/usr/include/OpenMS/COMPARISON/CLUSTERING/SingleLinkage.h is in libopenms-dev 1.11.1-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 | // --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// 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<Real> 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 Real value to meet Baseclass 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<Real> & original_distance, std::vector<BinaryTreeNode> & cluster_tree, const Real threshold = 1) const;
/// creates a new instance of a SingleLinkage object
static ClusterFunctor * create()
{
return new SingleLinkage();
}
/// get the identifier for this object
static const String getProductName()
{
return "SingleLinkage";
}
};
}
#endif //OPENMS_COMPARISON_CLUSTERING_SINGLELINKAGE_H
|