MRMAssay.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger $
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#pragma once

#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMIonSeries.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>

#include <boost/random/mersenne_twister.hpp>
#include <boost/random/uniform_int.hpp>
#include <boost/random/variate_generator.hpp>
#include <boost/unordered_map.hpp> // cannot remove this since tests fail otherwise

// #define DEBUG_MRMASSAY

namespace OpenMS
{
  class OPENMS_DLLAPI MRMAssay :
    public ProgressLogger
  {

public:
    MRMAssay(); // empty, no members

    ~MRMAssay() override;

    typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType;
    typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType;
    typedef std::vector<OpenMS::TargetedExperiment::Compound> CompoundVectorType;
    typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType;

    typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > PeptideTransitionMapType;
    typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > CompoundTransitionMapType;

    typedef boost::unordered_map<String, std::set<std::string> > ModifiedSequenceMap; 
    typedef boost::unordered_map<size_t, ModifiedSequenceMap> SequenceMapT; 

    typedef std::vector<std::pair<double, std::string> > FragmentSeqMap; 
    typedef boost::unordered_map<size_t, boost::unordered_map<String, FragmentSeqMap > > IonMapT; 

    typedef std::vector<std::pair<std::string, double> > IonSeries; 
    typedef std::map<String, IonSeries > PeptideMapT; 

    typedef boost::unordered_map<String, TargetedExperiment::Peptide> TargetDecoyMapT; 

    void reannotateTransitions(OpenMS::TargetedExperiment& exp,
                               double precursor_mz_threshold,
                               double product_mz_threshold,
                               const std::vector<String>& fragment_types,
                               const std::vector<size_t>& fragment_charges,
                               bool enable_specific_losses,
                               bool enable_unspecific_losses,
                               int round_decPow = -4);

    void restrictTransitions(OpenMS::TargetedExperiment& exp,
        double lower_mz_limit, double upper_mz_limit,
        const std::vector<std::pair<double, double> >& swathes);

    void detectingTransitions(OpenMS::TargetedExperiment& exp, int min_transitions, int max_transitions);

    void uisTransitions(OpenMS::TargetedExperiment& exp,
                        const std::vector<String>& fragment_types,
                        const std::vector<size_t>& fragment_charges,
                        bool enable_specific_losses,
                        bool enable_unspecific_losses,
                        bool enable_ms2_precursors,
                        double mz_threshold,
                        const std::vector<std::pair<double, double> >& swathes,
                        int round_decPow = -4,
                        size_t max_num_alternative_localizations = 20,
                        int shuffle_seed = -1,
                        bool disable_decoy_transitions = false);

    void filterMinMaxTransitionsCompound(OpenMS::TargetedExperiment& exp, int min_transitions, int max_transitions);

    void filterUnreferencedDecoysCompound(OpenMS::TargetedExperiment &exp);

protected:

    std::vector<std::string> getMatchingPeptidoforms_(const double fragment_ion,
                                                      const FragmentSeqMap& ions,
                                                      const double mz_threshold);

    int getSwath_(const std::vector<std::pair<double, double> >& swathes, const double precursor_mz);

    bool isInSwath_(const std::vector<std::pair<double, double> >& swathes, const double precursor_mz, const double product_mz);

    std::string getRandomSequence_(size_t sequence_size, boost::variate_generator<boost::mt19937&, boost::uniform_int<> > pseudoRNG);

    std::vector<std::vector<size_t> > nchoosekcombinations_(const std::vector<size_t>& n, size_t k);

    std::vector<OpenMS::AASequence> addModificationsSequences_(const std::vector<OpenMS::AASequence>& sequences,
                                                               const std::vector<std::vector<size_t> >& mods_combs,
                                                               const OpenMS::String& modification);

    std::vector<OpenMS::AASequence> generateTheoreticalPeptidoforms_(const OpenMS::AASequence& sequence);

    std::vector<OpenMS::AASequence> generateTheoreticalPeptidoformsDecoy_(const OpenMS::AASequence& sequence, const OpenMS::AASequence& decoy_sequence);

    void generateTargetInSilicoMap_(const OpenMS::TargetedExperiment& exp,
                                    const std::vector<String>& fragment_types,
                                    const std::vector<size_t>& fragment_charges,
                                    bool enable_specific_losses,
                                    bool enable_unspecific_losses,
                                    bool enable_ms2_precursors,
                                    const std::vector<std::pair<double, double> >& swathes,
                                    int round_decPow,
                                    size_t max_num_alternative_localizations,
                                    SequenceMapT& TargetSequenceMap,
                                    IonMapT& TargetIonMap,
                                    PeptideMapT& TargetPeptideMap);

    void generateDecoySequences_(const SequenceMapT& TargetSequenceMap,
                                 boost::unordered_map<String, String>& DecoySequenceMap,
                                 int shuffle_seed);

    void generateDecoyInSilicoMap_(const OpenMS::TargetedExperiment& exp,
                                   const std::vector<String>& fragment_types,
                                   const std::vector<size_t>& fragment_charges,
                                   bool enable_specific_losses,
                                   bool enable_unspecific_losses,
                                   bool enable_ms2_precursors,
                                   const std::vector<std::pair<double, double> >& swathes,
                                   int round_decPow,
                                   TargetDecoyMapT& TargetDecoyMap,
                                   PeptideMapT& TargetPeptideMap,
                                   boost::unordered_map<String, String>& DecoySequenceMap,
                                   IonMapT& DecoyIonMap,
                                   PeptideMapT& DecoyPeptideMap);

   void generateTargetAssays_(const OpenMS::TargetedExperiment& exp,
                              TransitionVectorType& transitions,
                              double mz_threshold,
                              const std::vector<std::pair<double, double> >& swathes,
                              int round_decPow,
                              const PeptideMapT& TargetPeptideMap,
                              const IonMapT& TargetIonMap);

   void generateDecoyAssays_(const OpenMS::TargetedExperiment& exp,
                             TransitionVectorType& transitions,
                             double mz_threshold,
                             const std::vector<std::pair<double, double> >& swathes,
                             int round_decPow,
                             const PeptideMapT& DecoyPeptideMap,
                             TargetDecoyMapT& TargetDecoyMap,
                             const IonMapT& DecoyIonMap,
                             const IonMapT& TargetIonMap);

  };
}