ClusterAnalyzer.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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);
 
}