OpenMS  3.0.0
SingleLinkage.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2022.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Mathias Walzer $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35 #pragma once
36 
37 #include <vector>
38 #include <set>
39 
43 
44 namespace OpenMS
45 {
55  class OPENMS_DLLAPI SingleLinkage :
56  public ClusterFunctor, public ProgressLogger
57  {
58 public:
59 
61  SingleLinkage();
62 
64  SingleLinkage(const SingleLinkage & source);
65 
67  ~SingleLinkage() override;
68 
70  SingleLinkage & operator=(const SingleLinkage & source);
71 
82  void operator()(DistanceMatrix<float> & original_distance, std::vector<BinaryTreeNode> & cluster_tree, const float threshold = 1) const override;
83 
85  static ClusterFunctor * create();
86 
88  static const String getProductName();
89  };
90 
91 
92 
93 }
ClusterFunctor.h
DistanceMatrix.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::DistanceMatrix
A two-dimensional distance matrix, similar to OpenMS::Matrix.
Definition: DistanceMatrix.h:67
OpenMS::ClusterFunctor
Base class for cluster functors.
Definition: ClusterFunctor.h:53
OpenMS::SingleLinkage
SingleLinkage ClusterMethod.
Definition: SingleLinkage.h:55