MetaboTargetedAssay.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 2002-2020.
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// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
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#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <map> //insert
 
#include <OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/ANALYSIS/ID/SiriusMSConverter.h> //SiriusMSFile
#include <OpenMS/FORMAT/DATAACCESS/SiriusFragmentAnnotation.h> //SiriusTargetDecoySpectra
 
#include <OpenMS/CONCEPT/Exception.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI MetaboTargetedAssay
  {
    public:
 
    double precursor_int;
    double transition_quality_score;
    String compound_name;
    String compound_adduct;
    TargetedExperiment::Compound potential_cmp;
    std::vector<ReactionMonitoringTransition> potential_rmts;
 
    struct CompoundTargetDecoyPair
    {
      SiriusMSFile::CompoundInfo compound_info;
      SiriusFragmentAnnotation::SiriusTargetDecoySpectra target_decoy_spectra;
 
      CompoundTargetDecoyPair() = default;
      CompoundTargetDecoyPair(SiriusMSFile::CompoundInfo info, SiriusFragmentAnnotation::SiriusTargetDecoySpectra td_spectra) : compound_info(info), target_decoy_spectra(td_spectra) {}
    };
 
 
    static std::vector<MetaboTargetedAssay> extractMetaboTargetedAssay(const MSExperiment& spectra,
                                                                       const FeatureMapping::FeatureToMs2Indices& feature_ms2_index,
                                                                       const double& precursor_rt_tol,
                                                                       const double& precursor_mz_distance,
                                                                       const double& cosine_sim_threshold,
                                                                       const double& transition_threshold,
                                                                       const double& min_fragment_mz,
                                                                       const double& max_fragment_mz,
                                                                       const bool& method_consensus_spectrum,
                                                                       const bool& exclude_ms2_precursor,
                                                                       const unsigned int& file_counter);
 
    static std::vector<MetaboTargetedAssay> extractMetaboTargetedAssayFragmentAnnotation(const std::vector< CompoundTargetDecoyPair >& v_cmp_spec,
                                                                                         const double& transition_threshold,
                                                                                         const double& min_fragment_mz,
                                                                                         const double& max_fragment_mz,
                                                                                         const bool& use_exact_mass,
                                                                                         const bool& exclude_ms2_precursor,
                                                                                         const unsigned int& file_counter);
 
 
 
 
    static std::vector< MetaboTargetedAssay::CompoundTargetDecoyPair > pairCompoundWithAnnotatedSpectra(const std::vector<SiriusMSFile::CompoundInfo>& v_cmpinfo,
                                                                                                        const std::vector<SiriusFragmentAnnotation::SiriusTargetDecoySpectra>& annotated_spectra);
 
 
    protected:
 
    static bool intensityLess_(Peak1D a, Peak1D b);
 
    static int getChargeFromAdduct_(const String& adduct);
 
};
 
} // namespace OpenMS