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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/TRANSFORMATIONS/RAW2PEAK/PeakPickerCWT.h>
#include <OpenMS/FORMAT/MzMLFile.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]);
PeakMap exp_raw;
PeakMap exp_picked;
MzMLFile mzml_file;
mzml_file.load(tutorial_data_path + "/data/Tutorial_PeakPickerCWT.mzML", exp_raw);
PeakPickerCWT pp;
Param param;
param.setValue("peak_width", 0.1);
pp.setParameters(param);
pp.pickExperiment(exp_raw, exp_picked);
exp_picked.updateRanges();
cout << "\nMinimal fwhm of a mass spectrometric peak: " << (double)param.getValue("peak_width")
<< "\n\nNumber of picked peaks " << exp_picked.getSize() << std::endl;
return 0;
} //end of main
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