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/FORMAT/MzMLFile.h>
  #include <OpenMS/KERNEL/MSExperiment.h>
  #include <OpenMS/KERNEL/ConsensusMap.h>
  #include <OpenMS/FORMAT/ParamXMLFile.h>
  
  #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderMultiplexAlgorithm.h>
  
  using namespace OpenMS;
  using namespace std;
  
  START_TEST(FeatureFinderMultiplexAlgorithm, "$Id$")
  
  FeatureFinderMultiplexAlgorithm* ptr = 0;
  FeatureFinderMultiplexAlgorithm* null_ptr = 0;
  START_SECTION(FeatureFinderMultiplexAlgorithm())
  {
    ptr = new FeatureFinderMultiplexAlgorithm();
    TEST_NOT_EQUAL(ptr, null_ptr);
  }
  END_SECTION
  
  START_SECTION(~FeatureFinderMultiplexAlgorithm())
  {
    delete ptr;
  }
  END_SECTION
  
  START_SECTION((virtual void run()))
  {
    MzMLFile mzml_file;
    MSExperiment exp;
    ConsensusMap result;
    
    mzml_file.getOptions().addMSLevel(1);
    mzml_file.load(OPENMS_GET_TEST_DATA_PATH("FeatureFinderMultiplex_1_input.mzML"), exp);
    exp.updateRanges(1);
    
    Param param;
    ParamXMLFile paramFile;
    paramFile.load(OPENMS_GET_TEST_DATA_PATH("FeatureFinderMultiplex_1_parameters.ini"), param);
    param = param.copy("FeatureFinderMultiplex:1:",true);
    param.remove("in");
    param.remove("out");
    param.remove("out_multiplets");
    param.remove("log");
    param.remove("debug");
    param.remove("threads");
    param.remove("no_progress");
    param.remove("force");
    param.remove("test");
    
    FeatureFinderMultiplexAlgorithm algorithm;
    algorithm.setParameters(param);
    algorithm.run(exp, true);
    result = algorithm.getConsensusMap();
    
    TEST_EQUAL(result.size(), 2);
    
    double L = result[0].getFeatures().begin()->getIntensity();
    double H = (++(result[0].getFeatures().begin()))->getIntensity();
  
    // Check that the HEAVY:LIGHT ratio is close to the expected 4:1 ratio
    TOLERANCE_ABSOLUTE(0.2);
    TEST_REAL_SIMILAR(H/L, 4.0);
  }
  END_SECTION
  
  END_TEST
  