| OpenMS 2.5.0

ClusterAnalyzer.h
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31 // $Maintainer: Mathias Walzer $
32 // $Authors: $
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34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DistanceMatrix.h>
38 #include <OpenMS/DATASTRUCTURES/BinaryTreeNode.h>
39
40 #include <vector>
41
42 namespace OpenMS
43 {
44 class String;
45
51 class OPENMS_DLLAPI ClusterAnalyzer
52 {
53 public:
55 ClusterAnalyzer();
56
58 ClusterAnalyzer(const ClusterAnalyzer & source);
59
61 virtual ~ClusterAnalyzer();
62
73 std::vector<float> averageSilhouetteWidth(const std::vector<BinaryTreeNode> & tree, const DistanceMatrix<float> & original);
74
83 std::vector<float> dunnIndices(const std::vector<BinaryTreeNode> & tree, const DistanceMatrix<float> & original, const bool tree_from_singlelinkage = false);
84
92 std::vector<float> cohesion(const std::vector<std::vector<Size> > & clusters, const DistanceMatrix<float> & original);
93
103 float averagePopulationAberration(Size cluster_quantity, std::vector<BinaryTreeNode> & tree);
104
120 void cut(const Size cluster_quantity, const std::vector<BinaryTreeNode> & tree, std::vector<std::vector<Size> > & clusters);
121
133 void cut(const Size cluster_quantity, const std::vector<BinaryTreeNode> & tree, std::vector<std::vector<BinaryTreeNode> > & subtrees);
134
143 String newickTree(const std::vector<BinaryTreeNode> & tree, const bool include_distance = false);
144
145 private:
147 ClusterAnalyzer & operator=(const ClusterAnalyzer & source);
148
149 };
151 bool compareBinaryTreeNode(const BinaryTreeNode & x, const BinaryTreeNode & y);
152
153 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
BinaryTreeNode.h
OpenMS::ClusterAnalyzer
Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode&#39;s)
Definition: ClusterAnalyzer.h:51
OpenMS::DistanceMatrix
A two-dimensional distance matrix, similar to OpenMS::Matrix.
Definition: DistanceMatrix.h:67
DistanceMatrix.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::compareBinaryTreeNode
bool compareBinaryTreeNode(const BinaryTreeNode &x, const BinaryTreeNode &y)
returns the value of (x.distance < y.distance) for use with sort
OpenMS::BinaryTreeNode
Elements of a binary tree used to represent a hierarchical clustering process.
Definition: BinaryTreeNode.h:48
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127