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<a href="RawMSSignalSimulation_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">// $Maintainer: Stephan Aiche$</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_RAWMSSIGNALSIMULATION_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_RAWMSSIGNALSIMULATION_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="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</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="EGHModel_8h.html">OpenMS/SIMULATION/EGHModel.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="preprocessor">#include <<a class="code" href="ProductModel_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/ProductModel.h</a>></span></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">namespace </span>OpenMS</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> {</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>  <span class="keyword">class </span>IsotopeModel;</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html"> 61</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> :</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>,</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  {</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> & rng);</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> & source);</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a>();</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> & source);</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">void</span> loadContaminants();</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordtype">void</span> generateRawSignals(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapSim</a> & features, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment_ct, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapSim</a> & contaminants);</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a35d6cf42451e70ae0298555699c807c4"> 92</a></span>  <span class="keyword">enum</span> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a35d6cf42451e70ae0298555699c807c4">IONIZATIONMETHOD</a> {IM_ESI = 0, IM_MALDI = 1, IM_ALL = 2};</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a118b7b87c79b44b10112206841e9fa99ae950ac3b5ed4f0c15e08535f6f61defc"> 93</a></span>  <span class="keyword">enum</span> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a118b7b87c79b44b10112206841e9fa99">PROFILESHAPE</a> {<a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a118b7b87c79b44b10112206841e9fa99ae950ac3b5ed4f0c15e08535f6f61defc">RT_RECTANGULAR</a>, RT_GAUSSIAN};</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1"> 94</a></span>  <span class="keyword">enum</span> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1">RESOLUTIONMODEL</a> {RES_CONSTANT, RES_LINEAR, RES_SQRT};</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a>();</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">void</span> setDefaultParams_();</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordtype">void</span> add1DSignal_(<a class="code" href="classOpenMS_1_1Feature.html">Feature</a> & feature, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment_ct);</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordtype">void</span> add2DSignal_(<a class="code" href="classOpenMS_1_1Feature.html">Feature</a> & feature, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment_ct);</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordtype">void</span> samplePeptideModel1D_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IsotopeModel.html">IsotopeModel</a> & iso,</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keyword">const</span> <a class="code" href="classdouble.html">SimCoordinateType</a> mz_start,</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keyword">const</span> <a class="code" href="classdouble.html">SimCoordinateType</a> mz_end,</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment,</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment_ct,</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> & activeFeature);</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> </div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordtype">void</span> samplePeptideModel2D_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html">ProductModel<2></a> & pm,</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keyword">const</span> <a class="code" href="classdouble.html">SimCoordinateType</a> mz_start,</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keyword">const</span> <a class="code" href="classdouble.html">SimCoordinateType</a> mz_end,</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <a class="code" href="classdouble.html">SimCoordinateType</a> rt_start,</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <a class="code" href="classdouble.html">SimCoordinateType</a> rt_end,</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment,</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment_ct,</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> & activeFeature);</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> </div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordtype">void</span> chooseElutionProfile_(<a class="code" href="classOpenMS_1_1EGHModel.html">EGHModel</a> * <span class="keyword">const</span> elutionmodel, <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> & feature, <span class="keyword">const</span> <span class="keywordtype">double</span> scale, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> rt_sampling_rate, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment);</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordtype">void</span> createContaminants_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapSim</a> & contaminants, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & exp, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & exp_ct);</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordtype">void</span> addShotNoise_(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment, <a class="code" href="classdouble.html">SimCoordinateType</a> minimal_mz_measurement_limit, <a class="code" href="classdouble.html">SimCoordinateType</a> maximal_mz_measurement_limit);</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> </div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="keywordtype">void</span> addWhiteNoise_(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment);</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span> </div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordtype">void</span> addDetectorNoise_(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment);</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span> </div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keywordtype">void</span> addBaseLine_(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment, <a class="code" href="classdouble.html">SimCoordinateType</a> minimal_mz_measurement_limit);</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span> </div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="keywordtype">void</span> getSamplingGrid_(std::vector<SimCoordinateType> & grid, <span class="keyword">const</span> <a class="code" href="classdouble.html">SimCoordinateType</a> mz_min, <span class="keyword">const</span> <a class="code" href="classdouble.html">SimCoordinateType</a> mz_max, <span class="keyword">const</span> <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> step_Da);</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> </div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="keywordtype">void</span> compressSignals_(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a> & experiment);</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span> </div>
<div class="line"><a name="l00191"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#aa5172269ee939c487130758cadcd4cfb"> 191</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#aa5172269ee939c487130758cadcd4cfb">sampling_points_per_FWHM_</a>;</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span> </div>
<div class="line"><a name="l00194"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a9230fb31da1a74d4242603f43ec837d2"> 194</a></span>  <a class="code" href="classdouble.html">SimCoordinateType</a> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a9230fb31da1a74d4242603f43ec837d2">mz_error_mean_</a>;</div>
<div class="line"><a name="l00196"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a6f24877bfac4bb851db844d4d64bc70b"> 196</a></span>  <a class="code" href="classdouble.html">SimCoordinateType</a> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a6f24877bfac4bb851db844d4d64bc70b">mz_error_stddev_</a>;</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> </div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <a class="code" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> getFeatureScaledIntensity_(<span class="keyword">const</span> <a class="code" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> feature_intensity, <span class="keyword">const</span> <a class="code" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> natural_scaling_factor);</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> </div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <a class="code" href="classdouble.html">DoubleReal</a> getResolution_(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> query_mz, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> resolution, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1">RESOLUTIONMODEL</a> model) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  <a class="code" href="classdouble.html">DoubleReal</a> getPeakWidth_(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> mz, <span class="keyword">const</span> <span class="keywordtype">bool</span> is_gaussian) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span> </div>
<div class="line"><a name="l00228"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a6779ed53a1a1cea178001f2e6a6d19c8"> 228</a></span>  <a class="code" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a6779ed53a1a1cea178001f2e6a6d19c8">intensity_scale_</a>;</div>
<div class="line"><a name="l00230"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a6e56e3a5bdaa0417bb08f9687b79b3da"> 230</a></span>  <a class="code" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a6e56e3a5bdaa0417bb08f9687b79b3da">intensity_scale_stddev_</a>;</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> </div>
<div class="line"><a name="l00234"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a3f60891f90436d076f7219221ff2b963"> 234</a></span>  <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1">RESOLUTIONMODEL</a> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a3f60891f90436d076f7219221ff2b963">res_model_</a>;</div>
<div class="line"><a name="l00236"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#adbfbec82b64e1711adf583d967462c6a"> 236</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#adbfbec82b64e1711adf583d967462c6a">res_base_</a>;</div>
<div class="line"><a name="l00238"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#ae65a24617ce997568df4171fb42332a3"> 238</a></span>  std::vector<SimCoordinateType> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#ae65a24617ce997568df4171fb42332a3">grid_</a>;</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_1RawMSSignalSimulation.html#a1755a34bd4d88feb6a87a209273177eb"> 241</a></span>  <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> <span class="keyword">const</span> * <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a1755a34bd4d88feb6a87a209273177eb">rnd_gen_</a>;</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span> </div>
<div class="line"><a name="l00243"></a><span class="lineno"><a class="line" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html"> 243</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html">ContaminantInfo</a></div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  {</div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a9a2326f35466e54c36c070829245c557"> 245</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a9a2326f35466e54c36c070829245c557">name</a>;</div>
<div class="line"><a name="l00246"></a><span class="lineno"><a class="line" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a3e3c33a9edff8dd3f451e9560defa539"> 246</a></span>  <a class="code" href="classOpenMS_1_1EmpiricalFormula.html">EmpiricalFormula</a> <a class="code" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a3e3c33a9edff8dd3f451e9560defa539">sf</a>;</div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a2810664da1ca109eecd2c9cd2fcaa733"> 247</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a2810664da1ca109eecd2c9cd2fcaa733">rt_start</a>, rt_end, intensity;</div>
<div class="line"><a name="l00248"></a><span class="lineno"><a class="line" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a1770476217a2958fbbe681225b6455c8"> 248</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a1770476217a2958fbbe681225b6455c8">q</a>;</div>
<div class="line"><a name="l00249"></a><span class="lineno"><a class="line" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a4f092a93751a0a02214d7ee8d8693178"> 249</a></span>  <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a118b7b87c79b44b10112206841e9fa99">PROFILESHAPE</a> <a class="code" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a4f092a93751a0a02214d7ee8d8693178">shape</a>;</div>
<div class="line"><a name="l00250"></a><span class="lineno"><a class="line" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a979efc903adb01c0801fe7efdd698dbd"> 250</a></span>  <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a35d6cf42451e70ae0298555699c807c4">IONIZATIONMETHOD</a> <a class="code" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a979efc903adb01c0801fe7efdd698dbd">im</a>;</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  };</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span> </div>
<div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a5d74c3f1b030f8633a63cc9cbd1e255c"> 253</a></span>  std::vector<ContaminantInfo> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a5d74c3f1b030f8633a63cc9cbd1e255c">contaminants_</a>;</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span> </div>
<div class="line"><a name="l00258"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a0ab3b2ea50a415b711d57ef6c888da8e"> 258</a></span>  std::vector<std::vector<double> > <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a0ab3b2ea50a415b711d57ef6c888da8e">threaded_random_numbers_</a>;</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span> </div>
<div class="line"><a name="l00264"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a515ff53e001edd54753be797f9da72aa"> 264</a></span>  std::vector<Size> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a515ff53e001edd54753be797f9da72aa">threaded_random_numbers_index_</a>;</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span> </div>
<div class="line"><a name="l00266"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#ab49500496d9f3af2a1d4c0ced31118ff"> 266</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> THREADED_RANDOM_NUMBER_POOL_SIZE_ = 500;</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span> </div>
<div class="line"><a name="l00268"></a><span class="lineno"><a class="line" href="classOpenMS_1_1RawMSSignalSimulation.html#a6dbbe280d54cf3dd4962dd7c3e5cb059"> 268</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1RawMSSignalSimulation.html#a6dbbe280d54cf3dd4962dd7c3e5cb059">contaminants_loaded_</a>;</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  };</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span> </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> </div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span> <span class="preprocessor">#endif</span></div>
<div class="ttc" id="ProductModel_8h_html"><div class="ttname"><a href="ProductModel_8h.html">ProductModel.h</a></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_1RawMSSignalSimulation_html_a35d6cf42451e70ae0298555699c807c4"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a35d6cf42451e70ae0298555699c807c4">OpenMS::RawMSSignalSimulation::IONIZATIONMETHOD</a></div><div class="ttdeci">IONIZATIONMETHOD</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_a3f60891f90436d076f7219221ff2b963"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a3f60891f90436d076f7219221ff2b963">OpenMS::RawMSSignalSimulation::res_model_</a></div><div class="ttdeci">RESOLUTIONMODEL res_model_</div><div class="ttdoc">model of how resolution behaves with increasing m/z </div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:234</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeModel_html"><div class="ttname"><a href="classOpenMS_1_1IsotopeModel.html">OpenMS::IsotopeModel</a></div><div class="ttdoc">Isotope distribution approximated using linear interpolation. </div><div class="ttdef"><b>Definition:</b> IsotopeModel.h:59</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_1RawMSSignalSimulation_html_a118b7b87c79b44b10112206841e9fa99ae950ac3b5ed4f0c15e08535f6f61defc"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a118b7b87c79b44b10112206841e9fa99ae950ac3b5ed4f0c15e08535f6f61defc">OpenMS::RawMSSignalSimulation::RT_RECTANGULAR</a></div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_a0ab3b2ea50a415b711d57ef6c888da8e"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a0ab3b2ea50a415b711d57ef6c888da8e">OpenMS::RawMSSignalSimulation::threaded_random_numbers_</a></div><div class="ttdeci">std::vector< std::vector< double > > threaded_random_numbers_</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:258</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="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_ad2e04a1a86912fd63b00661e2348d3b1"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1">OpenMS::RawMSSignalSimulation::RESOLUTIONMODEL</a></div><div class="ttdeci">RESOLUTIONMODEL</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1ProductModel_3_012_01_4_html"><div class="ttname"><a href="classOpenMS_1_1ProductModel_3_012_01_4.html">OpenMS::ProductModel< 2 ></a></div><div class="ttdoc">The class template is only implemented for D=2 because we use Peak2D here. </div><div class="ttdef"><b>Definition:</b> ProductModel.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_ae65a24617ce997568df4171fb42332a3"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#ae65a24617ce997568df4171fb42332a3">OpenMS::RawMSSignalSimulation::grid_</a></div><div class="ttdeci">std::vector< SimCoordinateType > grid_</div><div class="ttdoc">m/z sampling grid for all signals </div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:238</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_a5d74c3f1b030f8633a63cc9cbd1e255c"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a5d74c3f1b030f8633a63cc9cbd1e255c">OpenMS::RawMSSignalSimulation::contaminants_</a></div><div class="ttdeci">std::vector< ContaminantInfo > contaminants_</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:253</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="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo_html"><div class="ttname"><a href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html">OpenMS::RawMSSignalSimulation::ContaminantInfo</a></div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:243</div></div>
<div class="ttc" id="classOpenMS_1_1EmpiricalFormula_html"><div class="ttname"><a href="classOpenMS_1_1EmpiricalFormula.html">OpenMS::EmpiricalFormula</a></div><div class="ttdoc">Representation of an empirical formula. </div><div class="ttdef"><b>Definition:</b> EmpiricalFormula.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_a9230fb31da1a74d4242603f43ec837d2"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a9230fb31da1a74d4242603f43ec837d2">OpenMS::RawMSSignalSimulation::mz_error_mean_</a></div><div class="ttdeci">SimCoordinateType mz_error_mean_</div><div class="ttdoc">Mean of peak m/z error. </div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:194</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_adbfbec82b64e1711adf583d967462c6a"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#adbfbec82b64e1711adf583d967462c6a">OpenMS::RawMSSignalSimulation::res_base_</a></div><div class="ttdeci">DoubleReal res_base_</div><div class="ttdoc">base resolution at 400 Th </div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:236</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_aa5172269ee939c487130758cadcd4cfb"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#aa5172269ee939c487130758cadcd4cfb">OpenMS::RawMSSignalSimulation::sampling_points_per_FWHM_</a></div><div class="ttdeci">Int sampling_points_per_FWHM_</div><div class="ttdoc">number of points sampled per peak&#39;s FWHM </div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:191</div></div>
<div class="ttc" id="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo_html_a979efc903adb01c0801fe7efdd698dbd"><div class="ttname"><a href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a979efc903adb01c0801fe7efdd698dbd">OpenMS::RawMSSignalSimulation::ContaminantInfo::im</a></div><div class="ttdeci">IONIZATIONMETHOD im</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:250</div></div>
<div class="ttc" id="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo_html_a1770476217a2958fbbe681225b6455c8"><div class="ttname"><a href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a1770476217a2958fbbe681225b6455c8">OpenMS::RawMSSignalSimulation::ContaminantInfo::q</a></div><div class="ttdeci">Int q</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:248</div></div>
<div class="ttc" id="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo_html_a3e3c33a9edff8dd3f451e9560defa539"><div class="ttname"><a href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a3e3c33a9edff8dd3f451e9560defa539">OpenMS::RawMSSignalSimulation::ContaminantInfo::sf</a></div><div class="ttdeci">EmpiricalFormula sf</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:246</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_a118b7b87c79b44b10112206841e9fa99"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a118b7b87c79b44b10112206841e9fa99">OpenMS::RawMSSignalSimulation::PROFILESHAPE</a></div><div class="ttdeci">PROFILESHAPE</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:93</div></div>
<div class="ttc" id="EGHModel_8h_html"><div class="ttname"><a href="EGHModel_8h.html">EGHModel.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1EGHModel_html"><div class="ttname"><a href="classOpenMS_1_1EGHModel.html">OpenMS::EGHModel</a></div><div class="ttdoc">Exponential-Gaussian hybrid distribution model for elution profiles. </div><div class="ttdef"><b>Definition:</b> EGHModel.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_a1755a34bd4d88feb6a87a209273177eb"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a1755a34bd4d88feb6a87a209273177eb">OpenMS::RawMSSignalSimulation::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> RawMSSignalSimulation.h:241</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_1RawMSSignalSimulation_html_a6f24877bfac4bb851db844d4d64bc70b"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a6f24877bfac4bb851db844d4d64bc70b">OpenMS::RawMSSignalSimulation::mz_error_stddev_</a></div><div class="ttdeci">SimCoordinateType mz_error_stddev_</div><div class="ttdoc">Standard deviation of peak m/z error. </div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:196</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_a6dbbe280d54cf3dd4962dd7c3e5cb059"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a6dbbe280d54cf3dd4962dd7c3e5cb059">OpenMS::RawMSSignalSimulation::contaminants_loaded_</a></div><div class="ttdeci">bool contaminants_loaded_</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:268</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_1RawMSSignalSimulation_html"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html">OpenMS::RawMSSignalSimulation</a></div><div class="ttdoc">Simulates MS signals for a given set of peptides. </div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:61</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="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo_html_a2810664da1ca109eecd2c9cd2fcaa733"><div class="ttname"><a href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a2810664da1ca109eecd2c9cd2fcaa733">OpenMS::RawMSSignalSimulation::ContaminantInfo::rt_start</a></div><div class="ttdeci">DoubleReal rt_start</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:247</div></div>
<div class="ttc" id="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo_html_a4f092a93751a0a02214d7ee8d8693178"><div class="ttname"><a href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a4f092a93751a0a02214d7ee8d8693178">OpenMS::RawMSSignalSimulation::ContaminantInfo::shape</a></div><div class="ttdeci">PROFILESHAPE shape</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:249</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="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo_html_a9a2326f35466e54c36c070829245c557"><div class="ttname"><a href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html#a9a2326f35466e54c36c070829245c557">OpenMS::RawMSSignalSimulation::ContaminantInfo::name</a></div><div class="ttdeci">String name</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:245</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_1RawMSSignalSimulation_html_a6779ed53a1a1cea178001f2e6a6d19c8"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a6779ed53a1a1cea178001f2e6a6d19c8">OpenMS::RawMSSignalSimulation::intensity_scale_</a></div><div class="ttdeci">SimIntensityType intensity_scale_</div><div class="ttdoc">Scaling factor of peak intensities. </div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:228</div></div>
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_a6e56e3a5bdaa0417bb08f9687b79b3da"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a6e56e3a5bdaa0417bb08f9687b79b3da">OpenMS::RawMSSignalSimulation::intensity_scale_stddev_</a></div><div class="ttdeci">SimIntensityType intensity_scale_stddev_</div><div class="ttdoc">Standard deviation of peak intensity scaling. </div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:230</div></div>
<div class="ttc" id="classOpenMS_1_1RawMSSignalSimulation_html_a515ff53e001edd54753be797f9da72aa"><div class="ttname"><a href="classOpenMS_1_1RawMSSignalSimulation.html#a515ff53e001edd54753be797f9da72aa">OpenMS::RawMSSignalSimulation::threaded_random_numbers_index_</a></div><div class="ttdeci">std::vector< Size > threaded_random_numbers_index_</div><div class="ttdef"><b>Definition:</b> RawMSSignalSimulation.h:264</div></div>
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