35 #ifndef OPENMS_COMPARISON_CLUSTERING_CLUSTERANALYZER_H 
   36 #define OPENMS_COMPARISON_CLUSTERING_CLUSTERANALYZER_H 
   80     std::vector<Real> averageSilhouetteWidth(
const std::vector<BinaryTreeNode> & tree, 
const DistanceMatrix<Real> & original);
 
   90     std::vector<Real> dunnIndices(
const std::vector<BinaryTreeNode> & tree, 
const DistanceMatrix<Real> & original, 
const bool tree_from_singlelinkage = 
false);
 
   99     std::vector<Real> cohesion(
const std::vector<std::vector<Size> > & clusters, 
const DistanceMatrix<Real> & original);
 
  110     Real averagePopulationAberration(
Size cluster_quantity, std::vector<BinaryTreeNode> & tree);
 
  127     void cut(
const Size cluster_quantity, 
const std::vector<BinaryTreeNode> & tree, std::vector<std::vector<Size> > & clusters);
 
  140     void cut(
const Size cluster_quantity, 
const std::vector<BinaryTreeNode> & tree, std::vector<std::vector<BinaryTreeNode> > & subtrees);
 
  150     String newickTree(
const std::vector<BinaryTreeNode> & tree, 
const bool include_distance = 
false);
 
  161 #endif //OPENMS_COMPARISON_CLUSTERING_CLUSTERANALYZER_H 
float Real
Real type. 
Definition: Types.h:109
A more convenient string class. 
Definition: String.h:56
Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's) 
Definition: ClusterAnalyzer.h:58
A two-dimensional distance matrix, similar to OpenMS::Matrix. 
Definition: DistanceMatrix.h:57
bool compareBinaryTreeNode(const BinaryTreeNode &x, const BinaryTreeNode &y)
returns the value of (x.distance < y.distance) for use with sort 
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
Elements of a binary tree used to represent a hierarchical clustering process. 
Definition: BinaryTreeNode.h:50