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<a href="QuantitativeExperimentalDesign_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>
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<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Immanuel Luhn $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Immanuel Luhn$</span></div>
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<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_ANALYSIS_QUANTITATION_QUANTITATIVEEXPERIMENTALDESIGN_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_ANALYSIS_QUANTITATION_QUANTITATIVEEXPERIMENTALDESIGN_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="preprocessor">#include &lt;<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="TextFile_8h.html">OpenMS/FORMAT/TextFile.h</a>&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="PeptideAndProteinQuant_8h.html">OpenMS/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.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="ProteinResolver_8h.html">OpenMS/ANALYSIS/QUANTITATION/ProteinResolver.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="comment">//#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;{</div>
<div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="classOpenMS_1_1QuantitativeExperimentalDesign.html">   57</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1QuantitativeExperimentalDesign.html">QuantitativeExperimentalDesign</a> :</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;    <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>&#160;  {</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    <a class="code" href="classOpenMS_1_1QuantitativeExperimentalDesign.html">QuantitativeExperimentalDesign</a>();</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">//Destructor</span></div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1QuantitativeExperimentalDesign.html">QuantitativeExperimentalDesign</a>();</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    <span class="keywordtype">void</span> applyDesign2Resolver(<a class="code" href="classOpenMS_1_1ProteinResolver.html">ProteinResolver</a> &amp; resolver, <a class="code" href="classOpenMS_1_1TextFile.html">TextFile</a> &amp; file, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> &amp; fileNames);</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;    <span class="keywordtype">void</span> applyDesign2Quantifier(<a class="code" href="classOpenMS_1_1PeptideAndProteinQuant.html">PeptideAndProteinQuant</a> &amp; quantifier, <a class="code" href="classOpenMS_1_1TextFile.html">TextFile</a> &amp; file, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> &amp; fileNames);</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    <span class="comment">//std::vector&lt; std::pair&lt;PeptideAndProteinQuant::PeptideData,PeptideAndProteinQuant::ProteinQuant&gt; &gt;&amp; result);</span></div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;    <a class="code" href="classOpenMS_1_1QuantitativeExperimentalDesign.html">QuantitativeExperimentalDesign</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1QuantitativeExperimentalDesign.html">QuantitativeExperimentalDesign</a> &amp;);</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;    <a class="code" href="classOpenMS_1_1QuantitativeExperimentalDesign.html">QuantitativeExperimentalDesign</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1QuantitativeExperimentalDesign.html">QuantitativeExperimentalDesign</a> &amp;);</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;    <span class="keywordtype">void</span> mergeFeatureMaps_(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; map, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; experiment, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> &amp; file_paths);</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;    <span class="keywordtype">void</span> mergeConsensusMaps_(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp; map, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; experiment, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> &amp; file_paths);</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;    <span class="keywordtype">void</span> mergeIDFiles_(std::vector&lt;ProteinIdentification&gt; &amp; proteins, std::vector&lt;PeptideIdentification&gt; &amp; peptides, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; experiment, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> &amp; file_paths);</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    <span class="keywordtype">void</span> findRelevantFilePaths_(std::map&lt;String, StringList&gt; &amp; design2FileBaseName, std::map&lt;String, StringList&gt; &amp; design2FilePath, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> &amp; filePaths);</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    <span class="keywordtype">void</span> analyzeHeader_(<a class="code" href="classunsigned_01int.html">UInt</a> &amp; expCol, <a class="code" href="classunsigned_01int.html">UInt</a> &amp; fileCol, <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> &amp; header);</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;    <span class="keywordtype">void</span> getSeparator_(<a class="code" href="classOpenMS_1_1String.html">String</a> &amp; separator);</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;    <span class="keywordtype">void</span> mapFiles2Design_(std::map&lt;String, StringList&gt; &amp; experiments, <a class="code" href="classOpenMS_1_1TextFile.html">TextFile</a> &amp; file);</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;  };</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">// namespace OpenMS</span></div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;<span class="preprocessor">#endif // OPENMS_ANALYSIS_QUANTITATION_QUANTITATIVEEXPERIMENTALDESIGN_H</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_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="classOpenMS_1_1QuantitativeExperimentalDesign_html"><div class="ttname"><a href="classOpenMS_1_1QuantitativeExperimentalDesign.html">OpenMS::QuantitativeExperimentalDesign</a></div><div class="ttdoc">Merge files according to experimental design. </div><div class="ttdef"><b>Definition:</b> QuantitativeExperimentalDesign.h:57</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="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="PeptideAndProteinQuant_8h_html"><div class="ttname"><a href="PeptideAndProteinQuant_8h.html">PeptideAndProteinQuant.h</a></div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="ProteinResolver_8h_html"><div class="ttname"><a href="ProteinResolver_8h.html">ProteinResolver.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ProteinResolver_html"><div class="ttname"><a href="classOpenMS_1_1ProteinResolver.html">OpenMS::ProteinResolver</a></div><div class="ttdoc">Helper class for peptide and protein quantification based on feature data annotated with IDs...</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideAndProteinQuant_html"><div class="ttname"><a href="classOpenMS_1_1PeptideAndProteinQuant.html">OpenMS::PeptideAndProteinQuant</a></div><div class="ttdoc">Helper class for peptide and protein quantification based on feature data annotated with IDs...</div><div class="ttdef"><b>Definition:</b> PeptideAndProteinQuant.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html"><div class="ttname"><a href="classOpenMS_1_1StringList.html">OpenMS::StringList</a></div><div class="ttdoc">String list. </div><div class="ttdef"><b>Definition:</b> StringList.h:56</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="TextFile_8h_html"><div class="ttname"><a href="TextFile_8h.html">TextFile.h</a></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_1TextFile_html"><div class="ttname"><a href="classOpenMS_1_1TextFile.html">OpenMS::TextFile</a></div><div class="ttdoc">This class provides some basic file handling methods for text files. </div><div class="ttdef"><b>Definition:</b> TextFile.h:47</div></div>
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