span> </div>
<div class="line"><a name="l00172"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#a48d22c472cd233ffad028d415844c578"> 172</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1IonizationSimulation.html#a48d22c472cd233ffad028d415844c578">max_adduct_charge_</a>;</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span> </div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="comment">// important: leave that as vector<double> because gsl expects 'double' and not 'DoubleReal' (which might be something different)</span></div>
<div class="line"><a name="l00178"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#aa62f04e217a478e55bea5af98c7a6466"> 178</a></span>  std::vector<double> <a class="code" href="classOpenMS_1_1IonizationSimulation.html#aa62f04e217a478e55bea5af98c7a6466">maldi_probabilities_</a>;</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span> </div>
<div class="line"><a name="l00181"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#a25f7afe44ba229946b369a2f218dc10d"> 181</a></span>  <a class="code" href="classdouble.html">SimCoordinateType</a> <a class="code" href="classOpenMS_1_1IonizationSimulation.html#a25f7afe44ba229946b369a2f218dc10d">maximal_mz_measurement_limit_</a>;</div>
<div class="line"><a name="l00183"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#aedc4995317c2015ae20711edf457c22a"> 183</a></span>  <a class="code" href="classdouble.html">SimCoordinateType</a> <a class="code" href="classOpenMS_1_1IonizationSimulation.html#aedc4995317c2015ae20711edf457c22a">minimal_mz_measurement_limit_</a>;</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> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00187"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IonizationSimulation.html#a1755a34bd4d88feb6a87a209273177eb"> 187</a></span>  <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> <span class="keyword">const</span> * <a class="code" href="classOpenMS_1_1IonizationSimulation.html#a1755a34bd4d88feb6a87a209273177eb">rnd_gen_</a>;</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  };</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span> </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="preprocessor">#endif</span></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="namespaceOpenMS_html_aeeb197e95f7bd1ada2cca075468bab8f"><div class="ttname"><a href="namespaceOpenMS.html#aeeb197e95f7bd1ada2cca075468bab8f">OpenMS::SimChargeType</a></div><div class="ttdeci">Feature::ChargeType SimChargeType</div><div class="ttdoc">Charge of a peptide. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:65</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_1IonizationSimulation_html"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html">OpenMS::IonizationSimulation</a></div><div class="ttdoc">Simulates Protein ionization. </div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:64</div></div>
<div class="ttc" id="ConsensusMap_8h_html"><div class="ttname"><a href="ConsensusMap_8h.html">ConsensusMap.h</a></div></div>
<div class="ttc" id="SimTypes_8h_html"><div class="ttname"><a href="SimTypes_8h.html">SimTypes.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap</a></div><div class="ttdoc">A container for features. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1IonizationSimulation_html_a84655a74f51157d0db787c89bdfcef46"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#a84655a74f51157d0db787c89bdfcef46">OpenMS::IonizationSimulation::IonizationType</a></div><div class="ttdeci">IonizationType</div><div class="ttdoc">possible ionization methods </div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:71</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html">OpenMS::ConsensusMap</a></div><div class="ttdoc">A container for consensus elements. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:60</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_1AASequence_html"><div class="ttname"><a href="classOpenMS_1_1AASequence.html">OpenMS::AASequence</a></div><div class="ttdoc">Representation of a peptide/protein sequence. </div><div class="ttdef"><b>Definition:</b> AASequence.h:84</div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Adduct_html_ac491cec851c0e0300106ac3bc8bfa460"><div class="ttname"><a href="classOpenMS_1_1Adduct.html#ac491cec851c0e0300106ac3bc8bfa460">OpenMS::Adduct::AdductsType</a></div><div class="ttdeci">std::vector< Adduct > AdductsType</div><div class="ttdef"><b>Definition:</b> Adduct.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1IonizationSimulation_html_a48d22c472cd233ffad028d415844c578"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#a48d22c472cd233ffad028d415844c578">OpenMS::IonizationSimulation::max_adduct_charge_</a></div><div class="ttdeci">Size max_adduct_charge_</div><div class="ttdoc">Maximal charge that any impure adduct from parameter list has. </div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:172</div></div>
<div class="ttc" id="classOpenMS_1_1IonizationSimulation_html_a59ee927a14ddb37ade8cf9b28f0404b3"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#a59ee927a14ddb37ade8cf9b28f0404b3">OpenMS::IonizationSimulation::esi_impurity_probabilities_</a></div><div class="ttdeci">std::vector< double > esi_impurity_probabilities_</div><div class="ttdoc">Discrete distribution of impure charge adducts like Na+, K+, Ca++ etc besides the usual H+...</div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:161</div></div>
<div class="ttc" id="classOpenMS_1_1IonizationSimulation_html_abe20ef41cf84a2353c11b006dc638201"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#abe20ef41cf84a2353c11b006dc638201">OpenMS::IonizationSimulation::basic_residues_</a></div><div class="ttdeci">std::set< String > basic_residues_</div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:150</div></div>
<div class="ttc" id="classOpenMS_1_1IonizationSimulation_html_aedc4995317c2015ae20711edf457c22a"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#aedc4995317c2015ae20711edf457c22a">OpenMS::IonizationSimulation::minimal_mz_measurement_limit_</a></div><div class="ttdeci">SimCoordinateType minimal_mz_measurement_limit_</div><div class="ttdoc">Minimum m/z detected by mass analyser. </div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:183</div></div>
<div class="ttc" id="classOpenMS_1_1IonizationSimulation_html_a9157248c2b0cf08dc059d90d5200f06f"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#a9157248c2b0cf08dc059d90d5200f06f">OpenMS::IonizationSimulation::esi_adducts_</a></div><div class="ttdeci">Adduct::AdductsType esi_adducts_</div><div class="ttdoc">Corresponding table to esi_impurity_probabilities_ holding the actual element and its charge...</div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:167</div></div>
<div class="ttc" id="Adduct_8h_html"><div class="ttname"><a href="Adduct_8h.html">Adduct.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1IonizationSimulation_html_aa62f04e217a478e55bea5af98c7a6466"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#aa62f04e217a478e55bea5af98c7a6466">OpenMS::IonizationSimulation::maldi_probabilities_</a></div><div class="ttdeci">std::vector< double > maldi_probabilities_</div><div class="ttdoc">Preprocessed table of discrete distribution (MALDI charges) </div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:178</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_1IonizationSimulation_html_a1ab0fe0248799c192b1084a377d5a978"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#a1ab0fe0248799c192b1084a377d5a978">OpenMS::IonizationSimulation::ionization_type_</a></div><div class="ttdeci">IonizationType ionization_type_</div><div class="ttdoc">ESI or MALDI ionization. </div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:145</div></div>
<div class="ttc" id="structOpenMS_1_1SimRandomNumberGenerator_html"><div class="ttname"><a href="structOpenMS_1_1SimRandomNumberGenerator.html">OpenMS::SimRandomNumberGenerator</a></div><div class="ttdoc">Wrapper class for random number generators used by the simulation classes. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:99</div></div>
<div class="ttc" id="namespaceOpenMS_html_a1c6dc92dcdd8dd005518ab11d341ae5f"><div class="ttname"><a href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">OpenMS::SimIntensityType</a></div><div class="ttdeci">Peak2D::IntensityType SimIntensityType</div><div class="ttdoc">Abundance of proteins/peptides. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment< SimPointType ></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="classOpenMS_1_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1IonizationSimulation_html_ae504db913e79d0f53604b13022d1b6d3"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#ae504db913e79d0f53604b13022d1b6d3">OpenMS::IonizationSimulation::esi_probability_</a></div><div class="ttdeci">DoubleReal esi_probability_</div><div class="ttdoc">Probability for the binomial distribution of ESI charge states. </div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:155</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_1IonizationSimulation_html_a25f7afe44ba229946b369a2f218dc10d"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#a25f7afe44ba229946b369a2f218dc10d">OpenMS::IonizationSimulation::maximal_mz_measurement_limit_</a></div><div class="ttdeci">SimCoordinateType maximal_mz_measurement_limit_</div><div class="ttdoc">Maximum m/z detected by mass analyser. </div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:181</div></div>
<div class="ttc" id="classOpenMS_1_1IonizationSimulation_html_a1755a34bd4d88feb6a87a209273177eb"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#a1755a34bd4d88feb6a87a209273177eb">OpenMS::IonizationSimulation::rnd_gen_</a></div><div class="ttdeci">SimRandomNumberGenerator const * rnd_gen_</div><div class="ttdoc">Random number generator. </div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:187</div></div>
<div class="ttc" id="classOpenMS_1_1IonizationSimulation_html_a84655a74f51157d0db787c89bdfcef46af44dbf64796c3c09b804546061c39258"><div class="ttname"><a href="classOpenMS_1_1IonizationSimulation.html#a84655a74f51157d0db787c89bdfcef46af44dbf64796c3c09b804546061c39258">OpenMS::IonizationSimulation::MALDI</a></div><div class="ttdef"><b>Definition:</b> IonizationSimulation.h:73</div></div>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:15 using doxygen 1.8.5</font></TD>
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