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 $
  // $Authors: Stephan Aiche$
  // --------------------------------------------------------------------------
  
  #pragma once
  
  #include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
  
  namespace OpenMS
  {
  
    /**
      @brief Simulate ICPL experiments
  
      Add modified features to MS1 scans. Highly Experimental.
  
      @htmlinclude OpenMS_ICPLLabeler.parameters
    */
    class OPENMS_DLLAPI ICPLLabeler :
      public BaseLabeler
    {
  public:
  
      /// default constructor
      ICPLLabeler();
  
      /// destructor
      ~ICPLLabeler() override;
  
      /// create new object (needed by Factory)
      static BaseLabeler* create()
      {
        return new ICPLLabeler();
      }
  
      /// name of the model (needed by Factory)
      static const String getProductName()
      {
        return "ICPL";
      }
  
      // redeclaration of virtual methods
      void preCheck(Param& param) const override;
  
      void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
  
      void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
  
      void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
  
      void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
  
      void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
  
      void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
  
      void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
  
  protected:
      void addModificationToPeptideHit_(Feature& feature, const String& modification) const;
  
      void addLabelToProteinHits_(SimTypes::FeatureMapSim& features, const String& label) const;
  
      Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, Map<String, Feature>& unlabeled_features_index) const;
  
      String light_channel_label_;
      String medium_channel_label_;
      String heavy_channel_label_;
  
      void updateMembers_() override;
  
      String getUnmodifiedAASequence_(const Feature& feature, const String& label) const;
  
  private:
      /// Map ID for the light/unlabeled channel
      static const int LIGHT_FEATURE_MAPID_;
      /// Map ID for the medium labeled channel
      static const int MEDIUM_FEATURE_MAPID_;
      /// Map ID for the heavy labeled channel
      static const int HEAVY_FEATURE_MAPID_;
    };
  } // namespace OpenMS
  
  