text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry               
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2016.
  // 
  // 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: Hendrik Weisser $
  // $Authors: Hendrik Weisser $
  // --------------------------------------------------------------------------
  
  #include <OpenMS/CONCEPT/ClassTest.h>
  #include <OpenMS/test_config.h>
  
  ///////////////////////////
  
  #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SeedListGenerator.h>
  #include <OpenMS/FORMAT/ConsensusXMLFile.h>
  #include <OpenMS/FORMAT/MzMLFile.h>
  
  
  using namespace OpenMS;
  using namespace std;
  
  ///////////////////////////
  
  START_TEST(SeedListGenerator, "$Id$")
  
  /////////////////////////////////////////////////////////////
  
  SeedListGenerator* slg_ptr = 0;
  SeedListGenerator* slg_nullPointer = 0;
  
  START_SECTION((SeedListGenerator()))
  {
  	slg_ptr = new SeedListGenerator();
    TEST_NOT_EQUAL(slg_ptr, slg_nullPointer);
  }
  END_SECTION
  
  
  START_SECTION(([EXTRA] ~SeedListGenerator()))
  {
  	delete slg_ptr;
  }
  END_SECTION
  
  
  START_SECTION((void generateSeedList(const MSExperiment<>& experiment, SeedList& seeds)))
  {
  	MSExperiment<> experiment;
  	String path = OPENMS_GET_TEST_DATA_PATH("PepXMLFile_test.mzML");
  	MzMLFile().load(path, experiment);
  	SeedListGenerator::SeedList seeds;
  	SeedListGenerator().generateSeedList(experiment, seeds);
  	TEST_EQUAL(seeds.size(), 9);
  	TEST_EQUAL(seeds[0], DPosition<2>(0.5927, 538.605));
  	TEST_EQUAL(seeds[1], DPosition<2>(0.5927, 637.885));
  	TEST_EQUAL(seeds[2], DPosition<2>(0.5927, 678.384));
  	// ...
  	TEST_EQUAL(seeds[8], DPosition<2>(3.7572, 512.784));
  }
  END_SECTION
  
  
  START_SECTION((void generateSeedList(vector<PeptideIdentification>& peptides, SeedList& seeds, bool use_peptide_mass = false)))
  {
  	vector<PeptideIdentification> peptides(3);
  	peptides[0].setRT(1.1);
  	peptides[0].setMZ(111.111);
  	peptides[1].setRT(2.2);
  	peptides[1].setMZ(222.222);
  	peptides[2].setRT(3.3);
  	peptides[2].setMZ(333.333);
  	SeedListGenerator::SeedList seeds;
  	SeedListGenerator().generateSeedList(peptides, seeds);
  	TEST_EQUAL(seeds.size(), 3);
  	TEST_EQUAL(seeds[0], DPosition<2>(1.1, 111.111));
  	TEST_EQUAL(seeds[1], DPosition<2>(2.2, 222.222));
  	TEST_EQUAL(seeds[2], DPosition<2>(3.3, 333.333));
  	PeptideHit hit;
  	hit.setSequence(AASequence::fromString("TEST"));
  	hit.setCharge(2);
  	peptides[0].insertHit(hit);
  	peptides.resize(1);
  	SeedListGenerator().generateSeedList(peptides, seeds, true);
  	TEST_EQUAL(seeds.size(), 1);
  	TEST_REAL_SIMILAR(seeds[0][1], 219.09755);
  }
  END_SECTION
  
  
  START_SECTION((void generateSeedLists(const ConsensusMap& consensus, Map<UInt64, SeedList>& seed_lists)))
  {
  	ConsensusMap consensus;
  	String path = OPENMS_GET_TEST_DATA_PATH("ConsensusXMLFile_1.consensusXML");
  	ConsensusXMLFile().load(path, consensus);
  	Map<UInt64, SeedListGenerator::SeedList> seed_lists;
  	SeedListGenerator().generateSeedLists(consensus, seed_lists);
  	TEST_EQUAL(seed_lists.size(), 2);
  	TEST_EQUAL(seed_lists[0].size(), 0);
  	TEST_EQUAL(seed_lists[1].size(), 2);
  	TEST_EQUAL(seed_lists[1][0], DPosition<2>(1273.27, 904.47));
  	TEST_EQUAL(seed_lists[1][1], DPosition<2>(1184.46, 953.368));
  }
  END_SECTION
  
  
  START_SECTION((void convertSeedList(const SeedList& seeds, FeatureMap& features)))
  {
  	SeedListGenerator::SeedList seeds(3);
  	seeds[0] = DPosition<2>(1.1, 111.111);
  	seeds[1] = DPosition<2>(2.2, 222.222);
  	seeds[2] = DPosition<2>(3.3, 333.333);
  	FeatureMap features;
  	SeedListGenerator().convertSeedList(seeds, features);
  	TEST_EQUAL(features.size(), 3);
  	TEST_EQUAL(features[0].getRT(), 1.1);
  	TEST_EQUAL(features[0].getMZ(), 111.111);
  	TEST_EQUAL(features[1].getRT(), 2.2);
  	TEST_EQUAL(features[1].getMZ(), 222.222);
  	TEST_EQUAL(features[2].getRT(), 3.3);
  	TEST_EQUAL(features[2].getMZ(), 333.333);
  }
  END_SECTION
  
  
  START_SECTION((void convertSeedList(const FeatureMap& features, SeedList& seeds)))
  {
  	FeatureMap features;
  	features.resize(3);
  	features[0].setRT(1.1);
  	features[0].setMZ(111.111);
  	features[1].setRT(2.2);
  	features[1].setMZ(222.222);
  	features[2].setRT(3.3);
  	features[2].setMZ(333.333);
  	SeedListGenerator::SeedList seeds;
  	SeedListGenerator().convertSeedList(features, seeds);
  	TEST_EQUAL(seeds.size(), 3);
  	TEST_EQUAL(seeds[0], DPosition<2>(1.1, 111.111));
  	TEST_EQUAL(seeds[1], DPosition<2>(2.2, 222.222));
  	TEST_EQUAL(seeds[2], DPosition<2>(3.3, 333.333));
  }
  END_SECTION
  
  
  END_TEST
  