MRMFeatureFinderScoring.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: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#define USE_SP_INTERFACE
 
// Actual scoring
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>
 
#include <OpenMS/ANALYSIS/OPENSWATH/DIAScoring.h>
#include <OpenMS/FEATUREFINDER/EmgScoring.h>
 
// Kernel classes
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MRMTransitionGroup.h>
#include <OpenMS/KERNEL/MRMFeature.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
 
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
 
#include <unordered_map>
 
#ifdef _OPENMP
#include <omp.h>
#endif
 
bool SortDoubleDoublePairFirst(const std::pair<double, double>& left, const std::pair<double, double>& right);
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI MRMFeatureFinderScoring :
    public DefaultParamHandler,
    public ProgressLogger
  {
 
public:
 
    typedef OpenSwath::LightTransition TransitionType;
    typedef OpenSwath::LightTargetedExperiment TargetedExpType;
    typedef OpenSwath::LightCompound PeptideType;
    typedef OpenSwath::LightProtein ProteinType;
    typedef OpenSwath::LightModification ModificationType;
    // a transition group holds the chromatographic data and peaks across
    // multiple chromatograms from the same compound
    typedef MRMTransitionGroup< MSChromatogram, TransitionType> MRMTransitionGroupType;
    typedef std::map<String, MRMTransitionGroupType> TransitionGroupMapType;
 
 
    MRMFeatureFinderScoring();
 
    ~MRMFeatureFinderScoring() override;
 
 
 
    void pickExperiment(const PeakMap & chromatograms,
                        FeatureMap& output,
                        const TargetedExperiment& transition_exp,
                        const TransformationDescription& trafo,
                        const PeakMap& swath_map);
 
    void pickExperiment(const OpenSwath::SpectrumAccessPtr& input,
                        FeatureMap& output,
                        const OpenSwath::LightTargetedExperiment& transition_exp,
                        const TransformationDescription& trafo,
                        const std::vector<OpenSwath::SwathMap>& swath_maps,
                        TransitionGroupMapType& transition_group_map);
 
    void prepareProteinPeptideMaps_(const OpenSwath::LightTargetedExperiment& transition_exp);
 
    void scorePeakgroups(MRMTransitionGroupType& transition_group,
                         const TransformationDescription & trafo,
                         const std::vector<OpenSwath::SwathMap>& swath_maps,
                         FeatureMap& output,
                         bool ms1only = false) const;
 
    void setStrictFlag(bool f)
    {
      strict_ = f;
    }
 
    void setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)
    {
      ms1_map_ = ms1_map;
    }
 
    void mapExperimentToTransitionList(const OpenSwath::SpectrumAccessPtr& input,
                                       const OpenSwath::LightTargetedExperiment& transition_exp,
                                       TransitionGroupMapType& transition_group_map,
                                       TransformationDescription trafo,
                                       double rt_extraction_window);
private:
 
    void splitTransitionGroupsDetection_(const MRMTransitionGroupType& transition_group,
                                         MRMTransitionGroupType& transition_group_detection) const;
 
    void splitTransitionGroupsIdentification_(const MRMTransitionGroupType& transition_group,
                                              MRMTransitionGroupType& transition_group_identification,
                                              MRMTransitionGroupType& transition_group_identification_decoy) const;
 
    OpenSwath_Ind_Scores scoreIdentification_(MRMTransitionGroupType& transition_group_identification,
                                              MRMTransitionGroupType& transition_group_detection,
                                              OpenSwathScoring& scorer,
                                              const size_t feature_idx,
                                              const std::vector<std::string> & native_ids_detection,
                                              const double det_intensity_ratio_score,
                                              const double det_mi_ratio_score,
                                              const std::vector<OpenSwath::SwathMap>& swath_maps,
                                              const double drift_target,
                                              RangeMobility& im_range) const;
 
    void prepareFeatureOutput_(OpenMS::MRMFeature& mrmfeature, bool ms1only, int charge) const;
 
    void updateMembers_() override;
 
    // parameters
    double rt_extraction_window_;
    double quantification_cutoff_;
    int stop_report_after_feature_;
    bool write_convex_hull_;
    bool strict_;
    bool use_ms1_ion_mobility_;
    bool apply_im_peak_picking_;
    String scoring_model_;
 
    // scoring parameters
    double rt_normalization_factor_;
    int add_up_spectra_;
    String spectrum_addition_method_ ;
    String spectrum_merge_method_type_;
    double spacing_for_spectra_resampling_;
    double merge_spectra_by_peak_width_fraction_;
    double uis_threshold_sn_;
    double uis_threshold_peak_area_;
 
    double sn_win_len_;
    unsigned int sn_bin_count_;
    bool write_log_messages_;
 
    double im_extra_drift_;
 
    // members (unordered_map for O(1) lookup performance)
    std::unordered_map<OpenMS::String, const PeptideType*> PeptideRefMap_;
    OpenSwath_Scores_Usage su_;
    OpenMS::DIAScoring diascoring_;
    OpenMS::EmgScoring emgscoring_;
 
    // data
    OpenSwath::SpectrumAccessPtr ms1_map_;
 
  };
}
 
#undef run_identifier