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<a href="ClusterAnalyzer_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>
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<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>
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<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: Mathias Walzer $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: $</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_COMPARISON_CLUSTERING_CLUSTERANALYZER_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_COMPARISON_CLUSTERING_CLUSTERANALYZER_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="DistanceMatrix_8h.html">OpenMS/DATASTRUCTURES/DistanceMatrix.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="String_8h.html">OpenMS/DATASTRUCTURES/String.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="BinaryTreeNode_8h.html">OpenMS/DATASTRUCTURES/BinaryTreeNode.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;set&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;list&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;iostream&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;fstream&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &lt;cfloat&gt;</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;{</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;  <span class="keyword">class </span>String;</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;</div>
<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ClusterAnalyzer.html">   58</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</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="l00062"></a><span class="lineno">   62</span>&#160;    <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a>();</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> &amp; source);</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a>();</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;    std::vector&lt;Real&gt; averageSilhouetteWidth(<span class="keyword">const</span> std::vector&lt;BinaryTreeNode&gt; &amp; tree, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix&lt;Real&gt;</a> &amp; original);</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;    std::vector&lt;Real&gt; dunnIndices(<span class="keyword">const</span> std::vector&lt;BinaryTreeNode&gt; &amp; tree, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix&lt;Real&gt;</a> &amp; original, <span class="keyword">const</span> <span class="keywordtype">bool</span> tree_from_singlelinkage = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    std::vector&lt;Real&gt; cohesion(<span class="keyword">const</span> std::vector&lt;std::vector&lt;Size&gt; &gt; &amp; clusters, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix&lt;Real&gt;</a> &amp; original);</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> averagePopulationAberration(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> cluster_quantity, std::vector&lt;BinaryTreeNode&gt; &amp; tree);</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;    <span class="keywordtype">void</span> cut(<span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> cluster_quantity, <span class="keyword">const</span> std::vector&lt;BinaryTreeNode&gt; &amp; tree, std::vector&lt;std::vector&lt;Size&gt; &gt; &amp; clusters);</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;    <span class="keywordtype">void</span> cut(<span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> cluster_quantity, <span class="keyword">const</span> std::vector&lt;BinaryTreeNode&gt; &amp; tree, std::vector&lt;std::vector&lt;BinaryTreeNode&gt; &gt; &amp; subtrees);</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> newickTree(<span class="keyword">const</span> std::vector&lt;BinaryTreeNode&gt; &amp; tree, <span class="keyword">const</span> <span class="keywordtype">bool</span> include_distance = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;    <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> &amp; source);</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;  };</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;  <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenMS.html#a58a825f137e452fa91ed983fddd61c8a">compareBinaryTreeNode</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> &amp; x, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> &amp; y);</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;}</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;<span class="preprocessor">#endif //OPENMS_COMPARISON_CLUSTERING_CLUSTERANALYZER_H</span></div>
<div class="ttc" id="group__Concept_html_gab685845059e8a2c92743427d9a698c70"><div class="ttname"><a href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">OpenMS::Real</a></div><div class="ttdeci">float Real</div><div class="ttdoc">Real type. </div><div class="ttdef"><b>Definition:</b> Types.h:109</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_1ClusterAnalyzer_html"><div class="ttname"><a href="classOpenMS_1_1ClusterAnalyzer.html">OpenMS::ClusterAnalyzer</a></div><div class="ttdoc">Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode&amp;#39;s) </div><div class="ttdef"><b>Definition:</b> ClusterAnalyzer.h:58</div></div>
<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>
<div class="ttc" id="namespaceOpenMS_html_a58a825f137e452fa91ed983fddd61c8a"><div class="ttname"><a href="namespaceOpenMS.html#a58a825f137e452fa91ed983fddd61c8a">OpenMS::compareBinaryTreeNode</a></div><div class="ttdeci">bool compareBinaryTreeNode(const BinaryTreeNode &amp;x, const BinaryTreeNode &amp;y)</div><div class="ttdoc">returns the value of (x.distance &amp;lt; y.distance) for use with sort </div></div>
<div class="ttc" id="DistanceMatrix_8h_html"><div class="ttname"><a href="DistanceMatrix_8h.html">DistanceMatrix.h</a></div></div>
<div class="ttc" id="BinaryTreeNode_8h_html"><div class="ttname"><a href="BinaryTreeNode_8h.html">BinaryTreeNode.h</a></div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1BinaryTreeNode_html"><div class="ttname"><a href="classOpenMS_1_1BinaryTreeNode.html">OpenMS::BinaryTreeNode</a></div><div class="ttdoc">Elements of a binary tree used to represent a hierarchical clustering process. </div><div class="ttdef"><b>Definition:</b> BinaryTreeNode.h:50</div></div>
<div class="ttc" id="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
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