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<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_d5c86c02180db504975e24557b30e7a8.html">COMPARISON</a></li><li class="navelem"><a class="el" href="dir_cb8dd6e02b22bc637c17697ac03360d1.html">CLUSTERING</a></li> </ul>
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<div class="title">ClusterHierarchical.h</div> </div>
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<a href="ClusterHierarchical_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
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<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
31
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
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<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
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<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
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<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
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<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
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<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
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<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
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<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
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<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
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<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
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<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
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<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
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<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
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<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
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<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
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<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
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<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
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<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
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<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
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<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">//</span></div>
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<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> </div>
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<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// You should have received a copy of the GNU Lesser General Public</span></div>
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<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// License along with this library; if not, write to the Free Software</span></div>
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<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="comment">// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA</span></div>
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<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="comment">//</span></div>
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<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="comment">// $Maintainer: Mathias Walzer $</span></div>
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<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="comment">// $Authors: $</span></div>
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<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
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<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="comment">//</span></div>
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<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#ifndef OPENMS_COMPARISON_CLUSTERING_CLUSTERHIERARCHICAL_H</span></div>
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<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_COMPARISON_CLUSTERING_CLUSTERHIERARCHICAL_H</span></div>
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<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor"></span></div>
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<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>></span></div>
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<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <<a class="code" href="DistanceMatrix_8h.html">OpenMS/DATASTRUCTURES/DistanceMatrix.h</a>></span></div>
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<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <<a class="code" href="ClusterFunctor_8h.html">OpenMS/COMPARISON/CLUSTERING/ClusterFunctor.h</a>></span></div>
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<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <<a class="code" href="ClusterAnalyzer_8h.html">OpenMS/COMPARISON/CLUSTERING/ClusterAnalyzer.h</a>></span></div>
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<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include <<a class="code" href="PeakSpectrumCompareFunctor_8h.html">OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h</a>></span></div>
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<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <<a class="code" href="BinnedSpectrum_8h.html">OpenMS/COMPARISON/SPECTRA/BinnedSpectrum.h</a>></span></div>
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<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">#include <<a class="code" href="BinnedSpectrumCompareFunctor_8h.html">OpenMS/COMPARISON/SPECTRA/BinnedSpectrumCompareFunctor.h</a>></span></div>
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<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#include <<a class="code" href="Exception_8h.html">OpenMS/CONCEPT/Exception.h</a>></span></div>
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<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
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<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#include <vector></span></div>
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<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div>
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<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="keyword">namespace </span>OpenMS</div>
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<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> {</div>
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<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
84
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ClusterHierarchical.html"> 64</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ClusterHierarchical.html">ClusterHierarchical</a></div>
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<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  {</div>
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<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="keyword">private</span>:</div>
87
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
88
<div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ClusterHierarchical.html#ad7f9420c5db55e41dcaf2e64df8153e0"> 69</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1ClusterHierarchical.html#ad7f9420c5db55e41dcaf2e64df8153e0">threshold_</a>;</div>
89
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
90
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="keyword">public</span>:</div>
91
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ClusterHierarchical.html#ad85aa8985d410cb639986b082cc30964"> 73</a></span>  <a class="code" href="classOpenMS_1_1ClusterHierarchical.html#ad85aa8985d410cb639986b082cc30964">ClusterHierarchical</a>() :</div>
92
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  threshold_(1.0)</div>
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<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  {</div>
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<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  }</div>
95
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
96
<div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ClusterHierarchical.html#abdf3b01293b44af5bd0c404951452e5c"> 79</a></span>  <a class="code" href="classOpenMS_1_1ClusterHierarchical.html#abdf3b01293b44af5bd0c404951452e5c">ClusterHierarchical</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ClusterHierarchical.html">ClusterHierarchical</a> & source) :</div>
97
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  threshold_(source.threshold_)</div>
98
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  {</div>
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<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  }</div>
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<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
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<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ClusterHierarchical.html#aa6462893a95594a2c87be316f8c620a8"> 85</a></span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1ClusterHierarchical.html#aa6462893a95594a2c87be316f8c620a8">~ClusterHierarchical</a>()</div>
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<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  {</div>
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<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  }</div>
104
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div>
105
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> Data, <span class="keyword">typename</span> SimilarityComparator></div>
106
<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ClusterHierarchical.html#ae2f71a927933400ed5ce71513352e9ae"> 108</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ClusterHierarchical.html#ae2f71a927933400ed5ce71513352e9ae">cluster</a>(std::vector<Data> & data, <span class="keyword">const</span> SimilarityComparator & comparator, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ClusterFunctor.html">ClusterFunctor</a> & clusterer, std::vector<BinaryTreeNode> & cluster_tree, <a class="code" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix<Real></a> & original_distance)</div>
107
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  {</div>
108
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordflow">if</span> (original_distance.<a class="code" href="classOpenMS_1_1DistanceMatrix.html#af7ead7da765bc700381795644e5336d9">dimensionsize</a>() != data.size())</div>
109
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  {</div>
110
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="comment">//create distancematrix for data with comparator</span></div>
111
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  original_distance.<a class="code" href="classOpenMS_1_1DistanceMatrix.html#ac8bb3912a3ce86b15842e79d0b421204">clear</a>();</div>
112
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  original_distance.<a class="code" href="classOpenMS_1_1DistanceMatrix.html#ae89192ad76ef6362bda69ab08117c3f2">resize</a>(data.size(), 1);</div>
113
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < data.size(); i++)</div>
114
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  {</div>
115
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < i; j++)</div>
116
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  {</div>
117
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="comment">//distance value is 1-similarity value, since similarity is in range of [0,1]</span></div>
118
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  original_distance.<a class="code" href="classOpenMS_1_1DistanceMatrix.html#a742fc7b1066ade8d0ba632ceec223c59">setValueQuick</a>(i, j, 1 - comparator(data[i], data[j]));</div>
119
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  }</div>
120
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  }</div>
121
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  }</div>
122
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div>
123
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="comment">//~ std::cout << "done" << std::endl; //maybe progress handler?</span></div>
124
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="comment">// create clustering with ClusterMethod, DistanceMatrix and Data</span></div>
125
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  clusterer(original_distance, cluster_tree, threshold_);</div>
126
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  }</div>
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<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div>
128
<div class="line"><a name="l00146"></a><span class="lineno"><a class="line" href="group__SpectraClustering.html#ga58561325974d89bab2c7ccbd25dfc5cc"> 146</a></span>  <span class="keywordtype">void</span> <a class="code" href="group__SpectraClustering.html#ga58561325974d89bab2c7ccbd25dfc5cc">cluster</a>(std::vector<PeakSpectrum> & data, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BinnedSpectrumCompareFunctor.html">BinnedSpectrumCompareFunctor</a> & comparator, <span class="keywordtype">double</span> sz, <a class="code" href="classunsigned_01int.html">UInt</a> sp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ClusterFunctor.html">ClusterFunctor</a> & clusterer, std::vector<BinaryTreeNode> & cluster_tree, <a class="code" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix<Real></a> & original_distance)</div>
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<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  {</div>
130
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> </div>
131
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  std::vector<BinnedSpectrum> binned_data;</div>
132
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  binned_data.reserve(data.size());</div>
133
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div>
134
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="comment">//transform each PeakSpectrum to a corresponding BinnedSpectrum with given settings of size and spread</span></div>
135
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < data.size(); i++)</div>
136
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  {</div>
137
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="comment">//double sz(2), UInt sp(1);</span></div>
138
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  binned_data.push_back(<a class="code" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a>(sz, sp, data[i]));</div>
139
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  }</div>
140
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> </div>
141
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="comment">//create distancematrix for data with comparator</span></div>
142
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  original_distance.<a class="code" href="classOpenMS_1_1DistanceMatrix.html#ac8bb3912a3ce86b15842e79d0b421204">clear</a>();</div>
143
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  original_distance.<a class="code" href="classOpenMS_1_1DistanceMatrix.html#ae89192ad76ef6362bda69ab08117c3f2">resize</a>(data.size(), 1);</div>
144
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span> </div>
145
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < binned_data.size(); i++)</div>
146
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  {</div>
147
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < i; j++)</div>
148
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  {</div>
149
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="comment">//distance value is 1-similarity value, since similarity is in range of [0,1]</span></div>
150
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  original_distance.<a class="code" href="classOpenMS_1_1DistanceMatrix.html#a2e841e704b21daa5788812746ee1cf7e">setValue</a>(i, j, 1 - comparator(binned_data[i], binned_data[j]));</div>
151
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  }</div>
152
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  }</div>
153
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div>
154
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="comment">// create Clustering with ClusterMethod, DistanceMatrix and Data</span></div>
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<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  clusterer(original_distance, cluster_tree, threshold_);</div>
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<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  }</div>
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<div class="line"><a name="l00175"></a><span class="lineno"> 175</span> </div>
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<div class="line"><a name="l00177"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ClusterHierarchical.html#aa7fd3c8c549d04d503fdda45e5a858b8"> 177</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1ClusterHierarchical.html#aa7fd3c8c549d04d503fdda45e5a858b8">getThreshold</a>()</div>
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<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  {</div>
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<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordflow">return</span> threshold_;</div>
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<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  }</div>
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<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div>
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<div class="line"><a name="l00185"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ClusterHierarchical.html#a778d694897c4eeb0687713ef07a4e36e"> 185</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ClusterHierarchical.html#a778d694897c4eeb0687713ef07a4e36e">setThreshold</a>(<span class="keywordtype">double</span> x)</div>
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<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  {</div>
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<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  threshold_ = x;</div>
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<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  }</div>
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<div class="line"><a name="l00189"></a><span class="lineno"> 189</span> </div>
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<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  };</div>
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<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> </div>
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<div class="line"><a name="l00197"></a><span class="lineno"><a class="line" href="classOpenMS_1_1UnnormalizedComparator.html"> 197</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1UnnormalizedComparator.html">UnnormalizedComparator</a> :</div>
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<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">Exception::BaseException</a></div>
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<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  {</div>
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<div class="line"><a name="l00200"></a><span class="lineno"> 200</span> <span class="keyword">public</span>:</div>
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<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <a class="code" href="classOpenMS_1_1UnnormalizedComparator.html">UnnormalizedComparator</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> * file, <span class="keywordtype">int</span> line, <span class="keyword">const</span> <span class="keywordtype">char</span> * <span class="keyword">function</span>, <span class="keyword">const</span> <span class="keywordtype">char</span> * message</div>
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<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  = <span class="stringliteral">"Clustering with unnormalized similarity measurement requested, normalized is mandatory"</span>) <span class="keywordflow">throw</span>();</div>
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<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1UnnormalizedComparator.html">UnnormalizedComparator</a>() <span class="keywordflow">throw</span>();</div>
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<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  };</div>
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<div class="line"><a name="l00205"></a><span class="lineno"> 205</span> </div>
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<div class="line"><a name="l00206"></a><span class="lineno"> 206</span> }</div>
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<div class="line"><a name="l00207"></a><span class="lineno"> 207</span> <span class="preprocessor">#endif //OPENMS_COMPARISON_CLUSTERING_CLUSTERHIERARCHICAL_H</span></div>
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<div class="ttc" id="classOpenMS_1_1BinnedSpectrumCompareFunctor_html"><div class="ttname"><a href="classOpenMS_1_1BinnedSpectrumCompareFunctor.html">OpenMS::BinnedSpectrumCompareFunctor</a></div><div class="ttdoc">Base class for compare functors of BinnedSpectra. </div><div class="ttdef"><b>Definition:</b> BinnedSpectrumCompareFunctor.h:58</div></div>
182
<div class="ttc" id="classOpenMS_1_1ClusterHierarchical_html_aa6462893a95594a2c87be316f8c620a8"><div class="ttname"><a href="classOpenMS_1_1ClusterHierarchical.html#aa6462893a95594a2c87be316f8c620a8">OpenMS::ClusterHierarchical::~ClusterHierarchical</a></div><div class="ttdeci">virtual ~ClusterHierarchical()</div><div class="ttdoc">destructor </div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:85</div></div>
183
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
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<div class="ttc" id="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
185
<div class="ttc" id="classOpenMS_1_1DistanceMatrix_html_ae89192ad76ef6362bda69ab08117c3f2"><div class="ttname"><a href="classOpenMS_1_1DistanceMatrix.html#ae89192ad76ef6362bda69ab08117c3f2">OpenMS::DistanceMatrix::resize</a></div><div class="ttdeci">void resize(SizeType dimensionsize, Value value=Value())</div><div class="ttdoc">resizing the container </div><div class="ttdef"><b>Definition:</b> DistanceMatrix.h:330</div></div>
186
<div class="ttc" id="BinnedSpectrumCompareFunctor_8h_html"><div class="ttname"><a href="BinnedSpectrumCompareFunctor_8h.html">BinnedSpectrumCompareFunctor.h</a></div></div>
187
<div class="ttc" id="classOpenMS_1_1DistanceMatrix_html"><div class="ttname"><a href="classOpenMS_1_1DistanceMatrix.html">OpenMS::DistanceMatrix</a></div><div class="ttdoc">A two-dimensional distance matrix, similar to OpenMS::Matrix. </div><div class="ttdef"><b>Definition:</b> DistanceMatrix.h:57</div></div>
188
<div class="ttc" id="classOpenMS_1_1ClusterHierarchical_html_aa7fd3c8c549d04d503fdda45e5a858b8"><div class="ttname"><a href="classOpenMS_1_1ClusterHierarchical.html#aa7fd3c8c549d04d503fdda45e5a858b8">OpenMS::ClusterHierarchical::getThreshold</a></div><div class="ttdeci">double getThreshold()</div><div class="ttdoc">get the threshold </div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:177</div></div>
189
<div class="ttc" id="classOpenMS_1_1UnnormalizedComparator_html"><div class="ttname"><a href="classOpenMS_1_1UnnormalizedComparator.html">OpenMS::UnnormalizedComparator</a></div><div class="ttdoc">Exception thrown if clustering is attempted without a normalized compare functor. ...</div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:197</div></div>
190
<div class="ttc" id="classOpenMS_1_1DistanceMatrix_html_ac8bb3912a3ce86b15842e79d0b421204"><div class="ttname"><a href="classOpenMS_1_1DistanceMatrix.html#ac8bb3912a3ce86b15842e79d0b421204">OpenMS::DistanceMatrix::clear</a></div><div class="ttdeci">void clear()</div><div class="ttdoc">reset all </div><div class="ttdef"><b>Definition:</b> DistanceMatrix.h:309</div></div>
191
<div class="ttc" id="DistanceMatrix_8h_html"><div class="ttname"><a href="DistanceMatrix_8h.html">DistanceMatrix.h</a></div></div>
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<div class="ttc" id="ClusterFunctor_8h_html"><div class="ttname"><a href="ClusterFunctor_8h.html">ClusterFunctor.h</a></div></div>
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<div class="ttc" id="ClusterAnalyzer_8h_html"><div class="ttname"><a href="ClusterAnalyzer_8h.html">ClusterAnalyzer.h</a></div></div>
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<div class="ttc" id="BinnedSpectrum_8h_html"><div class="ttname"><a href="BinnedSpectrum_8h.html">BinnedSpectrum.h</a></div></div>
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<div class="ttc" id="classOpenMS_1_1DistanceMatrix_html_a742fc7b1066ade8d0ba632ceec223c59"><div class="ttname"><a href="classOpenMS_1_1DistanceMatrix.html#a742fc7b1066ade8d0ba632ceec223c59">OpenMS::DistanceMatrix::setValueQuick</a></div><div class="ttdeci">void setValueQuick(SizeType i, SizeType j, ValueType value)</div><div class="ttdoc">sets a value at a given position: </div><div class="ttdef"><b>Definition:</b> DistanceMatrix.h:291</div></div>
196
<div class="ttc" id="classOpenMS_1_1ClusterHierarchical_html_a778d694897c4eeb0687713ef07a4e36e"><div class="ttname"><a href="classOpenMS_1_1ClusterHierarchical.html#a778d694897c4eeb0687713ef07a4e36e">OpenMS::ClusterHierarchical::setThreshold</a></div><div class="ttdeci">void setThreshold(double x)</div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:185</div></div>
197
<div class="ttc" id="classOpenMS_1_1ClusterHierarchical_html_abdf3b01293b44af5bd0c404951452e5c"><div class="ttname"><a href="classOpenMS_1_1ClusterHierarchical.html#abdf3b01293b44af5bd0c404951452e5c">OpenMS::ClusterHierarchical::ClusterHierarchical</a></div><div class="ttdeci">ClusterHierarchical(const ClusterHierarchical &source)</div><div class="ttdoc">copy constructor </div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:79</div></div>
198
<div class="ttc" id="classOpenMS_1_1ClusterHierarchical_html_ad85aa8985d410cb639986b082cc30964"><div class="ttname"><a href="classOpenMS_1_1ClusterHierarchical.html#ad85aa8985d410cb639986b082cc30964">OpenMS::ClusterHierarchical::ClusterHierarchical</a></div><div class="ttdeci">ClusterHierarchical()</div><div class="ttdoc">default constructor </div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:73</div></div>
199
<div class="ttc" id="classOpenMS_1_1ClusterHierarchical_html_ad7f9420c5db55e41dcaf2e64df8153e0"><div class="ttname"><a href="classOpenMS_1_1ClusterHierarchical.html#ad7f9420c5db55e41dcaf2e64df8153e0">OpenMS::ClusterHierarchical::threshold_</a></div><div class="ttdeci">double threshold_</div><div class="ttdoc">the threshold given to the ClusterFunctor </div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:69</div></div>
200
<div class="ttc" id="classOpenMS_1_1Exception_1_1BaseException_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1BaseException.html">OpenMS::Exception::BaseException</a></div><div class="ttdoc">Exception base class. </div><div class="ttdef"><b>Definition:</b> Exception.h:90</div></div>
201
<div class="ttc" id="classOpenMS_1_1BinnedSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1BinnedSpectrum.html">OpenMS::BinnedSpectrum</a></div><div class="ttdoc">This is a binned representation of a PeakSpectrum. </div><div class="ttdef"><b>Definition:</b> BinnedSpectrum.h:66</div></div>
202
<div class="ttc" id="classOpenMS_1_1DistanceMatrix_html_a2e841e704b21daa5788812746ee1cf7e"><div class="ttname"><a href="classOpenMS_1_1DistanceMatrix.html#a2e841e704b21daa5788812746ee1cf7e">OpenMS::DistanceMatrix::setValue</a></div><div class="ttdeci">void setValue(SizeType i, SizeType j, ValueType value)</div><div class="ttdoc">sets a value at a given position: </div><div class="ttdef"><b>Definition:</b> DistanceMatrix.h:246</div></div>
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<div class="ttc" id="group__SpectraClustering_html_ga58561325974d89bab2c7ccbd25dfc5cc"><div class="ttname"><a href="group__SpectraClustering.html#ga58561325974d89bab2c7ccbd25dfc5cc">OpenMS::ClusterHierarchical::cluster</a></div><div class="ttdeci">void cluster(std::vector< PeakSpectrum > &data, const BinnedSpectrumCompareFunctor &comparator, double sz, UInt sp, const ClusterFunctor &clusterer, std::vector< BinaryTreeNode > &cluster_tree, DistanceMatrix< Real > &original_distance)</div><div class="ttdoc">clustering function for binned PeakSpectrum </div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:146</div></div>
204
<div class="ttc" id="classOpenMS_1_1DistanceMatrix_html_af7ead7da765bc700381795644e5336d9"><div class="ttname"><a href="classOpenMS_1_1DistanceMatrix.html#af7ead7da765bc700381795644e5336d9">OpenMS::DistanceMatrix::dimensionsize</a></div><div class="ttdeci">SizeType dimensionsize() const </div><div class="ttdoc">gives the number of rows (i.e. number of columns) </div><div class="ttdef"><b>Definition:</b> DistanceMatrix.h:398</div></div>
205
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
206
<div class="ttc" id="PeakSpectrumCompareFunctor_8h_html"><div class="ttname"><a href="PeakSpectrumCompareFunctor_8h.html">PeakSpectrumCompareFunctor.h</a></div></div>
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<div class="ttc" id="classOpenMS_1_1ClusterHierarchical_html_ae2f71a927933400ed5ce71513352e9ae"><div class="ttname"><a href="classOpenMS_1_1ClusterHierarchical.html#ae2f71a927933400ed5ce71513352e9ae">OpenMS::ClusterHierarchical::cluster</a></div><div class="ttdeci">void cluster(std::vector< Data > &data, const SimilarityComparator &comparator, const ClusterFunctor &clusterer, std::vector< BinaryTreeNode > &cluster_tree, DistanceMatrix< Real > &original_distance)</div><div class="ttdoc">Clustering function. </div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:108</div></div>
208
<div class="ttc" id="classOpenMS_1_1ClusterHierarchical_html"><div class="ttname"><a href="classOpenMS_1_1ClusterHierarchical.html">OpenMS::ClusterHierarchical</a></div><div class="ttdoc">Hierarchical clustering with generic clustering functions. </div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:64</div></div>
209
<div class="ttc" id="Exception_8h_html"><div class="ttname"><a href="Exception_8h.html">Exception.h</a></div></div>
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<div class="ttc" id="classOpenMS_1_1ClusterFunctor_html"><div class="ttname"><a href="classOpenMS_1_1ClusterFunctor.html">OpenMS::ClusterFunctor</a></div><div class="ttdoc">Base class for cluster functors. </div><div class="ttdef"><b>Definition:</b> ClusterFunctor.h:54</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:12 using doxygen 1.8.5</font></TD>
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