text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry               
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2021.
  // 
  // 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.
  // 
  // --------------------------------------------------------------------------
  // $Maintainer: Timo Sachsenberg$
  // $Authors: Alexandra Zerck$
  // --------------------------------------------------------------------------
  
  #include <OpenMS/CONCEPT/ClassTest.h>
  #include <OpenMS/test_config.h>
  
  ///////////////////////////
  #include <OpenMS/ANALYSIS/TARGETED/PSProteinInference.h>
  #include <OpenMS/METADATA/ProteinIdentification.h>
  #include <OpenMS/FORMAT/IdXMLFile.h>
  ///////////////////////////
  
  using namespace OpenMS;
  using namespace std;
  
  START_TEST(PSProteinInference, "$Id$")
  
  /////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////
  
  PSProteinInference* ptr = nullptr;
  PSProteinInference* null_ptr = nullptr;
  START_SECTION(PSProteinInference())
  {
  	ptr = new PSProteinInference();
  	TEST_NOT_EQUAL(ptr, null_ptr)
  }
  END_SECTION
  
  START_SECTION((virtual ~PSProteinInference()))
  {
  	delete ptr;
  }
  END_SECTION
  
  vector<PeptideIdentification> pep_ids;
  vector<ProteinIdentification> prot_ids;
  String document_id;
  IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("PSProteinInference_test_input.iDXML"),prot_ids,pep_ids,document_id);
  ptr = new PSProteinInference();
  START_SECTION((Size findMinimalProteinList(const std::vector< PeptideIdentification > &peptide_ids)))
  {
    Size num = ptr->findMinimalProteinList(pep_ids);
    TEST_EQUAL(num,3)
  }
  END_SECTION
  
  START_SECTION((void calculateProteinProbabilities(const std::vector< PeptideIdentification > &ids)))
  {
    ptr->calculateProteinProbabilities(pep_ids);
    TEST_REAL_SIMILAR(ptr->getProteinProbability("A2RUR9"),1.)
    TEST_REAL_SIMILAR(ptr->getProteinProbability("O00762"),0.132644)
    TEST_REAL_SIMILAR(ptr->getProteinProbability("O14795"),0.99999)
    TEST_REAL_SIMILAR(ptr->getProteinProbability("O15085"),1.)
  }
  END_SECTION
  
  START_SECTION((double getProteinProbability(const String &acc)))
  {
    TEST_REAL_SIMILAR(ptr->getProteinProbability("A2RUR9"),1.)
  }
  END_SECTION
  
  START_SECTION((bool isProteinInMinimalList(const String &acc)))
  {
    TEST_EQUAL(ptr->isProteinInMinimalList("A2RUR9"),true)
    TEST_EQUAL(ptr->isProteinInMinimalList("O00762"),true)
    TEST_EQUAL(ptr->isProteinInMinimalList("O14795"),false)
    TEST_EQUAL(ptr->isProteinInMinimalList("O15085"),true)
  }
  END_SECTION
  
  START_SECTION((Int getNumberOfProtIds(double protein_id_threshold)))
  {
    TEST_EQUAL(ptr->getNumberOfProtIds(.95),2)
  }
  END_SECTION
  
  START_SECTION((Int getNumberOfProtIdsPeptideRule(Int min_peptides, std::map< String, std::set< String > > &prot_id_counter)))
  {
    std::map< String, std::set< String > > prot_id_counter;
    set< String > peps;
    peps.insert("PEPTIDEONE");
    prot_id_counter.insert(make_pair("A2RUR9",peps));
    peps.insert("PEPTIDETWO");
    prot_id_counter.insert(make_pair("O00762",peps));
    peps.insert("PEPTIDETHREE");
    prot_id_counter.insert(make_pair("O15085",peps));
    TEST_EQUAL(ptr->getNumberOfProtIdsPeptideRule(3,prot_id_counter),1)
  }
  END_SECTION
  
  START_SECTION((LPWrapper::SOLVER getSolver()))
  {
  #if COINOR_SOLVER == 1
    TEST_EQUAL(ptr->getSolver(),LPWrapper::SOLVER_GLPK)
  #else
    TEST_EQUAL(ptr->getSolver(), LPWrapper::SOLVER_GLPK)
  #endif
  }
  END_SECTION
  
  delete ptr;
  
  /////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////
  END_TEST
  
  
  
  