ClusterAnalyzer.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Mathias Walzer $
// $Authors: $
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#pragma once

#include <OpenMS/DATASTRUCTURES/DistanceMatrix.h>
#include <OpenMS/DATASTRUCTURES/BinaryTreeNode.h>

#include <vector>

namespace OpenMS
{
  class String;

  class OPENMS_DLLAPI ClusterAnalyzer
  {
public:
    ClusterAnalyzer();

    ClusterAnalyzer(const ClusterAnalyzer & source);

    virtual ~ClusterAnalyzer();

    std::vector<float> averageSilhouetteWidth(const std::vector<BinaryTreeNode> & tree, const DistanceMatrix<float> & original);

    std::vector<float> dunnIndices(const std::vector<BinaryTreeNode> & tree, const DistanceMatrix<float> & original, const bool tree_from_singlelinkage = false);

    std::vector<float> cohesion(const std::vector<std::vector<Size> > & clusters, const DistanceMatrix<float> & original);

    float averagePopulationAberration(Size cluster_quantity, std::vector<BinaryTreeNode> & tree);

    void cut(const Size cluster_quantity, const std::vector<BinaryTreeNode> & tree, std::vector<std::vector<Size> > & clusters);

    void cut(const Size cluster_quantity, const std::vector<BinaryTreeNode> & tree, std::vector<std::vector<BinaryTreeNode> > & subtrees);

    String newickTree(const std::vector<BinaryTreeNode> & tree, const bool include_distance = false);

private:
    ClusterAnalyzer & operator=(const ClusterAnalyzer & source);

  };
  bool compareBinaryTreeNode(const BinaryTreeNode & x, const BinaryTreeNode & y);

}