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.
  //
  // --------------------------------------------------------------------------
  // $Maintainer: Chris Bielow$
  // $Authors: Stephan Aiche, Chris Bielow$
  // --------------------------------------------------------------------------
  
  #pragma once
  
  #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
  #include <OpenMS/SIMULATION/SimTypes.h>
  
  namespace OpenMS
  {
  
    /**
      @brief Simulates protein digestion
  
      Supports all enzymes supported by EnzymaticDigestion.h
      and additionally incorporates abundance values, which
      are distributed evenly among digestion products of each
      protein.
  
      @htmlinclude OpenMS_DigestSimulation.parameters
  
      @ingroup Simulation
    */
    class OPENMS_DLLAPI DigestSimulation :
      public DefaultParamHandler
    {
  
  public:
      /** @name Constructors and Destructors
        */
      //@{
      /// Default constructor
      DigestSimulation();
  
      /// Copy constructor
      DigestSimulation(const DigestSimulation& source);
  
      /// Destructor
      ~DigestSimulation() override;
      //@}
  
      /// Assignment operator
      DigestSimulation& operator=(const DigestSimulation& source);
  
  
      /**
          @brief Digest a set of proteins into peptides
  
          Digest proteins to peptides, with protein abundance distributes equally among
          created sibling peptides (this also applies for peptides with missed cleavages).
          Should a peptide be non-unique the abundances of its instances from proteins are summed up.
  
          @param feature_map Input FeatureMap containing the proteins that should be digested as ProteinIdentification
      **/
      void digest(SimTypes::FeatureMapSim& feature_map);
  
  private:
      /// set defaults
      void setDefaultParams_();
  
    };
  
  }
  
  