// --------------------------------------------------------------------------
//                   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: Andreas Bertsch $
// --------------------------------------------------------------------------


#pragma once

// OpenMS includes
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/COMPARISON/SPECTRA/ZhangSimilarityScore.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecomposition.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecompositionAlgorithm.h>
#include <OpenMS/ANALYSIS/DENOVO/CompNovoIonScoringBase.h>

// stl includes
#include <vector>
#include <map>

namespace OpenMS
{
  /**
    @brief  run with CompNovoIdentificationBase

      @ingroup Analysis_ID
  */
  class OPENMS_DLLAPI CompNovoIdentificationBase :
    public DefaultParamHandler
  {

public:

    /** @name constructors and destructors
     */
    //@{
    /// default constructor
    CompNovoIdentificationBase();

    /// copy constructor
    CompNovoIdentificationBase(const CompNovoIdentificationBase & source);

    /// destructor
    ~CompNovoIdentificationBase() override;
    //@}

    /// assignment operator
    CompNovoIdentificationBase & operator=(const CompNovoIdentificationBase & source);

    /** @name Accessors
     */
    //@{
    /// performs an ProteinIdentification run on a PeakMap
    virtual void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp) = 0;
    //@}

    typedef CompNovoIonScoringBase::IonScore IonScore;

protected:

    /// update members method from DefaultParamHandler to update the members
    void updateMembers_() override;

    /// filters the permutations
    void filterPermuts_(std::set<String> & permut) const;

    /// selects pivot ion of the given range using the scores given in CID_nodes
    void selectPivotIons_(std::vector<Size> & pivots, Size left, Size right, std::map<double, IonScore> & CID_nodes, const PeakSpectrum & CID_orig_spec, double precursor_weight, bool full_range = false);

    /// filters the decomps by the amino acid frequencies
    void filterDecomps_(std::vector<MassDecomposition> & decomps);

    /// produces mass decompositions using the given mass
    void getDecompositions_(std::vector<MassDecomposition> & decomps, double mass, bool no_caching = false);

    /// permutes the String s adds the prefix and stores the results in permutations
    static void permute_(const String& prefix, String s, std::set<String> & permutations);

    Size countMissedCleavagesTryptic_(const String & peptide) const;

    /// fills the spec with b and y ions, no other ion types or doubly charged variants are used
    void getCIDSpectrumLight_(PeakSpectrum & spec, const String & sequence, double prefix, double suffix);

    /// fills the spectrum with b,y ions, multiple charged variants; if prefix and suffix weights are given, the sequence is treated as tag
    void getCIDSpectrum_(PeakSpectrum & spec, const String & sequence, Size charge, double prefix = 0.0, double suffix = 0.0);

    /// fills the spectrum with c and z type ions
    void getETDSpectrum_(PeakSpectrum & spec, const String &sequence, Size /* charge */, double prefix = 0.0, double suffix = 0.0);

    /// initializes the score distribution pre-calculated for the use in spectrum generation
    void initIsotopeDistributions_();

    /// keep for each window of size windowsize in the m/z range of the spectrum exactly no_peaks
    void windowMower_(PeakSpectrum & spec, double windowsize, Size no_peaks);

    /// compares two spectra
    double compareSpectra_(const PeakSpectrum & s1, const PeakSpectrum & s2) const;

    /// returns a modified AASequence from a given internal representation
    AASequence getModifiedAASequence_(const String & sequence);

    /// returns the internal representation of a given AASequence
    String getModifiedStringFromAASequence_(const AASequence & sequence);

    /// mapping for the internal representation character to the actual residue
    std::map<char, const Residue *> name_to_residue_;

    /// mapping of the actual residue to the internal representing character
    std::map<const Residue *, char> residue_to_name_;

    /// masses of the amino acids
    std::map<char, double> aa_to_weight_;

    MassDecompositionAlgorithm mass_decomp_algorithm_;

    double min_aa_weight_{};

    ZhangSimilarityScore zhang_;

    std::map<Size, std::map<Size, std::set<String> > > subspec_to_sequences_;

    Size max_number_aa_per_decomp_;

    bool tryptic_only_;

    double fragment_mass_tolerance_;

    Size max_number_pivot_;

    double decomp_weights_precision_;

    double max_mz_;

    double min_mz_;

    double max_decomp_weight_;

    Size max_subscore_number_;

    Size max_isotope_;

    std::map<double, std::vector<MassDecomposition> > decomp_cache_;

    std::map<String, std::set<String> > permute_cache_;

  private:
    ///
    std::map<Size, std::vector<double> > isotope_distributions_;

public:

    /** @brief Simple class to store permutations and a score

            This class is used to store the generated permutations
            and a score to them
    */
    class Permut
    {
private:

      Permut() :
        score_(0)
      {
      }

public:

      Permut(const std::set<String>::const_iterator & permut, double s) :
        permut_(permut),
        score_(s)
      {
      }

      Permut(const Permut & rhs) = default;
      virtual ~Permut() = default;

      Permut & operator=(const Permut & rhs)
      {
        if (&rhs != this)
        {
          permut_ = rhs.permut_;
          score_ = rhs.score_;
        }
        return *this;
      }

      const std::set<String>::const_iterator & getPermut() const
      {
        return permut_;
      }

      void setPermut(const std::set<String>::const_iterator & it)
      {
        permut_ = it;
      }

      double getScore() const
      {
        return score_;
      }

      void setScore(double score)
      {
        score_ = score;
      }

protected:

      std::set<String>::const_iterator permut_;
      double score_;
    };

  };

  namespace Internal
  {
    bool PermutScoreComparator(const CompNovoIdentificationBase::Permut & p1, const CompNovoIdentificationBase::Permut & p2);
  }
}

