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CompleteLinkage.h
Go to the documentation of this file.
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// --------------------------------------------------------------------------
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// OpenMS -- Open-Source Mass Spectrometry
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// --------------------------------------------------------------------------
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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//
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// This software is released under a three-clause BSD license:
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above copyright
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// notice, this list of conditions and the following disclaimer in the
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// documentation and/or other materials provided with the distribution.
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// * Neither the name of any author or any participating institution
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// may be used to endorse or promote products derived from this software
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// without specific prior written permission.
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// For a full list of authors, refer to the file AUTHORS.
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// --------------------------------------------------------------------------
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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// --------------------------------------------------------------------------
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// $Maintainer: Mathias Walzer $
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// $Authors: $
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// --------------------------------------------------------------------------
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//
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#pragma once
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#include <vector>
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#include <set>
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#include <cmath>
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#include <
OpenMS/CONCEPT/ProgressLogger.h
>
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#include <
OpenMS/DATASTRUCTURES/DistanceMatrix.h
>
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#include <
OpenMS/COMPARISON/CLUSTERING/ClusterFunctor.h
>
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namespace
OpenMS
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{
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class
OPENMS_DLLAPI
CompleteLinkage
:
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public
ClusterFunctor
,
public
ProgressLogger
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{
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public
:
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CompleteLinkage
();
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CompleteLinkage
(
const
CompleteLinkage
& source);
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~
CompleteLinkage
()
override
;
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CompleteLinkage
& operator=(
const
CompleteLinkage
& source);
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void
operator()(
DistanceMatrix<float>
& original_distance, std::vector<BinaryTreeNode> & cluster_tree,
const
float
threshold = 1)
const override
;
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static
ClusterFunctor
* create();
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static
const
String
getProductName();
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};
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}
ClusterFunctor.h
DistanceMatrix.h
OpenMS::CompleteLinkage
CompleteLinkage ClusterMethod.
Definition:
CompleteLinkage.h:57
OpenMS::String
A more convenient string class.
Definition:
String.h:58
OpenMS
Main OpenMS namespace.
Definition:
FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition:
ProgressLogger.h:54
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
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