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<a href="ItraqQuantifier_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: Chris Bielow $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: 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_ITRAQQUANTIFIER_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_ITRAQQUANTIFIER_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 <vector></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="ItraqConstants_8h.html">OpenMS/ANALYSIS/QUANTITATION/ItraqConstants.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="ConsensusMap_8h.html">OpenMS/KERNEL/ConsensusMap.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="ProteinIdentification_8h.html">OpenMS/METADATA/ProteinIdentification.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.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> </div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> {</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
<div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ItraqQuantifier.html"> 57</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> :</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>,</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ItraqConstants.html">ItraqConstants</a></div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  {</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ItraqQuantifier.html#a2db6873392e87c6d42bb6466354d05e4"> 64</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1ItraqConstants_1_1ChannelInfo.html">ItraqConstants::ChannelInfo</a> <a class="code" href="classOpenMS_1_1ItraqQuantifier.html#a2db6873392e87c6d42bb6466354d05e4">ChannelInfo</a>;</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ItraqQuantifier.html#a90c9c7b0430f6c9821987d342595f45b"> 65</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1Map.html">ItraqConstants::ChannelMapType</a> <a class="code" href="classOpenMS_1_1ItraqQuantifier.html#a90c9c7b0430f6c9821987d342595f45b">ChannelMapType</a>;</div>
<div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ItraqQuantifier.html#a2977e178aa82b51a5d30ca756e503afd"> 66</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">ItraqConstants::IsotopeMatrices</a> <a class="code" href="classOpenMS_1_1ItraqQuantifier.html#a2977e178aa82b51a5d30ca756e503afd">IsotopeMatrices</a>;</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <a class="code" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a>();</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keyword">explicit</span> <a class="code" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a>(<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> itraq_type);</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <a class="code" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a>(<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> itraq_type, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> & param);</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <a class="code" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> & cp);</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <a class="code" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> & rhs);</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordtype">void</span> run(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & consensus_map_in,</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & consensus_map_out</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> </div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html"> 99</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html">ItraqQuantifierStats</a></div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  {</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a9686fe0eca18f675003906e6ab152d6e"> 101</a></span>  <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a9686fe0eca18f675003906e6ab152d6e">ItraqQuantifierStats</a>() :</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  channel_count(0),</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  iso_number_ms2_negative(0),</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  iso_number_reporter_negative(0),</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  iso_number_reporter_different(0),</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  iso_solution_different_intensity(0),</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  iso_total_intensity_negative(0),</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  number_ms2_total(0),</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  number_ms2_empty(0),</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  empty_channels()</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  {</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  }</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a name="l00114"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a38852688a32eab0f036dbc020ccfd797"> 114</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a38852688a32eab0f036dbc020ccfd797">channel_count</a>; <span class="comment">//< 4plex, 6plex, or 8 plex?!</span></div>
<div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#ac7e6a7cd7908d50290867e87a0a2bdb1"> 115</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#ac7e6a7cd7908d50290867e87a0a2bdb1">iso_number_ms2_negative</a>; <span class="comment">//< number of MS2 spectra where one or more channels had negative solution</span></div>
<div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#aa18934d89944556021f39387e8d53347"> 116</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#aa18934d89944556021f39387e8d53347">iso_number_reporter_negative</a>; <span class="comment">//< number of channels where naive solution was negative</span></div>
<div class="line"><a name="l00117"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a43d8ac69065095aa5d7e5b6b0c798d6a"> 117</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a43d8ac69065095aa5d7e5b6b0c798d6a">iso_number_reporter_different</a>; <span class="comment">//< number of channels >0 where naive solution was different; happens when naive solution is negative in other channels</span></div>
<div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a04cebfa5e2b505c16b3746651528a189"> 118</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a04cebfa5e2b505c16b3746651528a189">iso_solution_different_intensity</a>; <span class="comment">//< absolute intensity difference between both solutions (for channels > 0)</span></div>
<div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#aeb6cda3de6570b7e072fbb48aee7f4c6"> 119</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#aeb6cda3de6570b7e072fbb48aee7f4c6">iso_total_intensity_negative</a>; <span class="comment">//< only for spectra where naive solution is negative</span></div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a1de4edd4b171bf46d4edfac51d92d6e8"> 120</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a1de4edd4b171bf46d4edfac51d92d6e8">number_ms2_total</a>; <span class="comment">//< total number of MS2 spectra</span></div>
<div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a915e3f5eba5df2e5ab4ea0c49183e1df"> 121</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a915e3f5eba5df2e5ab4ea0c49183e1df">number_ms2_empty</a>; <span class="comment">//< number of empty MS2 (no reporters at all)</span></div>
<div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a6a87c6d5c9c6976e235a8110f37d3225"> 122</a></span>  std::map<Size, Size> <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a6a87c6d5c9c6976e235a8110f37d3225">empty_channels</a>; <span class="comment">//< Channel_ID -> Missing; indicating the number of empty channels from all MS2 scans, i.e., numbers are between number_ms2_empty and number_ms2_total</span></div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  };</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html">ItraqQuantifierStats</a> getStats() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> </div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> </div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordtype">void</span> setDefaultParams_();</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span> </div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span> </div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keywordtype">void</span> initIsotopeCorrections_();</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span> </div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="keywordtype">void</span> reconstructChannelInfo_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & consensus_map);</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keywordtype">bool</span> isIdentityCorrectionMatrix_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Matrix.html">Matrix<double></a>& channel_frequency) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  </div>
<div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ItraqQuantifier.html#ac0dd3c18dae25b85f52e27eae758046f"> 148</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1ItraqQuantifier.html#ac0dd3c18dae25b85f52e27eae758046f">itraq_type_</a>;</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> </div>
<div class="line"><a name="l00152"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ItraqQuantifier.html#a580627b7de9396a221f5156261902f88"> 152</a></span>  <a class="code" href="classOpenMS_1_1Map.html">ChannelMapType</a> <a class="code" href="classOpenMS_1_1ItraqQuantifier.html#a580627b7de9396a221f5156261902f88">channel_map_</a>;</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> </div>
<div class="line"><a name="l00155"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ItraqQuantifier.html#a536e27ec83eafb6e43ed1e71ffdce2b5"> 155</a></span>  <a class="code" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">IsotopeMatrices</a> <a class="code" href="classOpenMS_1_1ItraqQuantifier.html#a536e27ec83eafb6e43ed1e71ffdce2b5">isotope_corrections_</a>;</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div>
<div class="line"><a name="l00158"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ItraqQuantifier.html#aeab1440c4c51bf9ece15d6a94e4ddbdf"> 158</a></span>  <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html">ItraqQuantifierStats</a> <a class="code" href="classOpenMS_1_1ItraqQuantifier.html#aeab1440c4c51bf9ece15d6a94e4ddbdf">stats_</a>;</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  }; <span class="comment">// !class</span></div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> </div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  OPENMS_DLLAPI std::ostream & <a class="code" href="namespaceOpenMS.html#a74df8b74439d1f76961c8d987fb074fd">operator<<</a>(std::ostream & os, <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html">ItraqQuantifier::ItraqQuantifierStats</a> & stats);</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> } <span class="comment">// !namespace</span></div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> </div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> <span class="preprocessor">#endif // OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H</span></div>
<div class="ttc" id="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html_aeb6cda3de6570b7e072fbb48aee7f4c6"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#aeb6cda3de6570b7e072fbb48aee7f4c6">OpenMS::ItraqQuantifier::ItraqQuantifierStats::iso_total_intensity_negative</a></div><div class="ttdeci">DoubleReal iso_total_intensity_negative</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:119</div></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="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html_a38852688a32eab0f036dbc020ccfd797"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a38852688a32eab0f036dbc020ccfd797">OpenMS::ItraqQuantifier::ItraqQuantifierStats::channel_count</a></div><div class="ttdeci">Size channel_count</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1ItraqQuantifier_html_ac0dd3c18dae25b85f52e27eae758046f"><div class="ttname"><a href="classOpenMS_1_1ItraqQuantifier.html#ac0dd3c18dae25b85f52e27eae758046f">OpenMS::ItraqQuantifier::itraq_type_</a></div><div class="ttdeci">Int itraq_type_</div><div class="ttdoc">either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX </div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:148</div></div>
<div class="ttc" id="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html_a1de4edd4b171bf46d4edfac51d92d6e8"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a1de4edd4b171bf46d4edfac51d92d6e8">OpenMS::ItraqQuantifier::ItraqQuantifierStats::number_ms2_total</a></div><div class="ttdeci">Size number_ms2_total</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:120</div></div>
<div class="ttc" id="classOpenMS_1_1ItraqQuantifier_html_a90c9c7b0430f6c9821987d342595f45b"><div class="ttname"><a href="classOpenMS_1_1ItraqQuantifier.html#a90c9c7b0430f6c9821987d342595f45b">OpenMS::ItraqQuantifier::ChannelMapType</a></div><div class="ttdeci">ItraqConstants::ChannelMapType ChannelMapType</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:65</div></div>
<div class="ttc" id="namespaceOpenMS_html_a74df8b74439d1f76961c8d987fb074fd"><div class="ttname"><a href="namespaceOpenMS.html#a74df8b74439d1f76961c8d987fb074fd">OpenMS::operator<<</a></div><div class="ttdeci">std::ostream & operator<<(std::ostream &os, const ItraqQuantifier::ItraqQuantifierStats &stats)</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="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html">OpenMS::ItraqQuantifier::ItraqQuantifierStats</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> ItraqQuantifier.h:99</div></div>
<div class="ttc" id="classOpenMS_1_1ItraqConstants_html"><div class="ttname"><a href="classOpenMS_1_1ItraqConstants.html">OpenMS::ItraqConstants</a></div><div class="ttdoc">Some constants used throughout iTRAQ classes. </div><div class="ttdef"><b>Definition:</b> ItraqConstants.h:53</div></div>
<div class="ttc" id="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html_a43d8ac69065095aa5d7e5b6b0c798d6a"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a43d8ac69065095aa5d7e5b6b0c798d6a">OpenMS::ItraqQuantifier::ItraqQuantifierStats::iso_number_reporter_different</a></div><div class="ttdeci">Size iso_number_reporter_different</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:117</div></div>
<div class="ttc" id="structOpenMS_1_1ItraqConstants_1_1ChannelInfo_html"><div class="ttname"><a href="structOpenMS_1_1ItraqConstants_1_1ChannelInfo.html">OpenMS::ItraqConstants::ChannelInfo</a></div><div class="ttdoc">stores information on an iTRAQ channel </div><div class="ttdef"><b>Definition:</b> ItraqConstants.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1ItraqQuantifier_html_a580627b7de9396a221f5156261902f88"><div class="ttname"><a href="classOpenMS_1_1ItraqQuantifier.html#a580627b7de9396a221f5156261902f88">OpenMS::ItraqQuantifier::channel_map_</a></div><div class="ttdeci">ChannelMapType channel_map_</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:152</div></div>
<div class="ttc" id="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html_a915e3f5eba5df2e5ab4ea0c49183e1df"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a915e3f5eba5df2e5ab4ea0c49183e1df">OpenMS::ItraqQuantifier::ItraqQuantifierStats::number_ms2_empty</a></div><div class="ttdeci">Size number_ms2_empty</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:121</div></div>
<div class="ttc" id="classOpenMS_1_1ItraqQuantifier_html_a2977e178aa82b51a5d30ca756e503afd"><div class="ttname"><a href="classOpenMS_1_1ItraqQuantifier.html#a2977e178aa82b51a5d30ca756e503afd">OpenMS::ItraqQuantifier::IsotopeMatrices</a></div><div class="ttdeci">ItraqConstants::IsotopeMatrices IsotopeMatrices</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1ItraqQuantifier_html_a536e27ec83eafb6e43ed1e71ffdce2b5"><div class="ttname"><a href="classOpenMS_1_1ItraqQuantifier.html#a536e27ec83eafb6e43ed1e71ffdce2b5">OpenMS::ItraqQuantifier::isotope_corrections_</a></div><div class="ttdeci">IsotopeMatrices isotope_corrections_</div><div class="ttdoc">Matrices with isotope correction values (one for each plex-type) </div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:155</div></div>
<div class="ttc" id="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html_a04cebfa5e2b505c16b3746651528a189"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a04cebfa5e2b505c16b3746651528a189">OpenMS::ItraqQuantifier::ItraqQuantifierStats::iso_solution_different_intensity</a></div><div class="ttdeci">DoubleReal iso_solution_different_intensity</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:118</div></div>
<div class="ttc" id="ProteinIdentification_8h_html"><div class="ttname"><a href="ProteinIdentification_8h.html">ProteinIdentification.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ItraqQuantifier_html_aeab1440c4c51bf9ece15d6a94e4ddbdf"><div class="ttname"><a href="classOpenMS_1_1ItraqQuantifier.html#aeab1440c4c51bf9ece15d6a94e4ddbdf">OpenMS::ItraqQuantifier::stats_</a></div><div class="ttdeci">ItraqQuantifierStats stats_</div><div class="ttdoc">stats for isotope correction </div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:158</div></div>
<div class="ttc" id="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html_aa18934d89944556021f39387e8d53347"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#aa18934d89944556021f39387e8d53347">OpenMS::ItraqQuantifier::ItraqQuantifierStats::iso_number_reporter_negative</a></div><div class="ttdeci">Size iso_number_reporter_negative</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1ItraqQuantifier_html"><div class="ttname"><a href="classOpenMS_1_1ItraqQuantifier.html">OpenMS::ItraqQuantifier</a></div><div class="ttdoc">Does post-processing on raw iTRAQ channel quantitation. </div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:57</div></div>
<div class="ttc" id="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html_a9686fe0eca18f675003906e6ab152d6e"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a9686fe0eca18f675003906e6ab152d6e">OpenMS::ItraqQuantifier::ItraqQuantifierStats::ItraqQuantifierStats</a></div><div class="ttdeci">ItraqQuantifierStats()</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:101</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="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="PeptideIdentification_8h_html"><div class="ttname"><a href="PeptideIdentification_8h.html">PeptideIdentification.h</a></div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html_ac7e6a7cd7908d50290867e87a0a2bdb1"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#ac7e6a7cd7908d50290867e87a0a2bdb1">OpenMS::ItraqQuantifier::ItraqQuantifierStats::iso_number_ms2_negative</a></div><div class="ttdeci">Size iso_number_ms2_negative</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:115</div></div>
<div class="ttc" id="classOpenMS_1_1ItraqConstants_html_aad56172226aab6ec420d03d72e692a17"><div class="ttname"><a href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">OpenMS::ItraqConstants::IsotopeMatrices</a></div><div class="ttdeci">std::vector< Matrix< double > > IsotopeMatrices</div><div class="ttdoc">(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style </div><div class="ttdef"><b>Definition:</b> ItraqConstants.h:75</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_1ItraqQuantifier_html_a2db6873392e87c6d42bb6466354d05e4"><div class="ttname"><a href="classOpenMS_1_1ItraqQuantifier.html#a2db6873392e87c6d42bb6466354d05e4">OpenMS::ItraqQuantifier::ChannelInfo</a></div><div class="ttdeci">ItraqConstants::ChannelInfo ChannelInfo</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:64</div></div>
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats_html_a6a87c6d5c9c6976e235a8110f37d3225"><div class="ttname"><a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#a6a87c6d5c9c6976e235a8110f37d3225">OpenMS::ItraqQuantifier::ItraqQuantifierStats::empty_channels</a></div><div class="ttdeci">std::map< Size, Size > empty_channels</div><div class="ttdef"><b>Definition:</b> ItraqQuantifier.h:122</div></div>
<div class="ttc" id="classOpenMS_1_1Matrix_html"><div class="ttname"><a href="classOpenMS_1_1Matrix.html">OpenMS::Matrix< double ></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 11:19:15 using doxygen 1.8.5</font></TD>
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