// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// 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;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------

#ifndef OPENMS_SIMULATION_MSSIM_H
#define OPENMS_SIMULATION_MSSIM_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/SIMULATION/SimTypes.h>
#include <OpenMS/KERNEL/ConsensusMap.h>

#include <OpenMS/CONCEPT/ProgressLogger.h>

namespace OpenMS
{

  class BaseLabeler;

  /**
   @brief Central class for simulation of mass spectrometry experiments

   This implementation is an extended and rewritten version of the concepts and ideas presented in:<br>
   <p>
    Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gropl, Oliver Kohlbacher, and Knut Reinert.<br>
    LC-MSsim - A simulation software for liquid chromatography mass spectrometry data.<br>
    <em>BMC Bioinformatics</em> 9:423, 2008.
   </p>

   @htmlinclude OpenMS_MSSim.parameters

   @see DetectabilitySimulation
   @see DigestSimulation
   @see IonizationSimulation
   @see RawMSSignalSimulation
   @see RTSimulation

   @ingroup Simulation
  */
  class OPENMS_DLLAPI MSSim :
    public DefaultParamHandler,
    public ProgressLogger
  {

public:
    /** @name Constructors and Destructors
      */
    //@{
    /// Default constructor
    MSSim();

    /// Destructor
    virtual ~MSSim();
    //@}

    /**
     @brief General purpose function to simulate a mass spectrometry run

     @param rnd_gen random number generator which will be passed to the different classes
     @param peptides List of peptides and abundances that will be simulated
     */
    void simulate(SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen, SimTypes::SampleChannels& peptides);

    /// Access the simulated experiment
    const SimTypes::MSSimExperiment& getExperiment() const;

    /// Access the simulated features
    const SimTypes::FeatureMapSim& getSimulatedFeatures() const;

    /// Access the charge consensus map of simulated features
    ConsensusMap& getChargeConsensus();

    /// Access the contaminants feature map of simulated features
    const SimTypes::FeatureMapSim& getContaminants() const;

    /// Access the labeling consensus map of simulated features
    ConsensusMap& getLabelingConsensus();

    /// Access the picked (centroided) experiment
    const SimTypes::MSSimExperiment& getPeakMap() const;

    /**
      @brief Access the simulated identifications (proteins and peptides)

      If an MS2 signal has been simulated, identifications are generated based on
      their corresponding MS2 spectra. If MS2 simulation has been disabled,
      peptide IDs are generated from feature annotations. Otherwise, the -out_id
      idXML file would be empty if MS2 simulation is disabled (which is the default).

      @param proteins Will be filled with a single ProteinIdentification holding all ProteinHits.
      @param peptides Will be filled with PeptideIdentifications.
    */
    void getIdentifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;

    /**
      @brief Access the simulated MS2 identifications (proteins and peptides)

      @param proteins Will be filled with a single ProteinIdentification holding all ProteinHits used in the simulated MS2 spectra.
      @param peptides Will be filled with PeptideIdentifications for each simulated MS2 spectra holding all contributing peptides scored by their intensity contribution.
    */
    void getMS2Identifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;

    /**
      @brief Access the simulated identifications (proteins and peptides) from feature annotations

      @param proteins Will be filled with a single ProteinIdentification holding all ProteinHits.
      @param peptides Will be filled with PeptideIdentifications for all simulated features.
    */
    void getFeatureIdentifications(std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides) const;

    /// Returns the default parameters for simulation including the labeling technique with name @p labeling_name
    Param getParameters() const;

protected:
    /// handle global params
    void syncParams_(Param& p, bool to_outer);

    /// Convert a list of peptides with given abundance values into a FeatureMap
    void createFeatureMap_(const SimTypes::SampleProteins& peptides, SimTypes::FeatureMapSim& features, Size map_index);

    /// Synchronize members with param class
    void updateMembers_();

private:
    /// Holds the simulated data
    SimTypes::MSSimExperiment experiment_;

    /// Holds the ground-truth on generated peaks positions and intensities
    SimTypes::MSSimExperiment peak_map_;

    /// Holds the ground-truth on generated features
    SimTypes::FeatureMapSimVector feature_maps_;

    /// Holds consensus ground-truth about the charge associations
    ConsensusMap consensus_map_;

    /// Holds the ground-truth on generated contaminants
    SimTypes::FeatureMapSim contaminants_map_;

    /// Labeling functionality
    BaseLabeler* labeler_;
  };

}

#endif
