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// --------------------------------------------------------------------------
// 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.
//
#include <OpenMS/COMPARISON/CLUSTERING/ClusterAnalyzer.h>
#include <OpenMS/COMPARISON/CLUSTERING/ClusterHierarchical.h>
#include <OpenMS/COMPARISON/CLUSTERING/CompleteLinkage.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <vector>
#include <algorithm>
#include <iostream>
using namespace OpenMS;
using namespace std;
class LowLevelComparator
{
public:
double operator()(const double first, const double second) const
{
double x, y;
x = min(second, first);
y = max(first, second);
if ((y - x) > 1)
{
throw Exception::InvalidRange(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
}
return 1 - (y - x);
}
}; // end of LowLevelComparator
Int main()
{
// data
vector<double> data; // must be filled
srand(333);
Size nr = 12;
data.resize(nr);
for (Size i = 0; i < nr; ++i)
{
data[i] = (double)rand() / RAND_MAX;
}
LowLevelComparator llc;
CompleteLinkage sl;
vector<BinaryTreeNode> tree;
DistanceMatrix<float> dist; // will be filled
ClusterHierarchical ch;
ch.setThreshold(0.15);
// clustering
ch.cluster<double, LowLevelComparator>(data, llc, sl, tree, dist);
ClusterAnalyzer ca;
std::cout << ca.newickTree(tree) << std::endl;
return 0;
} //end of main
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