// --------------------------------------------------------------------------
//                   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
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// 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: Timo Sachsenberg $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>

namespace OpenMS
{
  class AASequence;
  class DigestionEnzymeProtein;

  /**
     @brief Methods to generate isobaric decoy sequences for DDA target-decoy searches.
  */
  class OPENMS_DLLAPI DecoyGenerator
  {
    public:
      // initializes random generator
      DecoyGenerator();

      // destructor
      ~DecoyGenerator() = default;

      // random seed for shuffling
      void setSeed(UInt64 seed);

      /* 
         @brief reverses the protein sequence. 
         note: modifications are discarded
      */
      AASequence reverseProtein(const AASequence& protein) const;
    
      /* 
          @brief reverses the protein's peptide sequences between enzymatic cutting positions. 
          note: modifications are discarded
      */
      AASequence reversePeptides(const AASequence& protein, const String& protease) const;

      /* 
          @brief shuffle the protein's peptide sequences between enzymatic cutting positions.
          each peptide is shuffled @param max_attempts times to minimize sequence identity.
          note: modifications are discarded 
      */
      AASequence shufflePeptides(
            const AASequence& aas,
            const String& protease,
            const int max_attempts = 100
            );
    
    private:
      // sequence identity by matching AAs
      static double SequenceIdentity_(const String& decoy, const String& target);

      // portable shuffle
      Math::RandomShuffler shuffler_;
  };
}

