MRMAssay.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger $
// --------------------------------------------------------------------------
 
#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 <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
#include <boost/random/mersenne_twister.hpp>
#include <boost/random/uniform_int.hpp>
#include <boost/random/variate_generator.hpp>
 
// #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 std::map<String, std::set<std::string> > ModifiedSequenceMap; 
    typedef std::map<size_t, ModifiedSequenceMap> SequenceMapT; 
 
    typedef std::vector<std::pair<double, std::string> > FragmentSeqMap; 
    typedef std::map<size_t, std::map<String, FragmentSeqMap > > IonMapT; 
 
    typedef std::vector<std::pair<std::string, double> > IonSeries; 
    typedef std::map<String, IonSeries > PeptideMapT; 
 
    typedef std::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);
 
    // =====================================================================
    // Light (memory-efficient) versions of the above methods
    // =====================================================================
 
    void reannotateTransitionsLight(OpenSwath::LightTargetedExperiment& 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 restrictTransitionsLight(OpenSwath::LightTargetedExperiment& exp,
                                  double lower_mz_limit,
                                  double upper_mz_limit,
                                  const std::vector<std::pair<double, double> >& swathes);
 
    void detectingTransitionsLight(OpenSwath::LightTargetedExperiment& exp,
                                   int min_transitions,
                                   int max_transitions);
 
    void uisTransitionsLight(OpenSwath::LightTargetedExperiment& 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);
 
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,
                                 std::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,
                                   std::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);
 
    // =====================================================================
    // Light (memory-efficient) versions of IPF helper methods
    // =====================================================================
 
    typedef std::map<String, OpenSwath::LightCompound> TargetDecoyMapLightT;
 
    void generateTargetInSilicoMapLight_(const OpenSwath::LightTargetedExperiment& 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 generateDecoyInSilicoMapLight_(const OpenSwath::LightTargetedExperiment& 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,
                                        TargetDecoyMapLightT& TargetDecoyMap,
                                        const PeptideMapT& TargetPeptideMap,
                                        const std::map<String, String>& DecoySequenceMap,
                                        IonMapT& DecoyIonMap,
                                        PeptideMapT& DecoyPeptideMap);
 
    void generateTargetAssaysLight_(const OpenSwath::LightTargetedExperiment& exp,
                                    std::vector<OpenSwath::LightTransition>& transitions,
                                    double mz_threshold,
                                    const std::vector<std::pair<double, double> >& swathes,
                                    int round_decPow,
                                    const PeptideMapT& TargetPeptideMap,
                                    const IonMapT& TargetIonMap);
 
    void generateDecoyAssaysLight_(const OpenSwath::LightTargetedExperiment& exp,
                                   std::vector<OpenSwath::LightTransition>& transitions,
                                   double mz_threshold,
                                   const std::vector<std::pair<double, double> >& swathes,
                                   int round_decPow,
                                   const PeptideMapT& DecoyPeptideMap,
                                   const TargetDecoyMapLightT& TargetDecoyMap,
                                   const IonMapT& DecoyIonMap,
                                   const IonMapT& TargetIonMap);
 
  };
}