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<a href="SimTypes_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>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<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>&#160;<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>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<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>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
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<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<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>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
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<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Stephan Aiche$</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Stephan Aiche, Chris Bielow$</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_SIMULATION_SIMTYPES_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_SIMULATION_SIMTYPES_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;utility&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;map&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;utility&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Peak2D_8h.html">OpenMS/KERNEL/Peak2D.h</a>&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="RichPeak1D_8h.html">OpenMS/KERNEL/RichPeak1D.h</a>&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="AASequence_8h.html">OpenMS/CHEMISTRY/AASequence.h</a>&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>&gt;</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FASTAFile_8h.html">OpenMS/FORMAT/FASTAFile.h</a>&gt;</span></div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ItraqConstants_8h.html">OpenMS/ANALYSIS/QUANTITATION/ItraqConstants.h</a>&gt;</span></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MetaInfoInterface_8h.html">OpenMS/METADATA/MetaInfoInterface.h</a>&gt;</span></div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;<span class="comment">// GSL includes (random number generation)</span></div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_rng.h&gt;</span></div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_randist.h&gt;</span></div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;{</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">   59</a></span>&#160;  <span class="keyword">typedef</span> <a class="code" href="classdouble.html">Peak2D::CoordinateType</a> <a class="code" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a>;</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;</div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">   62</a></span>&#160;  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> <a class="code" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a>;</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#aeeb197e95f7bd1ada2cca075468bab8f">   65</a></span>&#160;  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1BaseFeature.html#a87171116869a9f9511d7ce9ad7baf5d6">Feature::ChargeType</a> <a class="code" href="namespaceOpenMS.html#aeeb197e95f7bd1ada2cca075468bab8f">SimChargeType</a>;</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#ade9515c83ff4c03f40e7465d159daa67">   68</a></span>&#160;  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1Peak1D.html">Peak1D</a> <a class="code" href="namespaceOpenMS.html#ade9515c83ff4c03f40e7465d159daa67">SimPointType</a>;</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SampleProteins.html">   71</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SampleProteins.html">SampleProteins</a> : <span class="keyword">public</span> std::vector&lt;std::pair&lt;FASTAFile::FASTAEntry, MetaInfoInterface&gt; &gt; { }; </div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SampleChannels.html">   74</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SampleChannels.html">SampleChannels</a> : <span class="keyword">public</span> std::vector&lt;SampleProteins&gt; { }; </div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">   77</a></span>&#160;  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> <a class="code" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a>;</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;</div>
<div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">   80</a></span>&#160;  <span class="keyword">typedef</span> std::vector&lt;FeatureMapSim&gt; <a class="code" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">FeatureMapSimVector</a>;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;</div>
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">   83</a></span>&#160;  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;SimPointType&gt;</a> <a class="code" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a>;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;</div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SimRandomNumberGenerator.html">   99</a></span>&#160;  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a></div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;  {</div>
<div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">  102</a></span>&#160;    gsl_rng * <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a>;</div>
<div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">  104</a></span>&#160;    gsl_rng * <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a>;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;</div>
<div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SimRandomNumberGenerator.html#aeaf0195c71752fdcda29e355b362f143">  107</a></span>&#160;    <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#aeaf0195c71752fdcda29e355b362f143">SimRandomNumberGenerator</a>() :</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;      <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a>(<a class="code" href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>),</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;      <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a>(<a class="code" href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>)</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    {</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;    }</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;    <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#aeaf0195c71752fdcda29e355b362f143">SimRandomNumberGenerator</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> &amp; other) :</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;      <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a>(other.<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a>),</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;      <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a>(other.<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a>)</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;    {</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;    }</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;</div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SimRandomNumberGenerator.html#a5b9420ff81e904382d63a2f0db3bb9d7">  124</a></span>&#160;    <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a5b9420ff81e904382d63a2f0db3bb9d7">~SimRandomNumberGenerator</a>()</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;    {</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a> != 0)</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;      {</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;        gsl_rng_free(<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a>);</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;      }</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a> != 0)</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;      {</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;        gsl_rng_free(<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a>);</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;      }</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;    }</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;</div>
<div class="line"><a name="l00140"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SimRandomNumberGenerator.html#ad93e2ec7b4e761f3b62011681589cb80">  140</a></span>&#160;    <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> &amp; <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#ad93e2ec7b4e761f3b62011681589cb80">operator=</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> &amp; source)</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;    {</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;      this-&gt;<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a> = source.<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a>;</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;      this-&gt;<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a> = source.<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a>;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;      <span class="keywordflow">return</span> *<span class="keyword">this</span>;</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;    }</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;</div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SimRandomNumberGenerator.html#a2411805d760c5f01bbf46ad4cae5d3ad">  149</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a2411805d760c5f01bbf46ad4cae5d3ad">initialize</a>(<span class="keywordtype">bool</span> biological_random, <span class="keywordtype">bool</span> technical_random)</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;    {</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;      <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a> = gsl_rng_alloc(gsl_rng_mt19937);</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;      <span class="keywordflow">if</span> (biological_random)</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;      {</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;        gsl_rng_set(<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a>, time(0));</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;      }</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;      <span class="keywordflow">else</span> <span class="comment">// use gsl default seed to get reproducible experiments</span></div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;      {</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;        gsl_rng_set(<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">biological_rng</a>, 0);</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;      }</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;      <a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a> = gsl_rng_alloc(gsl_rng_mt19937);</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;      <span class="keywordflow">if</span> (technical_random)</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;      {</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;        gsl_rng_set(<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a>, time(0));</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;      }</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;      <span class="keywordflow">else</span> <span class="comment">// use gsl default seed to get reproducible experiments</span></div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;      {</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;        gsl_rng_set(<a class="code" href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">technical_rng</a>, 0);</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;      }</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;    }</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;  };</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;}</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;<span class="preprocessor">#endif</span></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="namespaceOpenMS_html_ade9515c83ff4c03f40e7465d159daa67"><div class="ttname"><a href="namespaceOpenMS.html#ade9515c83ff4c03f40e7465d159daa67">OpenMS::SimPointType</a></div><div class="ttdeci">Peak1D SimPointType</div><div class="ttdoc">Raw data point. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a4a8c5b2adc05e9ff96a007385bfe9b47"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">OpenMS::Peak2D::IntensityType</a></div><div class="ttdeci">Real IntensityType</div><div class="ttdoc">Intensity type. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:63</div></div>
<div class="ttc" id="structOpenMS_1_1SimRandomNumberGenerator_html_a2411805d760c5f01bbf46ad4cae5d3ad"><div class="ttname"><a href="structOpenMS_1_1SimRandomNumberGenerator.html#a2411805d760c5f01bbf46ad4cae5d3ad">OpenMS::SimRandomNumberGenerator::initialize</a></div><div class="ttdeci">void initialize(bool biological_random, bool technical_random)</div><div class="ttdoc">Initialize the RNGs. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:149</div></div>
<div class="ttc" id="namespaceOpenMS_html_a9396dc872898d760f035465bc56585d8"><div class="ttname"><a href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">OpenMS::FeatureMapSim</a></div><div class="ttdeci">FeatureMap FeatureMapSim</div><div class="ttdoc">Sim FeatureMap. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1BaseFeature_html_a87171116869a9f9511d7ce9ad7baf5d6"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html#a87171116869a9f9511d7ce9ad7baf5d6">OpenMS::BaseFeature::ChargeType</a></div><div class="ttdeci">Int ChargeType</div><div class="ttdoc">Type of charge values. </div><div class="ttdef"><b>Definition:</b> BaseFeature.h:64</div></div>
<div class="ttc" id="FASTAFile_8h_html"><div class="ttname"><a href="FASTAFile_8h.html">FASTAFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap&lt;&gt;</a></div></div>
<div class="ttc" id="RichPeak1D_8h_html"><div class="ttname"><a href="RichPeak1D_8h.html">RichPeak1D.h</a></div></div>
<div class="ttc" id="IsotopeWaveletParallelFor_8h_html_a070d2ce7b6bb7e5c05602aa8c308d0c4"><div class="ttname"><a href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a></div><div class="ttdeci">#define NULL</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletParallelFor.h:41</div></div>
<div class="ttc" id="classOpenMS_1_1SampleChannels_html"><div class="ttname"><a href="classOpenMS_1_1SampleChannels.html">OpenMS::SampleChannels</a></div><div class="ttdoc">Container for multiple channels of SampleProteins. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:74</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="AASequence_8h_html"><div class="ttname"><a href="AASequence_8h.html">AASequence.h</a></div></div>
<div class="ttc" id="Peak2D_8h_html"><div class="ttname"><a href="Peak2D_8h.html">Peak2D.h</a></div></div>
<div class="ttc" id="namespaceOpenMS_html_a375f999020e3ba21026a3f0be0c079f6"><div class="ttname"><a href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">OpenMS::SimCoordinateType</a></div><div class="ttdeci">Peak2D::CoordinateType SimCoordinateType</div><div class="ttdoc">Coordinate type in mz and rt dimension. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:59</div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1SimRandomNumberGenerator_html_a5b9420ff81e904382d63a2f0db3bb9d7"><div class="ttname"><a href="structOpenMS_1_1SimRandomNumberGenerator.html#a5b9420ff81e904382d63a2f0db3bb9d7">OpenMS::SimRandomNumberGenerator::~SimRandomNumberGenerator</a></div><div class="ttdeci">~SimRandomNumberGenerator()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:124</div></div>
<div class="ttc" id="structOpenMS_1_1SimRandomNumberGenerator_html_a8418c7661e9d110377e7160d01550954"><div class="ttname"><a href="structOpenMS_1_1SimRandomNumberGenerator.html#a8418c7661e9d110377e7160d01550954">OpenMS::SimRandomNumberGenerator::biological_rng</a></div><div class="ttdeci">gsl_rng * biological_rng</div><div class="ttdoc">GSL random number generator for biological variability. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:102</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html">OpenMS::Peak1D</a></div><div class="ttdoc">A 1-dimensional raw data point or peak. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:55</div></div>
<div class="ttc" id="structOpenMS_1_1SimRandomNumberGenerator_html_ad93e2ec7b4e761f3b62011681589cb80"><div class="ttname"><a href="structOpenMS_1_1SimRandomNumberGenerator.html#ad93e2ec7b4e761f3b62011681589cb80">OpenMS::SimRandomNumberGenerator::operator=</a></div><div class="ttdeci">SimRandomNumberGenerator &amp; operator=(const SimRandomNumberGenerator &amp;source)</div><div class="ttdoc">Assignment operator. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:140</div></div>
<div class="ttc" id="MetaInfoInterface_8h_html"><div class="ttname"><a href="MetaInfoInterface_8h.html">MetaInfoInterface.h</a></div></div>
<div class="ttc" id="namespaceOpenMS_html_ad8fab082e8d37c2f39ca13d92608d71d"><div class="ttname"><a href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">OpenMS::MSSimExperiment</a></div><div class="ttdeci">MSExperiment&lt; SimPointType &gt; MSSimExperiment</div><div class="ttdoc">Sim MSExperiment type. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:83</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="ItraqConstants_8h_html"><div class="ttname"><a href="ItraqConstants_8h.html">ItraqConstants.h</a></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&lt; SimPointType &gt;</a></div></div>
<div class="ttc" id="structOpenMS_1_1SimRandomNumberGenerator_html_aeaf0195c71752fdcda29e355b362f143"><div class="ttname"><a href="structOpenMS_1_1SimRandomNumberGenerator.html#aeaf0195c71752fdcda29e355b362f143">OpenMS::SimRandomNumberGenerator::SimRandomNumberGenerator</a></div><div class="ttdeci">SimRandomNumberGenerator()</div><div class="ttdoc">Default constructor. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1SampleProteins_html"><div class="ttname"><a href="classOpenMS_1_1SampleProteins.html">OpenMS::SampleProteins</a></div><div class="ttdoc">Container for FASTAEntry &amp;amp; abundance information. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:71</div></div>
<div class="ttc" id="structOpenMS_1_1SimRandomNumberGenerator_html_a8764fd4a009fc26b72180f667d09f1ec"><div class="ttname"><a href="structOpenMS_1_1SimRandomNumberGenerator.html#a8764fd4a009fc26b72180f667d09f1ec">OpenMS::SimRandomNumberGenerator::technical_rng</a></div><div class="ttdeci">gsl_rng * technical_rng</div><div class="ttdoc">GSL random number generator for technical variability. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:104</div></div>
<div class="ttc" id="namespaceOpenMS_html_a5377a8d620ef376a0b1eb2503b847e79"><div class="ttname"><a href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">OpenMS::FeatureMapSimVector</a></div><div class="ttdeci">std::vector&lt; FeatureMapSim &gt; FeatureMapSimVector</div><div class="ttdoc">Sim FeatureMap Vector. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:80</div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:20 using doxygen 1.8.5</font></TD>
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