OpenSwathScoring.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
 
// data access
#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
 
// Kernel classes
#include <OpenMS/KERNEL/MRMTransitionGroup.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
 
// scoring
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DIAScoring.h>
 
#include <vector>
#include <memory>
#include <boost/make_shared.hpp>
 
//logging
#include <OpenMS/CONCEPT/LogStream.h>
 
struct RangeMZ;
struct RangeMobility;
 
namespace OpenMS
{
  class MobilogramParquetConsumer;
 
  class OPENMS_DLLAPI OpenSwathScoring
  {
    typedef OpenSwath::LightCompound CompoundType;
    typedef OpenSwath::LightTransition TransitionType;
    typedef MRMTransitionGroup< MSChromatogram, TransitionType> MRMTransitionGroupType;
 
    enum class SpectrumAdditionMethod
    {
      ADDITION,
      RESAMPLE
    };
 
    enum class SpectrumMergeMethodType 
    { 
      FIXED, 
      DYNAMIC 
    };
 
    double rt_normalization_factor_;
    double spacing_for_spectra_resampling_;
    double merge_spectra_by_peak_width_fraction_;
    int add_up_spectra_;
    SpectrumAdditionMethod spectra_addition_method_;
    SpectrumMergeMethodType spectra_merge_method_type_;
    double im_drift_extra_pcnt_;
    OpenSwath_Scores_Usage su_;
    bool use_ms1_ion_mobility_; 
    bool apply_im_peak_picking_; 
 
  public:
 
    OpenSwathScoring();
 
    ~OpenSwathScoring();
 
    void initialize(double rt_normalization_factor,
                    int add_up_spectra,
                    double spacing_for_spectra_resampling,
                    double merge_spectra_by_peak_width_fraction,
                    const double drift_extra,
                    const OpenSwath_Scores_Usage & su,
                    const std::string& spectrum_addition_method,
                    const std::string& spectrum_merge_method_type,
                    bool use_ms1_ion_mobility,
                    bool apply_im_peak_picking);
 
    void calculateChromatographicScores(OpenSwath::IMRMFeature* imrmfeature,
                                        const std::vector<std::string>& native_ids,
                                        const std::vector<std::string>& precursor_ids,
                                        const std::vector<double>& normalized_library_intensity,
                                        std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
                                        OpenSwath_Scores & scores) const;
 
    void calculateChromatographicIdScores(OpenSwath::IMRMFeature* imrmfeature,
                                          const std::vector<std::string>& native_ids_identification,
                                          const std::vector<std::string>& native_ids_detection,
                                          std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
                                          OpenSwath_Ind_Scores & scores) const;
 
    void calculateLibraryScores(OpenSwath::IMRMFeature* imrmfeature,
                                const std::vector<TransitionType> & transitions,
                                const CompoundType& compound,
                                const double normalized_feature_rt,
                                OpenSwath_Scores & scores);
 
  void calculateDIAScores(OpenSwath::IMRMFeature* imrmfeature,
              const std::vector<TransitionType>& transitions,
              const std::vector<OpenSwath::SwathMap>& swath_maps,
              const OpenSwath::SpectrumAccessPtr& ms1_map,
              const OpenMS::DIAScoring& diascoring,
              const CompoundType& compound,
              OpenSwath_Scores& scores,
              std::vector<double>& mzerror_ppm,
              const double drift_target,
              const RangeMobility& range_im,
              MobilogramParquetConsumer* mobilogram_consumer = nullptr,
              Int64 feature_id = -1);
 
    void calculatePrecursorDIAScores(const OpenSwath::SpectrumAccessPtr& ms1_map,
                                     const OpenMS::DIAScoring& diascoring,
                                     double precursor_mz,
                                     double rt,
                                     const CompoundType& compound,
                                     RangeMobility im_range,
                                     OpenSwath_Scores& scores);
 
    void calculateDIAIdScores(OpenSwath::IMRMFeature* imrmfeature,
                              const TransitionType & transition,
                              MRMTransitionGroupType& transition_group_detection,
                              const std::vector<OpenSwath::SwathMap>& swath_maps,
                              RangeMobility& range_im,
                              const OpenMS::DIAScoring & diascoring,
                              OpenSwath_Scores & scores,
                              const double drift_target,
                              MobilogramParquetConsumer* mobilogram_consumer = nullptr,
                              Int64 feature_id = -1);
 
    void getNormalized_library_intensities_(const std::vector<TransitionType> & transitions,
                                            std::vector<double>& normalized_library_intensity);
 
    SpectrumSequence fetchSpectrumSwath(const std::vector<OpenSwath::SwathMap>& swath_maps, double RT, int nr_spectra_to_add, const RangeMobility& im_range);
 
 
    SpectrumSequence fetchSpectrumSwath(OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add, const RangeMobility& im_range);
  };
}