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<div class="title">SvmTheoreticalSpectrumGeneratorSet.h</div> </div>
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<a href="SvmTheoreticalSpectrumGeneratorSet_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>
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<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
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<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<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>
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<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>
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<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
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<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>
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<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
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<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
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<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Sandro Andreotti $</span></div>
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<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Sandro Andreotti $</span></div>
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<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
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<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> </div>
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<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#ifndef OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATORSET_H</span></div>
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<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATORSET_H</span></div>
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<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor"></span></div>
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<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="SimTypes_8h.html">OpenMS/SIMULATION/SimTypes.h</a>></span></div>
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<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>></span></div>
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<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="SvmTheoreticalSpectrumGenerator_8h.html">OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGenerator.h</a>></span></div>
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<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
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<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">namespace </span>OpenMS</div>
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<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> {</div>
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<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html"> 58</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html">SvmTheoreticalSpectrumGeneratorSet</a></div>
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<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  {</div>
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<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="keyword">public</span>:</div>
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<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div>
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<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html">SvmTheoreticalSpectrumGeneratorSet</a>();</div>
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<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
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<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html">SvmTheoreticalSpectrumGeneratorSet</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html">SvmTheoreticalSpectrumGeneratorSet</a> & source);</div>
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<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
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<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html">SvmTheoreticalSpectrumGeneratorSet</a>();</div>
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<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div>
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<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html">SvmTheoreticalSpectrumGeneratorSet</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html">SvmTheoreticalSpectrumGeneratorSet</a> & tsg);</div>
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<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
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<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordtype">void</span> simulate(<a class="code" href="classOpenMS_1_1MSSpectrum.html">RichPeakSpectrum</a> & spectrum, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> & peptide, <span class="keyword">const</span> gsl_rng * rng, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> precursor_charge);</div>
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<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
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<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordtype">void</span> load(<a class="code" href="classOpenMS_1_1String.html">String</a>);</div>
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<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
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<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">void</span> getSupportedCharges(std::set<Size> & charges);</div>
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<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
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<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> & getSvmModel(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>);</div>
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<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
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<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> <span class="keyword">protected</span>:</div>
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<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="comment">//map containing the simulator for each charge variant</span></div>
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<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html#a60d537cc4998816bcdd12fd450dc80d2"> 92</a></span>  std::map<Size, SvmTheoreticalSpectrumGenerator> <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html#a60d537cc4998816bcdd12fd450dc80d2">simulators_</a>;</div>
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<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
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<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  };</div>
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<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div>
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<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
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<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> }</div>
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<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div>
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<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
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<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> </div>
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<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> <span class="preprocessor">#endif</span></div>
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<div class="ttc" id="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
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<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>
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<div class="ttc" id="SimTypes_8h_html"><div class="ttname"><a href="SimTypes_8h.html">SimTypes.h</a></div></div>
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<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet_html"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html">OpenMS::SvmTheoreticalSpectrumGeneratorSet</a></div><div class="ttdoc">Loads SvmTheoreticalSpectrumGenerator instances for different charges. </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGeneratorSet.h:58</div></div>
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<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>
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<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">OpenMS::SvmTheoreticalSpectrumGenerator</a></div><div class="ttdoc">Simulates ms2 spectra with support vector machines. </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:69</div></div>
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<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< RichPeak1D ></a></div></div>
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<div class="ttc" id="SvmTheoreticalSpectrumGenerator_8h_html"><div class="ttname"><a href="SvmTheoreticalSpectrumGenerator_8h.html">SvmTheoreticalSpectrumGenerator.h</a></div></div>
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<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet_html_a60d537cc4998816bcdd12fd450dc80d2"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorSet.html#a60d537cc4998816bcdd12fd450dc80d2">OpenMS::SvmTheoreticalSpectrumGeneratorSet::simulators_</a></div><div class="ttdeci">std::map< Size, SvmTheoreticalSpectrumGenerator > simulators_</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGeneratorSet.h:92</div></div>
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<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>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:21 using doxygen 1.8.5</font></TD>
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