MetaboliteSpectralMatching.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: Timo Sachsenberg $
// $Authors: Erhan Kenar $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MassTrace.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/FORMAT/MzTab.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
 
#include <vector>
 
namespace OpenMS
{
 
  struct OPENMS_DLLAPI PrecursorMassComparator
  {
    bool operator() (const MSSpectrum& a, const MSSpectrum& b)
    {
      return a.getPrecursors()[0].getMZ() < b.getPrecursors()[0].getMZ();
    }
 
  } PrecursorMZLess;
 
  class OPENMS_DLLAPI SpectralMatch
  {
  public:
    SpectralMatch();
 
    ~SpectralMatch();
 
    SpectralMatch(const SpectralMatch&);
 
    SpectralMatch& operator=(const SpectralMatch&);
 
    double getObservedPrecursorMass() const;
    void setObservedPrecursorMass(const double&);
 
    double getObservedPrecursorRT() const;
    void setObservedPrecursorRT(const double&);
 
    double getFoundPrecursorMass() const;
    void setFoundPrecursorMass(const double&);
 
    Int getFoundPrecursorCharge() const;
    void setFoundPrecursorCharge(const Int&);
 
    double getMatchingScore() const;
    void setMatchingScore(const double&);
 
    Size getObservedSpectrumIndex() const;
    void setObservedSpectrumIndex(const Size&);
 
    Size getMatchingSpectrumIndex() const;
    void setMatchingSpectrumIndex(const Size&);
 
    std::string getObservedSpectrumNativeID() const;
    void setObservedSpectrumNativeID(const std::string&);
 
    std::string getPrimaryIdentifier() const;
    void setPrimaryIdentifier(const std::string&);
 
    std::string getSecondaryIdentifier() const;
    void setSecondaryIdentifier(const std::string&);
 
    std::string getCommonName() const;
    void setCommonName(const std::string&);
 
    std::string getSumFormula() const;
    void setSumFormula(const std::string&);
 
    std::string getInchiString() const;
    void setInchiString(const std::string&);
 
    std::string getSMILESString() const;
    void setSMILESString(const std::string&);
 
    std::string getPrecursorAdduct() const;
    void setPrecursorAdduct(const std::string&);
 
    double getObservedCCS() const;
    void setObservedCCS(const double&);
 
    double getFoundCCS() const;
    void setFoundCCS(const double&);
 
 
  private:
    double observed_precursor_mass_;   
    double observed_precursor_rt_;     
    double found_precursor_mass_;      
    Int found_precursor_charge_;       
    double matching_score_;            
    Size observed_spectrum_idx_;       
    Size matching_spectrum_idx_;       
    std::string observed_spectrum_native_id_; 
 
    // further meta information
    std::string primary_id_;     
    std::string secondary_id_;   
    std::string common_name_;    
    std::string sum_formula_;    
    std::string inchi_string_;   
    std::string smiles_string_;  
    std::string precursor_adduct_; 
 
    double observed_ccs_;   
    double found_ccs_;      
 
  };
 
  struct OPENMS_DLLAPI SpectralMatchScoreComparator
  {
    bool operator() (const SpectralMatch& a, const SpectralMatch& b)
    {
      return a.getMatchingScore() > b.getMatchingScore();
    }
 
  } SpectralMatchScoreGreater;
 
  class OPENMS_DLLAPI MetaboliteSpectralMatching :
  public DefaultParamHandler,
  public ProgressLogger
  {
  public:
    MetaboliteSpectralMatching();
 
    ~MetaboliteSpectralMatching() override;
 
    static double computeHyperScore(
      double fragment_mass_error,
      bool fragment_mass_tolerance_unit_ppm,
      const MSSpectrum& exp_spectrum,
      const MSSpectrum& db_spectrum,
      double mz_lower_bound = 0.0);
 
    static double computeHyperScore(
      double fragment_mass_error,
      bool fragment_mass_tolerance_unit_ppm,
      const MSSpectrum& exp_spectrum,
      const MSSpectrum& db_spectrum,
      std::vector<PeptideHit::PeakAnnotation>& annotations,
      double mz_lower_bound = 0.0);
 
    void run(PeakMap & msexp, PeakMap & spec_db, MzTab & mztab_out, std::string & out_spectra);
 
  protected:
    void updateMembers_() override;
 
    static double computeHyperScore_(
      double fragment_mass_error,
      bool fragment_mass_tolerance_unit_ppm,
      const MSSpectrum& exp_spectrum,
      const MSSpectrum& db_spectrum,
      std::vector<PeptideHit::PeakAnnotation>* annotations = 0,
      double mz_lower_bound = 0.0);
 
  private:
    void exportMzTab_(const std::vector<SpectralMatch>&, MzTab&);
 
    double precursor_mz_error_;     
    double fragment_mz_error_;      
    std::string mz_error_unit_;          
    std::string ion_mode_;               
 
    std::string report_mode_;            
 
    bool merge_spectra_;            
 
    double ccs_error_percent_;      
  };
 
}