text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2015.
  //
  // 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: $
  // --------------------------------------------------------------------------
  //
  #ifndef OPENMS_COMPARISON_CLUSTERING_SINGLELINKAGE_H
  #define OPENMS_COMPARISON_CLUSTERING_SINGLELINKAGE_H
  
  #include <vector>
  #include <set>
  #include <limits>
  #include <algorithm>
  
  #include <OpenMS/CONCEPT/ProgressLogger.h>
  #include <OpenMS/DATASTRUCTURES/DistanceMatrix.h>
  #include <OpenMS/COMPARISON/CLUSTERING/ClusterFunctor.h>
  
  namespace OpenMS
  {
    /**
        @brief SingleLinkage ClusterMethod
  
        The details of the method can be found in:
        SLINK: An optimally efficient algorithm for the single-link cluster method, The Computer Journal 1973 16(1):30-34; doi:10.1093/comjnl/16.1.30
        @see ClusterFunctor() base class.
  
        @ingroup SpectraClustering
    */
    class OPENMS_DLLAPI SingleLinkage :
      public ClusterFunctor, public ProgressLogger
    {
  public:
  
      /// default constructor
      SingleLinkage();
  
      /// copy constructor
      SingleLinkage(const SingleLinkage & source);
  
      /// destructor
      virtual ~SingleLinkage();
  
      /// assignment operator
      SingleLinkage & operator=(const SingleLinkage & source);
  
      /**
          @brief clusters the indices according to their respective element distances
  
      @param original_distance DistanceMatrix<float> containing the distances of the elements to be clustered
      @param cluster_tree vector< BinaryTreeNode >, represents the clustering, each node contains the next two clusters merged and their distance, strict order is kept: left_child < right_child
      @param threshold float value to meet Base class interface, will not be used because algorithm used is considerably fast and does not work by growing distances
      @throw ClusterFunctor::InsufficientInput thrown if input is <2
          The clustering method is single linkage, where the updated distances after merging two clusters are each the minimal distance between the elements of their clusters.
      @see ClusterFunctor , BinaryTreeNode
      */
      void operator()(DistanceMatrix<float> & original_distance, std::vector<BinaryTreeNode> & cluster_tree, const float threshold = 1) const;
  
      /// creates a new instance of a SingleLinkage object
      static ClusterFunctor * create();
  
      /// get the identifier for this object
      static const String getProductName();
    };
  
  
  
  }
  #endif //OPENMS_COMPARISON_CLUSTERING_SINGLELINKAGE_H
  