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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// 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/CONCEPT/Types.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmUnlabeled.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
using namespace OpenMS;
using namespace std;
int main(int argc, const char** argv)
{
if (argc < 2) return 1;
// the path to the data should be given on the command line
String tutorial_data_path(argv[1]);
vector<FeatureMap > maps;
maps.resize(2);
FeatureXMLFile feature_file;
feature_file.load(tutorial_data_path + "/data/Tutorial_Unlabeled_1.featureXML", maps[0]);
feature_file.load(tutorial_data_path + "/data/Tutorial_Unlabeled_2.featureXML", maps[1]);
ConsensusMap out;
out.getColumnHeaders()[0].filename = "/data/Tutorial_Unlabeled_1.mzML";
out.getColumnHeaders()[0].size = maps[0].size();
out.getColumnHeaders()[1].filename = "/data/Tutorial_Unlabeled_2.mzML";
out.getColumnHeaders()[1].size = maps[1].size();
FeatureGroupingAlgorithmUnlabeled algorithm;
// ... set parameters
algorithm.group(maps, out);
ConsensusXMLFile consensus_file;
consensus_file.store("Tutorial_Unlabeled.consensusXML", out);
return 0;
} //end of main
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