text: // --------------------------------------------------------------------------
  //                   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.
  //
  // --------------------------------------------------------------------------
  // $Maintainer: Lars Nilse $
  // $Authors: Lars Nilse $
  // --------------------------------------------------------------------------
  
  #include <OpenMS/CONCEPT/ClassTest.h>
  #include <OpenMS/test_config.h>
  
  #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFiltering.h>
  
  #include <OpenMS/FORMAT/MzMLFile.h>
  
  using namespace OpenMS;
  
  START_TEST(MultiplexFiltering, "$Id$")
  
  // read data
  MSExperiment exp;
  MzMLFile().load(OPENMS_GET_TEST_DATA_PATH("MultiplexFiltering.mzML"), exp);
  exp.updateRanges();
  
  // pick data
  PeakPickerHiRes picker;
  Param param = picker.getParameters();
  param.setValue("ms_levels", ListUtils::create<Int>("1"));
  param.setValue("signal_to_noise", 0.0);
  picker.setParameters(param);
  std::vector<PeakPickerHiRes::PeakBoundary> boundaries;
  std::vector<std::vector<PeakPickerHiRes::PeakBoundary> > boundaries_exp_s;
  std::vector<std::vector<PeakPickerHiRes::PeakBoundary> > boundaries_exp_c;
  MSExperiment exp_picked;
  picker.pickExperiment(exp, exp_picked, boundaries_exp_s, boundaries_exp_c);
  
  // set parameters
  int charge_min = 1;
  int charge_max = 6;
  int isotopes_per_peptide_min = 3;
  int isotopes_per_peptide_max = 6;
  double intensity_cutoff = 10.0;
  double rt_band = 2.0;
  double mz_tolerance = 40;
  bool mz_tolerance_unit = true;    // ppm (true), Da (false)
  double peptide_similarity = 0.8;
  double averagine_similarity = 0.75;
  double averagine_similarity_scaling = 0.75;
  String averagine_type="peptide";
  
  // construct list of peak patterns
  MultiplexDeltaMasses shifts1;
  shifts1.getDeltaMasses().push_back(MultiplexDeltaMasses::DeltaMass(0, "no_label"));
  shifts1.getDeltaMasses().push_back(MultiplexDeltaMasses::DeltaMass(8.0443702794, "Arg8"));
  MultiplexDeltaMasses shifts2;
  shifts2.getDeltaMasses().push_back(MultiplexDeltaMasses::DeltaMass(0, "no_label"));
  MultiplexDeltaMasses::LabelSet label_set;
  label_set.insert("Arg8");
  label_set.insert("Arg8");
  shifts2.getDeltaMasses().push_back(MultiplexDeltaMasses::DeltaMass(2*8.0443702794, label_set));
  std::vector<MultiplexIsotopicPeakPattern> patterns;
  for (int c = charge_max; c >= charge_min; --c)
  {
      MultiplexIsotopicPeakPattern pattern1(c, isotopes_per_peptide_max, shifts1, 0);
      patterns.push_back(pattern1);
      MultiplexIsotopicPeakPattern pattern2(c, isotopes_per_peptide_max, shifts2, 1);
      patterns.push_back(pattern2);
  }
  
  MultiplexFiltering* nullPointer = nullptr;
  MultiplexFiltering* ptr;
  
  START_SECTION(MultiplexFiltering(const MSExperiment& exp_picked, const std::vector<MultiplexIsotopicPeakPattern>& patterns, int isotopes_per_peptide_min, int isotopes_per_peptide_max, double intensity_cutoff, double rt_band, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide"))
    MultiplexFiltering filtering(exp_picked, patterns, isotopes_per_peptide_min, isotopes_per_peptide_max, intensity_cutoff, rt_band, mz_tolerance, mz_tolerance_unit, peptide_similarity, averagine_similarity, averagine_similarity_scaling, averagine_type);
    ptr = new MultiplexFiltering(exp_picked, patterns, isotopes_per_peptide_min, isotopes_per_peptide_max, intensity_cutoff, rt_band, mz_tolerance, mz_tolerance_unit, peptide_similarity, averagine_similarity, averagine_similarity_scaling, averagine_type);
    TEST_NOT_EQUAL(ptr, nullPointer);
    delete ptr;
  END_SECTION
  
  END_TEST
  