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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_330fe73d44ce641f33dd6036f80161a5.html">ANALYSIS</a></li><li class="navelem"><a class="el" href="dir_bf7833e183117afcae6dca8df942d40c.html">QUANTITATION</a></li> </ul>
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<a href="IsobaricQuantifier_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>
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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>
<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_ANALYSIS_QUANTITATION_ISOBARICQUANTIFIER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_QUANTITATION_ISOBARICQUANTIFIER_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> </div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="ConsensusMap_8h.html">OpenMS/KERNEL/ConsensusMap.h</a>></span></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> <span class="preprocessor">#include <<a class="code" href="IsobaricQuantitationMethod_8h.html">OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantitationMethod.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="IsobaricQuantifierStatistics_8h.html">OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantifierStatistics.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> {</div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IsobaricQuantifier.html"> 53</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1IsobaricQuantifier.html">IsobaricQuantifier</a> :</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  {</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <a class="code" href="classOpenMS_1_1IsobaricQuantifier.html">IsobaricQuantifier</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IsobaricQuantitationMethod.html">IsobaricQuantitationMethod</a>* <span class="keyword">const</span> quant_method);</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <a class="code" href="classOpenMS_1_1IsobaricQuantifier.html">IsobaricQuantifier</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IsobaricQuantifier.html">IsobaricQuantifier</a>& other);</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <a class="code" href="classOpenMS_1_1IsobaricQuantifier.html">IsobaricQuantifier</a>& operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IsobaricQuantifier.html">IsobaricQuantifier</a>& rhs);</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordtype">void</span> quantify(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a>& consensus_map_in, <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a>& consensus_map_out);</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keywordtype">void</span> setDefaultParams_();</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordtype">void</span> updateMembers_();</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="keyword">private</span>:</div>
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IsobaricQuantifier.html#a820b4d6ccf0333ef634a12daeff75fc4"> 90</a></span>  <a class="code" href="structOpenMS_1_1IsobaricQuantifierStatistics.html">IsobaricQuantifierStatistics</a> <a class="code" href="classOpenMS_1_1IsobaricQuantifier.html#a820b4d6ccf0333ef634a12daeff75fc4">stats_</a>;</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IsobaricQuantifier.html#a1a4692b8454e929813cd695bb57c4fb3"> 93</a></span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IsobaricQuantitationMethod.html">IsobaricQuantitationMethod</a>* <a class="code" href="classOpenMS_1_1IsobaricQuantifier.html#a1a4692b8454e929813cd695bb57c4fb3">quant_method_</a>;</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IsobaricQuantifier.html#a0c2fe92c5ee2f1ec2ef1809dd9ffe26a"> 96</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1IsobaricQuantifier.html#a0c2fe92c5ee2f1ec2ef1809dd9ffe26a">isotope_correction_enabled_</a>;</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IsobaricQuantifier.html#afa4076b98c61825612fff0b5ce709beb"> 99</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1IsobaricQuantifier.html#afa4076b98c61825612fff0b5ce709beb">normalization_enabled_</a>;</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> </div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordtype">void</span> computeLabelingStatistics_(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a>& consensus_map_out);</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  };</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> } <span class="comment">// namespace</span></div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> <span class="preprocessor">#endif // OPENMS_ANALYSIS_QUANTITATION_ISOBARICQUANTIFIER_H</span></div>
<div class="ttc" id="ConsensusMap_8h_html"><div class="ttname"><a href="ConsensusMap_8h.html">ConsensusMap.h</a></div></div>
<div class="ttc" id="IsobaricQuantifierStatistics_8h_html"><div class="ttname"><a href="IsobaricQuantifierStatistics_8h.html">IsobaricQuantifierStatistics.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html">OpenMS::ConsensusMap</a></div><div class="ttdoc">A container for consensus elements. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:60</div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1IsobaricQuantifierStatistics_html"><div class="ttname"><a href="structOpenMS_1_1IsobaricQuantifierStatistics.html">OpenMS::IsobaricQuantifierStatistics</a></div><div class="ttdoc">Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion...</div><div class="ttdef"><b>Definition:</b> IsobaricQuantifierStatistics.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1IsobaricQuantifier_html_afa4076b98c61825612fff0b5ce709beb"><div class="ttname"><a href="classOpenMS_1_1IsobaricQuantifier.html#afa4076b98c61825612fff0b5ce709beb">OpenMS::IsobaricQuantifier::normalization_enabled_</a></div><div class="ttdeci">bool normalization_enabled_</div><div class="ttdoc">Is true if normalization is enabled, false otherwise. </div><div class="ttdef"><b>Definition:</b> IsobaricQuantifier.h:99</div></div>
<div class="ttc" id="IsobaricQuantitationMethod_8h_html"><div class="ttname"><a href="IsobaricQuantitationMethod_8h.html">IsobaricQuantitationMethod.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1IsobaricQuantifier_html_a820b4d6ccf0333ef634a12daeff75fc4"><div class="ttname"><a href="classOpenMS_1_1IsobaricQuantifier.html#a820b4d6ccf0333ef634a12daeff75fc4">OpenMS::IsobaricQuantifier::stats_</a></div><div class="ttdeci">IsobaricQuantifierStatistics stats_</div><div class="ttdoc">Stats of current quantitation run. </div><div class="ttdef"><b>Definition:</b> IsobaricQuantifier.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1IsobaricQuantifier_html_a1a4692b8454e929813cd695bb57c4fb3"><div class="ttname"><a href="classOpenMS_1_1IsobaricQuantifier.html#a1a4692b8454e929813cd695bb57c4fb3">OpenMS::IsobaricQuantifier::quant_method_</a></div><div class="ttdeci">const IsobaricQuantitationMethod * quant_method_</div><div class="ttdoc">The quantification method used for the dataset to be analyzed. </div><div class="ttdef"><b>Definition:</b> IsobaricQuantifier.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1IsobaricQuantifier_html_a0c2fe92c5ee2f1ec2ef1809dd9ffe26a"><div class="ttname"><a href="classOpenMS_1_1IsobaricQuantifier.html#a0c2fe92c5ee2f1ec2ef1809dd9ffe26a">OpenMS::IsobaricQuantifier::isotope_correction_enabled_</a></div><div class="ttdeci">bool isotope_correction_enabled_</div><div class="ttdoc">Is true if isotope correction is enabled, false otherwise. </div><div class="ttdef"><b>Definition:</b> IsobaricQuantifier.h:96</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_1IsobaricQuantitationMethod_html"><div class="ttname"><a href="classOpenMS_1_1IsobaricQuantitationMethod.html">OpenMS::IsobaricQuantitationMethod</a></div><div class="ttdoc">Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...</div><div class="ttdef"><b>Definition:</b> IsobaricQuantitationMethod.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1IsobaricQuantifier_html"><div class="ttname"><a href="classOpenMS_1_1IsobaricQuantifier.html">OpenMS::IsobaricQuantifier</a></div><div class="ttdoc">Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensitie...</div><div class="ttdef"><b>Definition:</b> IsobaricQuantifier.h:53</div></div>
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