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<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_0cb073f3ffc34c59e0f7dd814375c720.html">SIMULATION</a></li><li class="navelem"><a class="el" href="dir_5daaaa26cf350675d3033118b6f3b93f.html">LABELING</a></li> </ul>
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<div class="title">O18Labeler.h</div> </div>
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<a href="O18Labeler_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">// $Authors: Stephan Aiche$</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_LABELING_O18LABELER_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_LABELING_O18LABELER_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="BaseLabeler_8h.html">OpenMS/SIMULATION/LABELING/BaseLabeler.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> {</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
<div class="line"><a name="l00050"></a><span class="lineno"><a class="line" href="classOpenMS_1_1O18Labeler.html"> 50</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1O18Labeler.html">O18Labeler</a> :</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1BaseLabeler.html">BaseLabeler</a></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  {</div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <a class="code" href="classOpenMS_1_1O18Labeler.html">O18Labeler</a>();</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1O18Labeler.html">O18Labeler</a>();</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="classOpenMS_1_1O18Labeler.html#a4de43939ecee328ea4cd203a39fb3dc0"> 62</a></span>  <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1BaseLabeler.html">BaseLabeler</a>* <a class="code" href="classOpenMS_1_1O18Labeler.html#a4de43939ecee328ea4cd203a39fb3dc0">create</a>()</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  {</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1O18Labeler.html">O18Labeler</a>();</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> </div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1O18Labeler.html#af73fd15708e50e77665070023a09cc87"> 68</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1O18Labeler.html#af73fd15708e50e77665070023a09cc87">getProductName</a>()</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  {</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordflow">return</span> <span class="stringliteral">"o18"</span>;</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  }</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="comment">// redeclaration of virtual methods</span></div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordtype">void</span> preCheck(<a class="code" href="classOpenMS_1_1Param.html">Param</a>& param) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordtype">void</span> setUpHook(<a class="code" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">FeatureMapSimVector</a>& <span class="comment">/* channels */</span>);</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordtype">void</span> postDigestHook(<a class="code" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">FeatureMapSimVector</a>& <span class="comment">/* features_to_simulate */</span>);</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>  <span class="keywordtype">void</span> postRTHook(<a class="code" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">FeatureMapSimVector</a>& <span class="comment">/* features_to_simulate */</span>);</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordtype">void</span> postDetectabilityHook(<a class="code" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">FeatureMapSimVector</a>& <span class="comment">/* features_to_simulate */</span>);</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keywordtype">void</span> postIonizationHook(<a class="code" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">FeatureMapSimVector</a>& <span class="comment">/* features_to_simulate */</span>);</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordtype">void</span> postRawMSHook(<a class="code" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">FeatureMapSimVector</a>& <span class="comment">/* features_to_simulate */</span>);</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordtype">void</span> postRawTandemMSHook(<a class="code" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">FeatureMapSimVector</a>& <span class="comment">/* features_to_simulate */</span>, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSSimExperiment</a>& <span class="comment">/* simulated map */</span>);</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>  <span class="keywordtype">void</span> addModificationToPeptideHit_(<a class="code" href="classOpenMS_1_1Feature.html">Feature</a>& feature, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& modification) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> mergeFeatures_(<a class="code" href="classOpenMS_1_1Feature.html">Feature</a>& labeled_channel_feature, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a>& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="classOpenMS_1_1O18Labeler.html#ac7f2d49dc922a97884d6c0b66f5924b3"> 97</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1O18Labeler.html#ac7f2d49dc922a97884d6c0b66f5924b3">LIGHT_CHANNEL_ID_</a>;</div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="classOpenMS_1_1O18Labeler.html#af13308ade5d7d5e1cd99361920fedf01"> 99</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1O18Labeler.html#af13308ade5d7d5e1cd99361920fedf01">MEDIUM_CHANNEL_ID_</a>;</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1O18Labeler.html#a99a172d65ff67afb791c461c855d380e"> 101</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1O18Labeler.html#a99a172d65ff67afb791c461c855d380e">HEAVY_CHANNEL_ID_</a>;</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  };</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <span class="preprocessor">#endif //#ifndef OPENMS_SIMULATION_LABELING_O18LABELER_H</span></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="BaseLabeler_8h_html"><div class="ttname"><a href="BaseLabeler_8h.html">BaseLabeler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1AASequence_html"><div class="ttname"><a href="classOpenMS_1_1AASequence.html">OpenMS::AASequence</a></div><div class="ttdoc">Representation of a peptide/protein sequence. </div><div class="ttdef"><b>Definition:</b> AASequence.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1O18Labeler_html_af73fd15708e50e77665070023a09cc87"><div class="ttname"><a href="classOpenMS_1_1O18Labeler.html#af73fd15708e50e77665070023a09cc87">OpenMS::O18Labeler::getProductName</a></div><div class="ttdeci">static const String getProductName()</div><div class="ttdoc">name of the model (needed by Factory) </div><div class="ttdef"><b>Definition:</b> O18Labeler.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1O18Labeler_html_a99a172d65ff67afb791c461c855d380e"><div class="ttname"><a href="classOpenMS_1_1O18Labeler.html#a99a172d65ff67afb791c461c855d380e">OpenMS::O18Labeler::HEAVY_CHANNEL_ID_</a></div><div class="ttdeci">static const int HEAVY_CHANNEL_ID_</div><div class="ttdoc">Map ID for the heavy/bi-labeled channel. </div><div class="ttdef"><b>Definition:</b> O18Labeler.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1O18Labeler_html_af13308ade5d7d5e1cd99361920fedf01"><div class="ttname"><a href="classOpenMS_1_1O18Labeler.html#af13308ade5d7d5e1cd99361920fedf01">OpenMS::O18Labeler::MEDIUM_CHANNEL_ID_</a></div><div class="ttdeci">static const int MEDIUM_CHANNEL_ID_</div><div class="ttdoc">Map ID for the medium/mono-labeled channel. </div><div class="ttdef"><b>Definition:</b> O18Labeler.h:99</div></div>
<div class="ttc" id="classOpenMS_1_1O18Labeler_html"><div class="ttname"><a href="classOpenMS_1_1O18Labeler.html">OpenMS::O18Labeler</a></div><div class="ttdoc">Simulate O-18 experiments. </div><div class="ttdef"><b>Definition:</b> O18Labeler.h:50</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_1O18Labeler_html_ac7f2d49dc922a97884d6c0b66f5924b3"><div class="ttname"><a href="classOpenMS_1_1O18Labeler.html#ac7f2d49dc922a97884d6c0b66f5924b3">OpenMS::O18Labeler::LIGHT_CHANNEL_ID_</a></div><div class="ttdeci">static const int LIGHT_CHANNEL_ID_</div><div class="ttdoc">Map ID for the light/unlabeled channel. </div><div class="ttdef"><b>Definition:</b> O18Labeler.h:97</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html"><div class="ttname"><a href="classOpenMS_1_1Param.html">OpenMS::Param</a></div><div class="ttdoc">Management and storage of parameters / INI files. </div><div class="ttdef"><b>Definition:</b> Param.h:69</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="namespaceOpenMS_html_a5377a8d620ef376a0b1eb2503b847e79"><div class="ttname"><a href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">OpenMS::FeatureMapSimVector</a></div><div class="ttdeci">std::vector< FeatureMapSim > FeatureMapSimVector</div><div class="ttdoc">Sim FeatureMap Vector. </div><div class="ttdef"><b>Definition:</b> SimTypes.h:80</div></div>
<div class="ttc" id="classOpenMS_1_1BaseLabeler_html"><div class="ttname"><a href="classOpenMS_1_1BaseLabeler.html">OpenMS::BaseLabeler</a></div><div class="ttdoc">Abstract base class for all kinds of labeling techniques. </div><div class="ttdef"><b>Definition:</b> BaseLabeler.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1O18Labeler_html_a4de43939ecee328ea4cd203a39fb3dc0"><div class="ttname"><a href="classOpenMS_1_1O18Labeler.html#a4de43939ecee328ea4cd203a39fb3dc0">OpenMS::O18Labeler::create</a></div><div class="ttdeci">static BaseLabeler * create()</div><div class="ttdoc">create new object (needed by Factory) </div><div class="ttdef"><b>Definition:</b> O18Labeler.h:62</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 11:19:18 using doxygen 1.8.5</font></TD>
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</TABLE>
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