OpenMS  3.0.0
ClusterAnalyzer.h
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31 // $Maintainer: Mathias Walzer $
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34 
35 #pragma once
36 
39 
40 #include <vector>
41 
42 namespace OpenMS
43 {
44  class String;
45 
51  class OPENMS_DLLAPI ClusterAnalyzer
52  {
53 public:
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 }
DistanceMatrix.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::compareBinaryTreeNode
bool compareBinaryTreeNode(const BinaryTreeNode &x, const BinaryTreeNode &y)
returns the value of (x.distance < y.distance) for use with sort
BinaryTreeNode.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ClusterAnalyzer
Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's)
Definition: ClusterAnalyzer.h:51
OpenMS::DistanceMatrix
A two-dimensional distance matrix, similar to OpenMS::Matrix.
Definition: DistanceMatrix.h:67
OpenMS::BinaryTreeNode
Elements of a binary tree used to represent a hierarchical clustering process.
Definition: BinaryTreeNode.h:48