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<a href="MapAlignmentAlgorithmPoseClustering_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: Clemens Groepl $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Eva Lange, Clemens Groepl $</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_MAPMATCHING_MAPALIGNMENTALGORITHMPOSECLUSTERING_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_MAPMATCHING_MAPALIGNMENTALGORITHMPOSECLUSTERING_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="MapAlignmentAlgorithm_8h.html">OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithm.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="TransformationDescription_8h.html">OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.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="StablePairFinder_8h.html">OpenMS/ANALYSIS/MAPMATCHING/StablePairFinder.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="PoseClusteringAffineSuperimposer_8h.html">OpenMS/ANALYSIS/MAPMATCHING/PoseClusteringAffineSuperimposer.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="ConsensusMap_8h.html">OpenMS/KERNEL/ConsensusMap.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="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;{</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">   65</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> :</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;  {</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a>();</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a>();</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    <span class="keywordtype">void</span> align(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; map, <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> &amp; trafo);</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;    <span class="keywordtype">void</span> align(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;&gt;</a> &amp; map, <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> &amp; trafo);</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    <span class="keywordtype">void</span> align(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp; map, <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> &amp; trafo);</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a6110872a350e1ac11924dcc470cb6714">   80</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a6110872a350e1ac11924dcc470cb6714">setReference</a>(<span class="keyword">const</span> MapType &amp; map)</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    {</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;      MapType map2 = map; <span class="comment">// todo: avoid copy (MSExperiment version of convert() demands non-const version)</span></div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;      <a class="code" href="classOpenMS_1_1ConsensusMap.html#addd3e7ab2d02c8ff9377da76cf2fcaff">ConsensusMap::convert</a>(0, map2, reference_, max_num_peaks_considered_);</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;    }</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div>
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a9584ec9238430832ac2c381039513247">   87</a></span>&#160;    <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a> * <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a9584ec9238430832ac2c381039513247">create</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="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a>();</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;</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a8d4600093afb26cff7d7db82a1837e9f">   93</a></span>&#160;    <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a8d4600093afb26cff7d7db82a1837e9f">getProductName</a>()</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;    {</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;      <span class="keywordflow">return</span> <span class="stringliteral">&quot;pose_clustering&quot;</span>;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    }</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">   98</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> updateMembers_();</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"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a58e8fabd0acee7c3d34db7c304db762e">  102</a></span>&#160;    <a class="code" href="classOpenMS_1_1PoseClusteringAffineSuperimposer.html">PoseClusteringAffineSuperimposer</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a58e8fabd0acee7c3d34db7c304db762e">superimposer_</a>;</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#afa65b41aa65348bd4396b9bef84e7ac7">  104</a></span>&#160;    <a class="code" href="classOpenMS_1_1StablePairFinder.html">StablePairFinder</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#afa65b41aa65348bd4396b9bef84e7ac7">pairfinder_</a>;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;</div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a0a180d56906b4980aa2719fc500cd2de">  106</a></span>&#160;    <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a0a180d56906b4980aa2719fc500cd2de">reference_</a>;</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"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a04e32c6e5d826c09e14323f0226f69b8">  108</a></span>&#160;    <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a04e32c6e5d826c09e14323f0226f69b8">max_num_peaks_considered_</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="keyword">private</span>:</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;    <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> &amp;);</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;    <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> &amp;);</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;  };</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;<span class="preprocessor">#endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMPOSECLUSTERING_H</span></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering_html_a58e8fabd0acee7c3d34db7c304db762e"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a58e8fabd0acee7c3d34db7c304db762e">OpenMS::MapAlignmentAlgorithmPoseClustering::superimposer_</a></div><div class="ttdeci">PoseClusteringAffineSuperimposer superimposer_</div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmPoseClustering.h:102</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering_html_afa65b41aa65348bd4396b9bef84e7ac7"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#afa65b41aa65348bd4396b9bef84e7ac7">OpenMS::MapAlignmentAlgorithmPoseClustering::pairfinder_</a></div><div class="ttdeci">StablePairFinder pairfinder_</div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmPoseClustering.h:104</div></div>
<div class="ttc" id="classOpenMS_1_1StablePairFinder_html"><div class="ttname"><a href="classOpenMS_1_1StablePairFinder.html">OpenMS::StablePairFinder</a></div><div class="ttdoc">This class implements a pair finding algorithm for consensus features. </div><div class="ttdef"><b>Definition:</b> StablePairFinder.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering_html_a6110872a350e1ac11924dcc470cb6714"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a6110872a350e1ac11924dcc470cb6714">OpenMS::MapAlignmentAlgorithmPoseClustering::setReference</a></div><div class="ttdeci">void setReference(const MapType &amp;map)</div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmPoseClustering.h:80</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="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_1MapAlignmentAlgorithm_html"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithm.html">OpenMS::MapAlignmentAlgorithm</a></div><div class="ttdoc">Base class for all map-alignment algorithms. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithm.h:58</div></div>
<div class="ttc" id="StablePairFinder_8h_html"><div class="ttname"><a href="StablePairFinder_8h.html">StablePairFinder.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html">OpenMS::ConsensusMap</a></div><div class="ttdoc">A container for consensus elements. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:60</div></div>
<div class="ttc" id="PoseClusteringAffineSuperimposer_8h_html"><div class="ttname"><a href="PoseClusteringAffineSuperimposer_8h.html">PoseClusteringAffineSuperimposer.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering_html"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">OpenMS::MapAlignmentAlgorithmPoseClustering</a></div><div class="ttdoc">A map alignment algorithm based on pose clustering. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmPoseClustering.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering_html_a04e32c6e5d826c09e14323f0226f69b8"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a04e32c6e5d826c09e14323f0226f69b8">OpenMS::MapAlignmentAlgorithmPoseClustering::max_num_peaks_considered_</a></div><div class="ttdeci">Int max_num_peaks_considered_</div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmPoseClustering.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering_html_a8d4600093afb26cff7d7db82a1837e9f"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a8d4600093afb26cff7d7db82a1837e9f">OpenMS::MapAlignmentAlgorithmPoseClustering::getProductName</a></div><div class="ttdeci">static String getProductName()</div><div class="ttdoc">Returns the product name (for the Factory) </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmPoseClustering.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="TransformationDescription_8h_html"><div class="ttname"><a href="TransformationDescription_8h.html">TransformationDescription.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html_addd3e7ab2d02c8ff9377da76cf2fcaff"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html#addd3e7ab2d02c8ff9377da76cf2fcaff">OpenMS::ConsensusMap::convert</a></div><div class="ttdeci">static void convert(UInt64 const input_map_index, FeatureMap&lt; FeatureT &gt; const &amp;input_map, ConsensusMap &amp;output_map, Size n=-1)</div><div class="ttdoc">Convert a FeatureMap (of any feature type) to a ConsensusMap. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:230</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationDescription_html"><div class="ttname"><a href="classOpenMS_1_1TransformationDescription.html">OpenMS::TransformationDescription</a></div><div class="ttdoc">Generic description of a coordinate transformation. </div><div class="ttdef"><b>Definition:</b> TransformationDescription.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering_html_a9584ec9238430832ac2c381039513247"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a9584ec9238430832ac2c381039513247">OpenMS::MapAlignmentAlgorithmPoseClustering::create</a></div><div class="ttdeci">static MapAlignmentAlgorithm * create()</div><div class="ttdoc">Creates a new instance of this class (for Factory) </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmPoseClustering.h:87</div></div>
<div class="ttc" id="MapAlignmentAlgorithm_8h_html"><div class="ttname"><a href="MapAlignmentAlgorithm_8h.html">MapAlignmentAlgorithm.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PoseClusteringAffineSuperimposer_html"><div class="ttname"><a href="classOpenMS_1_1PoseClusteringAffineSuperimposer.html">OpenMS::PoseClusteringAffineSuperimposer</a></div><div class="ttdoc">A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transf...</div><div class="ttdef"><b>Definition:</b> PoseClusteringAffineSuperimposer.h:65</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_1MapAlignmentAlgorithmPoseClustering_html_a0a180d56906b4980aa2719fc500cd2de"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a0a180d56906b4980aa2719fc500cd2de">OpenMS::MapAlignmentAlgorithmPoseClustering::reference_</a></div><div class="ttdeci">ConsensusMap reference_</div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmPoseClustering.h:106</div></div>
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