text: // --------------------------------------------------------------------------
  //                   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.
  //
  // --------------------------------------------------------------------------
  // $Maintainer: Timo Sachsenberg $
  // $Authors: Alexandra Zerck $
  // --------------------------------------------------------------------------
  //
  
  #pragma once
  
  #include <OpenMS/METADATA/PeptideIdentification.h>
  #include <OpenMS/DATASTRUCTURES/LPWrapper.h>
  
  namespace OpenMS
  {
  
    /**
         @brief This class implements protein inference for the precursor ion selection strategies.
  
  
  
  
  
    */
    class OPENMS_DLLAPI PSProteinInference
    {
  public:
  
      PSProteinInference();
  
      virtual ~PSProteinInference();
  
  
      Size findMinimalProteinList(const std::vector<PeptideIdentification> & peptide_ids);
  
      void calculateProteinProbabilities(const std::vector<PeptideIdentification> & ids);
  
  //     double getProteinProbability(const String& acc,const std::vector<String>& accessions, const std::vector<double>& probabilities);
  
      double getProteinProbability(const String & acc);
  
      bool isProteinInMinimalList(const String & acc);
      Int getNumberOfProtIds(double protein_id_threshold);
      Int getNumberOfProtIdsPeptideRule(Int min_peptides, std::map<String, std::set<String> > & prot_id_counter);
  
      void setSolver(LPWrapper::SOLVER solver)
      {
        solver_ = solver;
      }
  
      LPWrapper::SOLVER getSolver()
      {
        return solver_;
      }
  
  private:
      std::vector<String> minimal_protein_list_accessions_;
      std::vector<String> accessions_;
      std::vector<double> probabilities_;
      LPWrapper::SOLVER solver_;
    };
  
  }
  
  
  
  