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<a href="SILACAnalyzer_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Lars Nilse $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Lars Nilse, Steffen Sass, Holger Plattfaut, Bastian Blank $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_FILTERING_DATAREDUCTION_SILACANALYZER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FILTERING_DATAREDUCTION_SILACANALYZER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="comment">//OpenMS includes</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;OpenMS/config.h&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="comment">// #include &lt;OpenMS/APPLICATIONS/TOPPBase.h&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="DBoundingBox_8h.html">OpenMS/DATASTRUCTURES/DBoundingBox.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ConsensusMap_8h.html">OpenMS/KERNEL/ConsensusMap.h</a>&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MzMLFile_8h.html">OpenMS/FORMAT/MzMLFile.h</a>&gt;</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ConsensusXMLFile_8h.html">OpenMS/FORMAT/ConsensusXMLFile.h</a>&gt;</span></div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureXMLFile_8h.html">OpenMS/FORMAT/FeatureXMLFile.h</a>&gt;</span></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="LinearRegression_8h.html">OpenMS/MATH/STATISTICS/LinearRegression.h</a>&gt;</span></div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="RangeUtils_8h.html">OpenMS/KERNEL/RangeUtils.h</a>&gt;</span></div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ChromatogramTools_8h.html">OpenMS/KERNEL/ChromatogramTools.h</a>&gt;</span></div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MzQuantMLFile_8h.html">OpenMS/FORMAT/MzQuantMLFile.h</a>&gt;</span></div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSQuantifications_8h.html">OpenMS/METADATA/MSQuantifications.h</a>&gt;</span></div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SILACFilter_8h.html">OpenMS/FILTERING/DATAREDUCTION/SILACFilter.h</a>&gt;</span></div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SILACFiltering_8h.html">OpenMS/FILTERING/DATAREDUCTION/SILACFiltering.h</a>&gt;</span></div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SILACClustering_8h.html">OpenMS/COMPARISON/CLUSTERING/SILACClustering.h</a>&gt;</span></div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="PeakWidthEstimator_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/PeakWidthEstimator.h</a>&gt;</span></div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;<span class="comment">//Contrib includes</span></div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;<span class="preprocessor">#include &lt;boost/algorithm/string/split.hpp&gt;</span></div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;<span class="preprocessor">#include &lt;boost/algorithm/string/classification.hpp&gt;</span></div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;<span class="comment">//std includes</span></div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;<span class="preprocessor">#include &lt;cmath&gt;</span></div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;<span class="preprocessor">#include &lt;algorithm&gt;</span></div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;<span class="preprocessor">#include &lt;fstream&gt;</span></div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;<span class="preprocessor">#include &lt;limits&gt;</span></div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;<span class="preprocessor">#include &lt;locale&gt;</span></div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;<span class="preprocessor">#include &lt;iomanip&gt;</span></div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;{</div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html">   86</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SILACAnalyzer.html">SILACAnalyzer</a> :</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;  {</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;  <span class="keyword">private</span>:</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;    <span class="comment">// input and output files</span></div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a19a2651887fa4d874edfe6a94b54b2d5">   92</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a19a2651887fa4d874edfe6a94b54b2d5">in</a>;</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#ab64766cccc4f8fdf5c87b8bcc9493c4a">   93</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#ab64766cccc4f8fdf5c87b8bcc9493c4a">out</a>;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a09438f47c3b3ead847dd32c7d07e5c12">   94</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a09438f47c3b3ead847dd32c7d07e5c12">out_clusters</a>;</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#ac10a8fb6c9755533604f2f4efe5909f2">   95</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#ac10a8fb6c9755533604f2f4efe5909f2">out_features</a>;</div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#adc1a8255946606d602587c2796a17649">   96</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#adc1a8255946606d602587c2796a17649">out_mzq</a>;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;</div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#ac74fe586851d4a6f5fe80f8ca419e3a7">   98</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#ac74fe586851d4a6f5fe80f8ca419e3a7">out_filters</a>;</div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#aeb34d95776f7522f1c55d9a081f3c472">   99</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#aeb34d95776f7522f1c55d9a081f3c472">in_filters</a>;</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a64ac4995816f47f50bc0dd105ce4d350">  100</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a64ac4995816f47f50bc0dd105ce4d350">out_debug</a>;</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;    <span class="comment">// section &quot;sample&quot;</span></div>
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a5e0eb25e120d00ed27d0590f33660996">  103</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a5e0eb25e120d00ed27d0590f33660996">selected_labels</a>;</div>
<div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a145cf377400ce6b5c8760644f69163fe">  104</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a145cf377400ce6b5c8760644f69163fe">charge_min</a>;</div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#aa1d91c4a53814ce7340f949756029b1d">  105</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#aa1d91c4a53814ce7340f949756029b1d">charge_max</a>;</div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a96eb46acbedf9b5079712943fbbb797d">  106</a></span>&#160;    <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a96eb46acbedf9b5079712943fbbb797d">missed_cleavages</a>;</div>
<div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#abd95b60697a179a50679bcd4cace9225">  107</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#abd95b60697a179a50679bcd4cace9225">isotopes_per_peptide_min</a>;</div>
<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#aef0963ffe4c2330d785b8fede9e7e3cc">  108</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#aef0963ffe4c2330d785b8fede9e7e3cc">isotopes_per_peptide_max</a>;</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    <span class="comment">// section &quot;algorithm&quot;</span></div>
<div class="line"><a name="l00111"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a920f0e916452ca37d0b646e8e7ed7318">  111</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a920f0e916452ca37d0b646e8e7ed7318">rt_threshold</a>;</div>
<div class="line"><a name="l00112"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a4d532bb9efa7c2aeaedbcf5ff0c13826">  112</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a4d532bb9efa7c2aeaedbcf5ff0c13826">rt_min</a>;</div>
<div class="line"><a name="l00113"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a69a387a94bd4eed1e15560ff8b515af5">  113</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a69a387a94bd4eed1e15560ff8b515af5">intensity_cutoff</a>;</div>
<div class="line"><a name="l00114"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#ac8a7a5df4900eb88c011d402eb5a6255">  114</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#ac8a7a5df4900eb88c011d402eb5a6255">intensity_correlation</a>;</div>
<div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a385a39714b1ed807bdb5d7da14d63247">  115</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a385a39714b1ed807bdb5d7da14d63247">model_deviation</a>;</div>
<div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a0469ba5f938fd955f3bf73c1ef2e213b">  116</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a0469ba5f938fd955f3bf73c1ef2e213b">allow_missing_peaks</a>;</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;    <span class="comment">// section &quot;labels&quot;</span></div>
<div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a60b26944cbd02e52b1e137a7069c6f1a">  119</a></span>&#160;    std::vector&lt;std::vector&lt;String&gt; &gt; <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a60b26944cbd02e52b1e137a7069c6f1a">SILAClabels</a>;    <span class="comment">// list of SILAC labels, e.g. selected_labels=&quot;[Lys4,Arg6][Lys8,Arg10]&quot; =&gt; SILAClabels[0][1]=&quot;Arg6&quot;</span></div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a2eddf423e5ff345fb99fcfa45116f2f1">  120</a></span>&#160;    std::vector&lt;std::vector&lt;DoubleReal&gt; &gt; <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a2eddf423e5ff345fb99fcfa45116f2f1">massShifts</a>; <span class="comment">// list of mass shifts</span></div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;</div>
<div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#ab82579f850f8826ffe606b8855504348">  122</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1SILACClustering.html">SILACClustering</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#ab82579f850f8826ffe606b8855504348">Clustering</a>;</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;</div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#aa924369b7a4efee5ac3ab55a7501c983">  124</a></span>&#160;    <a class="code" href="classOpenMS_1_1MSQuantifications.html">MSQuantifications</a> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#aa924369b7a4efee5ac3ab55a7501c983">msq</a>;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;  <span class="keyword">public</span>:</div>
<div class="line"><a name="l00127"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a3ca615fc4cf75e66d68fdb94df4b94e9">  127</a></span>&#160;    <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a3ca615fc4cf75e66d68fdb94df4b94e9">SILACAnalyzer</a>() :</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;      allow_missing_peaks(true)</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;    {</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;    }</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;</div>
<div class="line"><a name="l00139"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a3df0796837f7699916b4e26fdb328b04">  139</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a3df0796837f7699916b4e26fdb328b04">initialize</a>(</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;      <span class="comment">// section &quot;sample&quot;</span></div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> selected_labels_,</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> charge_min_,</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> charge_max_,</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;      <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> missed_cleavages_,</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> isotopes_per_peptide_min_,</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> isotopes_per_peptide_max_, </div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;      <span class="comment">// section &quot;algorithm&quot;</span></div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> rt_threshold_,</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> rt_min_,</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> intensity_cutoff_,</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> intensity_correlation_,</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> model_deviation_,</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;      <span class="keywordtype">bool</span> allow_missing_peaks_,</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;      <span class="comment">// labels part</span></div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;      std::map&lt;String, DoubleReal&gt; label_identifiers)</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;    {</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;      selected_labels          = selected_labels_;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;      charge_min               = charge_min_;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;      charge_max               = charge_max_;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;      missed_cleavages         = missed_cleavages_;</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;      isotopes_per_peptide_min = isotopes_per_peptide_min_;</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;      isotopes_per_peptide_max = isotopes_per_peptide_max_;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;      rt_threshold           = rt_threshold_;</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;      rt_min                 = rt_min_;</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;      intensity_cutoff       = intensity_cutoff_;</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;      intensity_correlation  = intensity_correlation_;</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;      model_deviation        = model_deviation_;</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;      allow_missing_peaks    = allow_missing_peaks_;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;      calculateLabelsAndMassShifts(label_identifiers);</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;    }</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;    <span class="keywordtype">void</span> calculateLabelsAndMassShifts(std::map&lt;String, DoubleReal&gt; label_identifiers);</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;</div>
<div class="line"><a name="l00185"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a63ca5fae46c85b6bc06a1dc801c7467f">  185</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a63ca5fae46c85b6bc06a1dc801c7467f">run_all</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;Peak1D&gt;</a> &amp; exp, <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp; out_map)</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;    {</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;      <a class="code" href="classOpenMS_1_1PeakWidthEstimator_1_1Result.html">PeakWidthEstimator::Result</a> peak_width;</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;      std::vector&lt;std::vector&lt;SILACPattern&gt; &gt; data;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;      <a class="code" href="classOpenMS_1_1MSQuantifications.html">MSQuantifications</a> msq;</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;      std::vector&lt;Clustering *&gt; cluster_data;</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;      peak_width = estimatePeakWidth(exp);</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;      filterData(exp, peak_width, data); </div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;      clusterData(exp, peak_width, cluster_data, data);</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;      <span class="comment">// write output to consensus map</span></div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;      <span class="keywordflow">for</span> (std::vector&lt;Clustering *&gt;::const_iterator it = cluster_data.begin(); it != cluster_data.end(); ++it)</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;      {</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;        generateClusterConsensusByCluster(out_map, **it);</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;      }</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;    }</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;    <a class="code" href="classOpenMS_1_1PeakWidthEstimator_1_1Result.html">PeakWidthEstimator::Result</a> estimatePeakWidth(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;Peak1D&gt;</a> &amp; exp);</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;    <span class="keywordtype">void</span> filterData(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;Peak1D&gt;</a> &amp; exp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeakWidthEstimator_1_1Result.html">PeakWidthEstimator::Result</a> &amp; peak_width, std::vector&lt;std::vector&lt;SILACPattern&gt; &gt; &amp; data);</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;    <span class="keywordtype">void</span> clusterData(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;&gt;</a> &amp;, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeakWidthEstimator_1_1Result.html">PeakWidthEstimator::Result</a> &amp;, std::vector&lt;Clustering *&gt; &amp;, std::vector&lt;std::vector&lt;SILACPattern&gt; &gt; &amp; data);</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;</div>
<div class="line"><a name="l00223"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a76a3c66df61210b400938317c735098a">  223</a></span>&#160;    std::vector&lt;std::vector&lt;String&gt; &gt; &amp; <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a76a3c66df61210b400938317c735098a">getSILAClabels</a>()</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;    {</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;      <span class="keywordflow">return</span> SILAClabels;</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;    }</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;</div>
<div class="line"><a name="l00231"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#ab0a5d682b988df4438f71140a2e68275">  231</a></span>&#160;    std::vector&lt;std::vector&lt;DoubleReal&gt; &gt; &amp; <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#ab0a5d682b988df4438f71140a2e68275">getMassShifts</a>()</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;    {</div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;      <span class="keywordflow">return</span> massShifts;</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;    }</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;  <span class="keyword">public</span>:</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;    <span class="keywordtype">void</span> generateClusterConsensusByCluster(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;, <span class="keyword">const</span> Clustering &amp;) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;    <span class="keywordtype">void</span> generateClusterConsensusByPattern(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;, <span class="keyword">const</span> Clustering &amp;, <a class="code" href="classunsigned_01int.html">UInt</a> &amp; cluster_id) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;    <span class="keywordtype">void</span> generateClusterDebug(std::ostream &amp; out, <span class="keyword">const</span> Clustering &amp; clustering, <a class="code" href="classunsigned_01int.html">UInt</a> &amp; cluster_id) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;</div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;  <span class="keyword">public</span>:</div>
<div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;    <span class="keywordtype">void</span> generateFilterConsensusByPattern(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;, <span class="keyword">const</span> std::vector&lt;SILACPattern&gt; &amp;) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;</div>
<div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;  <span class="keyword">private</span>:</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;</div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;    <a class="code" href="classOpenMS_1_1ConsensusFeature.html">ConsensusFeature</a> generateSingleConsensusByPattern(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACPattern.html">SILACPattern</a> &amp;) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;  <span class="keyword">public</span>:</div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;    <span class="keywordtype">void</span> generateClusterFeatureByCluster(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp;, <span class="keyword">const</span> Clustering &amp;) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;    <span class="keywordtype">void</span> readFilterConsensusByPattern(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;, std::vector&lt;std::vector&lt;SILACPattern&gt; &gt; &amp;);</div>
<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;</div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;    <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; selectColor(<a class="code" href="classunsigned_01int.html">UInt</a> nr);</div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;</div>
<div class="line"><a name="l00284"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#ae930eb8197c8961725cdc3aacc6a1c09">  284</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#ae930eb8197c8961725cdc3aacc6a1c09">readConsensus</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp; in)<span class="keyword"> const</span></div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;      <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html">ConsensusXMLFile</a> c_file;</div>
<div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;      c_file.<a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a426f58285a6c7a6b81346bcc4cf58e2a">load</a>(filename, in);</div>
<div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;    }</div>
<div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;</div>
<div class="line"><a name="l00293"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#ae14ec0b9fd095ebe54c1e8cc75338548">  293</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#ae14ec0b9fd095ebe54c1e8cc75338548">writeConsensus</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp; out)<span class="keyword"> const</span></div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;      out.<a class="code" href="classOpenMS_1_1ConsensusMap.html#a86f7b200260209865e730a2e4fcaa628">sortByPosition</a>();</div>
<div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;      out.<a class="code" href="classOpenMS_1_1ConsensusMap.html#a2ba4cf095974c86863027d78210dc2fa">applyMemberFunction</a>(&amp;<a class="code" href="classOpenMS_1_1UniqueIdInterface.html#a9c908a735f82adb8f66a326547a9acf8">UniqueIdInterface::setUniqueId</a>);</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;      out.<a class="code" href="classOpenMS_1_1ConsensusMap.html#af3fc434b747ad4f686744aca8fe9ef84">setExperimentType</a>(<span class="stringliteral">&quot;silac&quot;</span>);</div>
<div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;</div>
<div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160;      <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html">ConsensusXMLFile</a> c_file;</div>
<div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;      c_file.<a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#af72f4966d65af7a802025d8640a0e570">store</a>(filename, out);</div>
<div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;    }</div>
<div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;</div>
<div class="line"><a name="l00306"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#a7d9066a1cc3461a21d32188728049cde">  306</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#a7d9066a1cc3461a21d32188728049cde">writeMzQuantML</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <a class="code" href="classOpenMS_1_1MSQuantifications.html">MSQuantifications</a> &amp; msq)<span class="keyword"> const</span></div>
<div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00308"></a><span class="lineno">  308</span>&#160;      <span class="comment">//~ TODO apply above to ConsensusMap befor putting into Msq</span></div>
<div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;      <span class="comment">//~ out.sortByPosition();</span></div>
<div class="line"><a name="l00310"></a><span class="lineno">  310</span>&#160;      <span class="comment">//~ out.applyMemberFunction(&amp;UniqueIdInterface::setUniqueId);</span></div>
<div class="line"><a name="l00311"></a><span class="lineno">  311</span>&#160;      <span class="comment">//~ out.setExperimentType(&quot;SILAC&quot;);</span></div>
<div class="line"><a name="l00312"></a><span class="lineno">  312</span>&#160;</div>
<div class="line"><a name="l00313"></a><span class="lineno">  313</span>&#160;      <a class="code" href="classOpenMS_1_1MzQuantMLFile.html">MzQuantMLFile</a> file;</div>
<div class="line"><a name="l00314"></a><span class="lineno">  314</span>&#160;      file.<a class="code" href="classOpenMS_1_1MzQuantMLFile.html#aafe60b67d30415c197f1ebfd10bf01c6">store</a>(filename, msq);</div>
<div class="line"><a name="l00315"></a><span class="lineno">  315</span>&#160;    }</div>
<div class="line"><a name="l00316"></a><span class="lineno">  316</span>&#160;</div>
<div class="line"><a name="l00320"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACAnalyzer.html#ade305f744c909667f3c6f4e2fed3262b">  320</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SILACAnalyzer.html#ade305f744c909667f3c6f4e2fed3262b">writeFeatures</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; out)<span class="keyword"> const</span></div>
<div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00322"></a><span class="lineno">  322</span>&#160;      out.<a class="code" href="classOpenMS_1_1FeatureMap.html#a86f7b200260209865e730a2e4fcaa628">sortByPosition</a>();</div>
<div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;      out.<a class="code" href="classOpenMS_1_1FeatureMap.html#a2ba4cf095974c86863027d78210dc2fa">applyMemberFunction</a>(&amp;<a class="code" href="classOpenMS_1_1UniqueIdInterface.html#a9c908a735f82adb8f66a326547a9acf8">UniqueIdInterface::setUniqueId</a>);</div>
<div class="line"><a name="l00324"></a><span class="lineno">  324</span>&#160;</div>
<div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureXMLFile.html">FeatureXMLFile</a> f_file;</div>
<div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;      f_file.<a class="code" href="classOpenMS_1_1FeatureXMLFile.html#ae05e70281bd2c24b9cfa431200669858">store</a>(filename, out);</div>
<div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;    }</div>
<div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;</div>
<div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;  };</div>
<div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;}</div>
<div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;</div>
<div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;<span class="preprocessor">#endif </span><span class="comment">/* SILACANALYZER_H_ */</span><span class="preprocessor"></span></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_ab82579f850f8826ffe606b8855504348"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#ab82579f850f8826ffe606b8855504348">OpenMS::SILACAnalyzer::Clustering</a></div><div class="ttdeci">SILACClustering Clustering</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:122</div></div>
<div class="ttc" id="FeatureXMLFile_8h_html"><div class="ttname"><a href="FeatureXMLFile_8h.html">FeatureXMLFile.h</a></div></div>
<div class="ttc" id="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
<div class="ttc" id="PeakWidthEstimator_8h_html"><div class="ttname"><a href="PeakWidthEstimator_8h.html">PeakWidthEstimator.h</a></div></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="ConsensusMap_8h_html"><div class="ttname"><a href="ConsensusMap_8h.html">ConsensusMap.h</a></div></div>
<div class="ttc" id="MSQuantifications_8h_html"><div class="ttname"><a href="MSQuantifications_8h.html">MSQuantifications.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a385a39714b1ed807bdb5d7da14d63247"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a385a39714b1ed807bdb5d7da14d63247">OpenMS::SILACAnalyzer::model_deviation</a></div><div class="ttdeci">DoubleReal model_deviation</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:115</div></div>
<div class="ttc" id="RangeUtils_8h_html"><div class="ttname"><a href="RangeUtils_8h.html">RangeUtils.h</a></div></div>
<div class="ttc" id="DBoundingBox_8h_html"><div class="ttname"><a href="DBoundingBox_8h.html">DBoundingBox.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_ae05e70281bd2c24b9cfa431200669858"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#ae05e70281bd2c24b9cfa431200669858">OpenMS::FeatureXMLFile::store</a></div><div class="ttdeci">void store(const String &amp;filename, const FeatureMap&lt;&gt; &amp;feature_map)</div><div class="ttdoc">stores the map feature_map in file with name filename. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap&lt;&gt;</a></div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_ab64766cccc4f8fdf5c87b8bcc9493c4a"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#ab64766cccc4f8fdf5c87b8bcc9493c4a">OpenMS::SILACAnalyzer::out</a></div><div class="ttdeci">String out</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a5e0eb25e120d00ed27d0590f33660996"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a5e0eb25e120d00ed27d0590f33660996">OpenMS::SILACAnalyzer::selected_labels</a></div><div class="ttdeci">String selected_labels</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_ae14ec0b9fd095ebe54c1e8cc75338548"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#ae14ec0b9fd095ebe54c1e8cc75338548">OpenMS::SILACAnalyzer::writeConsensus</a></div><div class="ttdeci">void writeConsensus(const String &amp;filename, ConsensusMap &amp;out) const </div><div class="ttdoc">Write consensusXML from ConsensusMap to file. </div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:293</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html">OpenMS::SILACAnalyzer</a></div><div class="ttdoc">Algorithm to use for SILACAnalysis. </div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_ac10a8fb6c9755533604f2f4efe5909f2"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#ac10a8fb6c9755533604f2f4efe5909f2">OpenMS::SILACAnalyzer::out_features</a></div><div class="ttdeci">String out_features</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:95</div></div>
<div class="ttc" id="classOpenMS_1_1UniqueIdInterface_html_a9c908a735f82adb8f66a326547a9acf8"><div class="ttname"><a href="classOpenMS_1_1UniqueIdInterface.html#a9c908a735f82adb8f66a326547a9acf8">OpenMS::UniqueIdInterface::setUniqueId</a></div><div class="ttdeci">Size setUniqueId()</div><div class="ttdoc">Assigns a new, valid unique id. Always returns 1. </div><div class="ttdef"><b>Definition:</b> UniqueIdInterface.h:150</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="classOpenMS_1_1ConsensusMap_html_a2ba4cf095974c86863027d78210dc2fa"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html#a2ba4cf095974c86863027d78210dc2fa">OpenMS::ConsensusMap::applyMemberFunction</a></div><div class="ttdeci">Size applyMemberFunction(Size(Type::*member_function)())</div><div class="ttdoc">Applies a member function of Type to the container itself and all consensus features. The returned values are accumulated. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:438</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a76a3c66df61210b400938317c735098a"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a76a3c66df61210b400938317c735098a">OpenMS::SILACAnalyzer::getSILAClabels</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; String &gt; &gt; &amp; getSILAClabels()</div><div class="ttdoc">Returns the list of SILAC labels, e.g. selected_labels=&amp;quot;[Lys4,Arg6][Lys8,Arg10]&amp;quot; =&amp;gt; SILAClabels[0][1]...</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:223</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_a2ba4cf095974c86863027d78210dc2fa"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#a2ba4cf095974c86863027d78210dc2fa">OpenMS::FeatureMap::applyMemberFunction</a></div><div class="ttdeci">Size applyMemberFunction(Size(Type::*member_function)())</div><div class="ttdoc">Applies a member function of Type to the container itself and all features (including subordinates)...</div><div class="ttdef"><b>Definition:</b> FeatureMap.h:496</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html_af3fc434b747ad4f686744aca8fe9ef84"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html#af3fc434b747ad4f686744aca8fe9ef84">OpenMS::ConsensusMap::setExperimentType</a></div><div class="ttdeci">void setExperimentType(const String &amp;experiment_type)</div><div class="ttdoc">Mutable access to the experiment type. </div></div>
<div class="ttc" id="classOpenMS_1_1SILACClustering_html"><div class="ttname"><a href="classOpenMS_1_1SILACClustering.html">OpenMS::SILACClustering</a></div><div class="ttdoc">Clustering implementation for SILAC stuff. </div><div class="ttdef"><b>Definition:</b> SILACClustering.h:52</div></div>
<div class="ttc" id="SILACFiltering_8h_html"><div class="ttname"><a href="SILACFiltering_8h.html">SILACFiltering.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_abd95b60697a179a50679bcd4cace9225"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#abd95b60697a179a50679bcd4cace9225">OpenMS::SILACAnalyzer::isotopes_per_peptide_min</a></div><div class="ttdeci">UInt isotopes_per_peptide_min</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:107</div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_ab0a5d682b988df4438f71140a2e68275"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#ab0a5d682b988df4438f71140a2e68275">OpenMS::SILACAnalyzer::getMassShifts</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; DoubleReal &gt; &gt; &amp; getMassShifts()</div><div class="ttdoc">Returns the list of mass shifts calcualted. </div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:231</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_ae930eb8197c8961725cdc3aacc6a1c09"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#ae930eb8197c8961725cdc3aacc6a1c09">OpenMS::SILACAnalyzer::readConsensus</a></div><div class="ttdeci">void readConsensus(const String &amp;filename, ConsensusMap &amp;in) const </div><div class="ttdoc">Read consensusXML from file to ConsensusMap. </div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:284</div></div>
<div class="ttc" id="MzQuantMLFile_8h_html"><div class="ttname"><a href="MzQuantMLFile_8h.html">MzQuantMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a3df0796837f7699916b4e26fdb328b04"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a3df0796837f7699916b4e26fdb328b04">OpenMS::SILACAnalyzer::initialize</a></div><div class="ttdeci">void initialize(String selected_labels_, UInt charge_min_, UInt charge_max_, Int missed_cleavages_, UInt isotopes_per_peptide_min_, UInt isotopes_per_peptide_max_, DoubleReal rt_threshold_, DoubleReal rt_min_, DoubleReal intensity_cutoff_, DoubleReal intensity_correlation_, DoubleReal model_deviation_, bool allow_missing_peaks_, std::map&lt; String, DoubleReal &gt; label_identifiers)</div><div class="ttdoc">Initializes the algorithm with parameters. </div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:139</div></div>
<div class="ttc" id="classOpenMS_1_1MzQuantMLFile_html"><div class="ttname"><a href="classOpenMS_1_1MzQuantMLFile.html">OpenMS::MzQuantMLFile</a></div><div class="ttdoc">File adapter for MzQuantML files. </div><div class="ttdef"><b>Definition:</b> MzQuantMLFile.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html">OpenMS::ConsensusXMLFile</a></div><div class="ttdoc">This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...</div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a63ca5fae46c85b6bc06a1dc801c7467f"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a63ca5fae46c85b6bc06a1dc801c7467f">OpenMS::SILACAnalyzer::run_all</a></div><div class="ttdeci">void run_all(MSExperiment&lt; Peak1D &gt; &amp;exp, ConsensusMap &amp;out_map)</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:185</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_aa924369b7a4efee5ac3ab55a7501c983"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#aa924369b7a4efee5ac3ab55a7501c983">OpenMS::SILACAnalyzer::msq</a></div><div class="ttdeci">MSQuantifications msq</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:124</div></div>
<div class="ttc" id="classOpenMS_1_1MSQuantifications_html"><div class="ttname"><a href="classOpenMS_1_1MSQuantifications.html">OpenMS::MSQuantifications</a></div><div class="ttdef"><b>Definition:</b> MSQuantifications.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_a86f7b200260209865e730a2e4fcaa628"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#a86f7b200260209865e730a2e4fcaa628">OpenMS::FeatureMap::sortByPosition</a></div><div class="ttdeci">void sortByPosition()</div><div class="ttdoc">Sort features by position. Lexicographical comparison (first RT then m/z) is done. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:310</div></div>
<div class="ttc" id="classOpenMS_1_1PeakWidthEstimator_1_1Result_html"><div class="ttname"><a href="classOpenMS_1_1PeakWidthEstimator_1_1Result.html">OpenMS::PeakWidthEstimator::Result</a></div><div class="ttdef"><b>Definition:</b> PeakWidthEstimator.h:60</div></div>
<div class="ttc" id="SILACFilter_8h_html"><div class="ttname"><a href="SILACFilter_8h.html">SILACFilter.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_ac74fe586851d4a6f5fe80f8ca419e3a7"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#ac74fe586851d4a6f5fe80f8ca419e3a7">OpenMS::SILACAnalyzer::out_filters</a></div><div class="ttdeci">String out_filters</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:98</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a64ac4995816f47f50bc0dd105ce4d350"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a64ac4995816f47f50bc0dd105ce4d350">OpenMS::SILACAnalyzer::out_debug</a></div><div class="ttdeci">String out_debug</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a7d9066a1cc3461a21d32188728049cde"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a7d9066a1cc3461a21d32188728049cde">OpenMS::SILACAnalyzer::writeMzQuantML</a></div><div class="ttdeci">void writeMzQuantML(const String &amp;filename, MSQuantifications &amp;msq) const </div><div class="ttdoc">Write MzQuantML from ConsensusMap to file. </div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:306</div></div>
<div class="ttc" id="ConsensusXMLFile_8h_html"><div class="ttname"><a href="ConsensusXMLFile_8h.html">ConsensusXMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment&lt; Peak1D &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a920f0e916452ca37d0b646e8e7ed7318"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a920f0e916452ca37d0b646e8e7ed7318">OpenMS::SILACAnalyzer::rt_threshold</a></div><div class="ttdeci">DoubleReal rt_threshold</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a60b26944cbd02e52b1e137a7069c6f1a"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a60b26944cbd02e52b1e137a7069c6f1a">OpenMS::SILACAnalyzer::SILAClabels</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; String &gt; &gt; SILAClabels</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:119</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_adc1a8255946606d602587c2796a17649"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#adc1a8255946606d602587c2796a17649">OpenMS::SILACAnalyzer::out_mzq</a></div><div class="ttdeci">String out_mzq</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:96</div></div>
<div class="ttc" id="classOpenMS_1_1MzQuantMLFile_html_aafe60b67d30415c197f1ebfd10bf01c6"><div class="ttname"><a href="classOpenMS_1_1MzQuantMLFile.html#aafe60b67d30415c197f1ebfd10bf01c6">OpenMS::MzQuantMLFile::store</a></div><div class="ttdeci">void store(const String &amp;filename, const MSQuantifications &amp;cmsq) const </div><div class="ttdoc">Stores a map in a MzQuantML file. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html">OpenMS::FeatureXMLFile</a></div><div class="ttdoc">This class provides Input/Output functionality for feature maps. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_aa1d91c4a53814ce7340f949756029b1d"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#aa1d91c4a53814ce7340f949756029b1d">OpenMS::SILACAnalyzer::charge_max</a></div><div class="ttdeci">UInt charge_max</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a96eb46acbedf9b5079712943fbbb797d"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a96eb46acbedf9b5079712943fbbb797d">OpenMS::SILACAnalyzer::missed_cleavages</a></div><div class="ttdeci">Int missed_cleavages</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:106</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_aeb34d95776f7522f1c55d9a081f3c472"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#aeb34d95776f7522f1c55d9a081f3c472">OpenMS::SILACAnalyzer::in_filters</a></div><div class="ttdeci">String in_filters</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:99</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="SILACClustering_8h_html"><div class="ttname"><a href="SILACClustering_8h.html">SILACClustering.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a0469ba5f938fd955f3bf73c1ef2e213b"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a0469ba5f938fd955f3bf73c1ef2e213b">OpenMS::SILACAnalyzer::allow_missing_peaks</a></div><div class="ttdeci">bool allow_missing_peaks</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a2eddf423e5ff345fb99fcfa45116f2f1"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a2eddf423e5ff345fb99fcfa45116f2f1">OpenMS::SILACAnalyzer::massShifts</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; DoubleReal &gt; &gt; massShifts</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:120</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_aef0963ffe4c2330d785b8fede9e7e3cc"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#aef0963ffe4c2330d785b8fede9e7e3cc">OpenMS::SILACAnalyzer::isotopes_per_peptide_max</a></div><div class="ttdeci">UInt isotopes_per_peptide_max</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a69a387a94bd4eed1e15560ff8b515af5"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a69a387a94bd4eed1e15560ff8b515af5">OpenMS::SILACAnalyzer::intensity_cutoff</a></div><div class="ttdeci">DoubleReal intensity_cutoff</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:113</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a09438f47c3b3ead847dd32c7d07e5c12"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a09438f47c3b3ead847dd32c7d07e5c12">OpenMS::SILACAnalyzer::out_clusters</a></div><div class="ttdeci">String out_clusters</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1SILACPattern_html"><div class="ttname"><a href="classOpenMS_1_1SILACPattern.html">OpenMS::SILACPattern</a></div><div class="ttdoc">A single SILAC pattern containing multiple found points. </div><div class="ttdef"><b>Definition:</b> SILACPattern.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html_a86f7b200260209865e730a2e4fcaa628"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html#a86f7b200260209865e730a2e4fcaa628">OpenMS::ConsensusMap::sortByPosition</a></div><div class="ttdeci">void sortByPosition()</div><div class="ttdoc">Lexicographically sorts the peaks by their position (First RT then m/z). </div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_af72f4966d65af7a802025d8640a0e570"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#af72f4966d65af7a802025d8640a0e570">OpenMS::ConsensusXMLFile::store</a></div><div class="ttdeci">void store(const String &amp;filename, const ConsensusMap &amp;consensus_map)</div><div class="ttdoc">Stores a consensus map to file. </div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_ac8a7a5df4900eb88c011d402eb5a6255"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#ac8a7a5df4900eb88c011d402eb5a6255">OpenMS::SILACAnalyzer::intensity_correlation</a></div><div class="ttdeci">DoubleReal intensity_correlation</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:114</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="ChromatogramTools_8h_html"><div class="ttname"><a href="ChromatogramTools_8h.html">ChromatogramTools.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a426f58285a6c7a6b81346bcc4cf58e2a"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a426f58285a6c7a6b81346bcc4cf58e2a">OpenMS::ConsensusXMLFile::load</a></div><div class="ttdeci">void load(const String &amp;filename, ConsensusMap &amp;map)</div><div class="ttdoc">Loads a consensus map from file and calls updateRanges. </div></div>
<div class="ttc" id="LinearRegression_8h_html"><div class="ttname"><a href="LinearRegression_8h.html">LinearRegression.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a4d532bb9efa7c2aeaedbcf5ff0c13826"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a4d532bb9efa7c2aeaedbcf5ff0c13826">OpenMS::SILACAnalyzer::rt_min</a></div><div class="ttdeci">DoubleReal rt_min</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:112</div></div>
<div class="ttc" id="MzMLFile_8h_html"><div class="ttname"><a href="MzMLFile_8h.html">MzMLFile.h</a></div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a19a2651887fa4d874edfe6a94b54b2d5"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a19a2651887fa4d874edfe6a94b54b2d5">OpenMS::SILACAnalyzer::in</a></div><div class="ttdeci">String in</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a3ca615fc4cf75e66d68fdb94df4b94e9"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a3ca615fc4cf75e66d68fdb94df4b94e9">OpenMS::SILACAnalyzer::SILACAnalyzer</a></div><div class="ttdeci">SILACAnalyzer()</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:127</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusFeature_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusFeature.html">OpenMS::ConsensusFeature</a></div><div class="ttdoc">A 2-dimensional consensus feature. </div><div class="ttdef"><b>Definition:</b> ConsensusFeature.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_ade305f744c909667f3c6f4e2fed3262b"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#ade305f744c909667f3c6f4e2fed3262b">OpenMS::SILACAnalyzer::writeFeatures</a></div><div class="ttdeci">void writeFeatures(const String &amp;filename, FeatureMap&lt;&gt; &amp;out) const </div><div class="ttdoc">Write featureXML from FeatureMap to file. </div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:320</div></div>
<div class="ttc" id="classOpenMS_1_1SILACAnalyzer_html_a145cf377400ce6b5c8760644f69163fe"><div class="ttname"><a href="classOpenMS_1_1SILACAnalyzer.html#a145cf377400ce6b5c8760644f69163fe">OpenMS::SILACAnalyzer::charge_min</a></div><div class="ttdeci">UInt charge_min</div><div class="ttdef"><b>Definition:</b> SILACAnalyzer.h:104</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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