ClusterAnalyzer.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
 
#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);
 
}