3
<TITLE>ClusterAnalyzer.h Source File</TITLE>
4
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
5
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
7
<BODY BGCOLOR="#FFFFFF">
8
<A href="index.html">Home</A> ·
9
<A href="classes.html">Classes</A> ·
10
<A href="annotated.html">Annotated Classes</A> ·
11
<A href="modules.html">Modules</A> ·
12
<A href="functions_func.html">Members</A> ·
13
<A href="namespaces.html">Namespaces</A> ·
14
<A href="pages.html">Related Pages</A>
15
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
16
<!-- Generated by Doxygen 1.8.5 -->
17
<div id="nav-path" class="navpath">
19
<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>
23
<div class="headertitle">
24
<div class="title">ClusterAnalyzer.h</div> </div>
26
<div class="contents">
27
<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> <span class="comment">// --------------------------------------------------------------------------</span></div>
28
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
29
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
30
<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>
32
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
33
<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>
34
<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>
35
<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>
36
<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>
37
<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>
38
<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>
39
<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>
40
<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>
41
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
42
<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>
43
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
44
<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>
45
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
46
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
47
<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>
48
<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>
49
<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>
50
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
51
<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>
52
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
53
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
54
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
55
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
56
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
57
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Mathias Walzer $</span></div>
58
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: $</span></div>
59
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
60
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
61
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_COMPARISON_CLUSTERING_CLUSTERANALYZER_H</span></div>
62
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_COMPARISON_CLUSTERING_CLUSTERANALYZER_H</span></div>
63
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
64
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="DistanceMatrix_8h.html">OpenMS/DATASTRUCTURES/DistanceMatrix.h</a>></span></div>
65
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>></span></div>
66
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="BinaryTreeNode_8h.html">OpenMS/DATASTRUCTURES/BinaryTreeNode.h</a>></span></div>
67
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> </div>
68
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <vector></span></div>
69
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <set></span></div>
70
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <list></span></div>
71
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <iostream></span></div>
72
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <fstream></span></div>
73
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <cfloat></span></div>
74
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
75
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="keyword">namespace </span>OpenMS</div>
76
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> {</div>
77
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keyword">class </span>String;</div>
78
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
79
<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ClusterAnalyzer.html"> 58</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a></div>
80
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  {</div>
81
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="keyword">public</span>:</div>
82
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a>();</div>
83
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div>
84
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <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> & source);</div>
85
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
86
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a>();</div>
87
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
88
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  std::vector<Real> averageSilhouetteWidth(<span class="keyword">const</span> std::vector<BinaryTreeNode> & tree, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix<Real></a> & original);</div>
89
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
90
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  std::vector<Real> dunnIndices(<span class="keyword">const</span> std::vector<BinaryTreeNode> & tree, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix<Real></a> & original, <span class="keyword">const</span> <span class="keywordtype">bool</span> tree_from_singlelinkage = <span class="keyword">false</span>);</div>
91
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div>
92
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  std::vector<Real> cohesion(<span class="keyword">const</span> std::vector<std::vector<Size> > & clusters, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix<Real></a> & original);</div>
93
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> </div>
94
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <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<BinaryTreeNode> & tree);</div>
95
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
96
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <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<BinaryTreeNode> & tree, std::vector<std::vector<Size> > & clusters);</div>
97
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> </div>
98
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <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<BinaryTreeNode> & tree, std::vector<std::vector<BinaryTreeNode> > & subtrees);</div>
99
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> </div>
100
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> newickTree(<span class="keyword">const</span> std::vector<BinaryTreeNode> & tree, <span class="keyword">const</span> <span class="keywordtype">bool</span> include_distance = <span class="keyword">false</span>);</div>
101
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div>
102
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> <span class="keyword">private</span>:</div>
103
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> & source);</div>
104
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span> </div>
105
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  };</div>
106
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <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> & x, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> & y);</div>
107
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div>
108
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> }</div>
109
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> <span class="preprocessor">#endif //OPENMS_COMPARISON_CLUSTERING_CLUSTERANALYZER_H</span></div>
110
<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>
111
<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>
112
<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&#39;s) </div><div class="ttdef"><b>Definition:</b> ClusterAnalyzer.h:58</div></div>
113
<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>
114
<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 &x, const BinaryTreeNode &y)</div><div class="ttdoc">returns the value of (x.distance &lt; y.distance) for use with sort </div></div>
115
<div class="ttc" id="DistanceMatrix_8h_html"><div class="ttname"><a href="DistanceMatrix_8h.html">DistanceMatrix.h</a></div></div>
116
<div class="ttc" id="BinaryTreeNode_8h_html"><div class="ttname"><a href="BinaryTreeNode_8h.html">BinaryTreeNode.h</a></div></div>
117
<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>
118
<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>
119
<div class="ttc" id="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
120
</div><!-- fragment --></div><!-- contents -->
121
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
122
<TABLE width="100%" border="0">
124
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
125
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:12 using doxygen 1.8.5</font></TD>
added
removed
doc/html/ClusterAnalyzer_8h_source.html
