// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
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//    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;
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche$
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>

namespace OpenMS
{

  /**
    @brief Simulate O-18 experiments

    Add modified features to MS1 scans.

        @htmlinclude OpenMS_O18Labeler.parameters
  */
  class OPENMS_DLLAPI O18Labeler :
    public BaseLabeler
  {
public:

    /// default constructor
    O18Labeler();

    /// destructor
    ~O18Labeler() override;

    /// create new object (needed by Factory)
    static BaseLabeler* create()
    {
      return new O18Labeler();
    }

    /// name of the model (needed by Factory)
    static const String getProductName()
    {
      return "o18";
    }

    // 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;

    Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;

private:
    /// Map ID for the light/unlabeled channel
    static const int LIGHT_CHANNEL_ID_;
    /// Map ID for the medium/mono-labeled channel
    static const int MEDIUM_CHANNEL_ID_;
    /// Map ID for the heavy/bi-labeled channel
    static const int HEAVY_CHANNEL_ID_;
  };
} // namespace OpenMS

