// --------------------------------------------------------------------------
//                   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:
//  * 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.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------

#pragma once

#include <vector>
#include <utility>
#include <map>
#include <utility>
#include <boost/shared_ptr.hpp>

#include <boost/random/mersenne_twister.hpp>

#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/Peak2D.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>

namespace OpenMS
{

  namespace SimTypes
  {
    /// Coordinate type in mz and rt dimension
    typedef Peak2D::CoordinateType SimCoordinateType;

    /// Abundance of proteins/peptides
    typedef Peak2D::IntensityType SimIntensityType;

    /// Charge of a peptide
    typedef Feature::ChargeType SimChargeType;

    /// Raw data point
    typedef Peak1D SimPointType;

    /**
      @brief Plain data object holding sequence and abundance information on a single protein.
    */
    struct SimProtein
    {
      /// FASTAEntry holding the sequence information
      FASTAFile::FASTAEntry entry;
      /// MetaInfoInterface holding the abundance information
      MetaInfoInterface meta;

      /**
        @brief c'tor
      */
      SimProtein(FASTAFile::FASTAEntry& e, MetaInfoInterface& m) :
       entry(e),
       meta(m)
      {}
    };

    /// Container for FASTAEntry & abundance information
    typedef std::vector<SimProtein> SampleProteins;

    /// Container for multiple channels of SampleProteins
    typedef std::vector<SampleProteins> SampleChannels;

    /// Sim FeatureMap
    typedef FeatureMap FeatureMapSim;

    /// Sim FeatureMap Vector
    typedef std::vector<FeatureMapSim> FeatureMapSimVector;

    /// Sim MSExperiment type
    typedef PeakMap MSSimExperiment;

    /**
      @brief Wrapper class for random number generators used by the simulation classes

      The random numbers are separated two sources of randomness:

      <ul>
        <li><em>technical random numbers</em> which should represent technical
            sources of variability like instrument noise and </li>
        <li><em>biological random numbers</em> which should represent biological
            sources of variability (e.g. between two samples of the same composition)</li>
      </ul>

      @ingroup Simulation
    */
    class SimRandomNumberGenerator
    {
public:

      boost::random::mt19937_64& getBiologicalRng()
      {
        return biological_rng_;
      }

      boost::random::mt19937_64& getTechnicalRng()
      {
        return technical_rng_;
      }

      void setBiologicalRngSeed(unsigned long int seed)
      {
        biological_rng_.seed(seed);
      }

      void setTechnicalRngSeed(unsigned long int seed)
      {
        technical_rng_.seed(seed);
      }

      /// Initialize the RNGs
      void initialize(bool biological_random, bool technical_random)
      {
        // use 0 as default seed to get reproducible experiments
        if (biological_random)
        {
          biological_rng_ = boost::random::mt19937_64(std::time(nullptr));
        }
        else
        {
          biological_rng_ = boost::random::mt19937_64(0);
        }

        if (technical_random)
        {
          technical_rng_ = boost::random::mt19937_64(std::time(nullptr));
        }
        else
        {
          technical_rng_ = boost::random::mt19937_64(0);
        }
      }

private:
      /// random number generator for biological variability
      boost::random::mt19937_64 biological_rng_;
      /// random number generator for technical variability
      boost::random::mt19937_64 technical_rng_;

    };

    //Sim Shared Pointer type
    typedef boost::shared_ptr<SimRandomNumberGenerator> MutableSimRandomNumberGeneratorPtr;

  }

}

