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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/FILTERING/CALIBRATION/TOFCalibration.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <iostream>
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]);
TOFCalibration ec;
PeakMap exp_raw, calib_exp;
MzMLFile mzml_file;
mzml_file.load(tutorial_data_path + "/data/Tutorial_TOFCalibration_peak.mzML", calib_exp);
mzml_file.load(tutorial_data_path + "/data/Tutorial_TOFCalibration_raw.mzML", exp_raw);
vector<double> ref_masses;
TextFile ref_file;
ref_file.load(tutorial_data_path + "/data/Tutorial_TOFCalibration_masses.txt", true);
for (TextFile::ConstIterator iter = ref_file.begin(); iter != ref_file.end(); ++iter)
{
ref_masses.push_back(String(iter->c_str()).toDouble());
}
std::vector<double> ml1;
ml1.push_back(418327.924993827);
std::vector<double> ml2;
ml2.push_back(253.645187196031);
std::vector<double> ml3;
ml3.push_back(-0.0414243465397252);
ec.setML1s(ml1);
ec.setML2s(ml2);
ec.setML3s(ml3);
Param param;
param.setValue("PeakPicker:peak_width", 0.1);
ec.setParameters(param);
ec.pickAndCalibrate(calib_exp, exp_raw, ref_masses);
return 0;
} //end of main
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