MRMFeatureFinderScoring.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $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/ANALYSIS/OPENSWATH/SONARScoring.h>
#include <OpenMS/TRANSFORMATIONS/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 <boost/shared_ptr.hpp>
#include <boost/make_shared.hpp>
#include <boost/unordered_map.hpp>

#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(PeakMap & chromatograms, FeatureMap& output, TargetedExperiment& transition_exp,
                        TransformationDescription trafo, PeakMap& swath_map);

    void pickExperiment(OpenSwath::SpectrumAccessPtr input,
                        FeatureMap& output,
                        OpenSwath::LightTargetedExperiment& transition_exp,
                        TransformationDescription trafo,
                        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);

    void setStrictFlag(bool f)
    {
      strict_ = f;
    }

    void setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)
    {
      ms1_map_ = ms1_map;
    }

    void mapExperimentToTransitionList(OpenSwath::SpectrumAccessPtr input,
                                       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);

    void splitTransitionGroupsIdentification_(const MRMTransitionGroupType& transition_group,
                                              MRMTransitionGroupType& transition_group_identification,
                                              MRMTransitionGroupType& transition_group_identification_decoy);

    OpenSwath_Scores scoreIdentification_(MRMTransitionGroupType& transition_group_identification,
                                          OpenSwathScoring& scorer,
                                          const size_t feature_idx,
                                          const std::vector<std::string> & native_ids_detection,
                                          const double sn_win_len_,
                                          const unsigned int sn_bin_count_,
                                          const double det_intensity_ratio_score,
                                          const double det_mi_ratio_score,
                                          bool write_log_messages,
                                          const std::vector<OpenSwath::SwathMap>& swath_maps);

    void updateMembers_() override;

    // parameters
    double rt_extraction_window_;
    double quantification_cutoff_;
    int stop_report_after_feature_;
    bool write_convex_hull_;
    bool strict_;
    String scoring_model_;

    // scoring parameters
    double rt_normalization_factor_;
    int add_up_spectra_;
    double spacing_for_spectra_resampling_;
    double uis_threshold_sn_;
    double uis_threshold_peak_area_;

    // members
    std::map<OpenMS::String, const PeptideType*> PeptideRefMap_;
    OpenSwath_Scores_Usage su_;
    OpenMS::DIAScoring diascoring_;
    OpenMS::SONARScoring sonarscoring_;
    OpenMS::EmgScoring emgscoring_;

    // data
    OpenSwath::SpectrumAccessPtr ms1_map_;

  };
}

#undef run_identifier