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 2002-2017.
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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/CONCEPT/LogStream.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMIonSeries.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>

#include <boost/bind.hpp>
#include <boost/lexical_cast.hpp>
#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();

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

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

    typedef boost::unordered_map<size_t, boost::unordered_map<String, std::set<std::string> > > SequenceMapT;
    typedef boost::unordered_map<size_t, boost::unordered_map<String, std::vector<std::pair<double, std::string> > > > IonMapT;
    typedef std::map<String, std::vector<std::pair<std::string, double> > > PeptideMapT;
    typedef boost::unordered_map<String, String> SequenceMap_T;

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

    void reannotateTransitions(OpenMS::TargetedExperiment& exp, double precursor_mz_threshold, double product_mz_threshold, std::vector<String> fragment_types, 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, std::vector<std::pair<double, double> > swathes);

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

    void uisTransitions(OpenMS::TargetedExperiment& exp,
                        std::vector<String> fragment_types,
                        std::vector<size_t> fragment_charges,
                        bool enable_specific_losses,
                        bool enable_unspecific_losses,
                        bool enable_ms2_precursors,
                        double mz_threshold,
                        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 std::vector<std::pair<double, std::string> >& 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_(std::vector<size_t> n, size_t k);

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

    std::vector<OpenMS::AASequence> combineModifications_(OpenMS::AASequence sequence);

    std::vector<OpenMS::AASequence> combineDecoyModifications_(OpenMS::AASequence sequence, OpenMS::AASequence decoy_sequence);

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

    void generateDecoySequences_(boost::unordered_map<size_t,
                                 boost::unordered_map<String, std::set<std::string> > >& TargetSequenceMap,
                                 boost::unordered_map<String, String>& DecoySequenceMap, 
                                 int shuffle_seed);

    void generateDecoyInSilicoMap_(OpenMS::TargetedExperiment& exp,
                                   std::vector<String> fragment_types, std::vector<size_t> fragment_charges,
                                   bool enable_specific_losses,
                                   bool enable_unspecific_losses,
                                   bool enable_ms2_precursors,
                                   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_(OpenMS::TargetedExperiment& exp,
                              TransitionVectorType& transitions, double mz_threshold,
                              std::vector<std::pair<double, double> > swathes,
                              int round_decPow,
                              PeptideMapT& TargetPeptideMap,
                              IonMapT& TargetIonMap);

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

  };
}