OpenSwathScoring.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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//    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

// 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>

// scoring
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DIAScoring.h>

#include <vector>
#include <boost/shared_ptr.hpp>
#include <boost/make_shared.hpp>

namespace OpenMS
{
  class OPENMS_DLLAPI OpenSwathScoring 
  {
    typedef OpenSwath::LightCompound CompoundType;
    typedef OpenSwath::LightTransition TransitionType;

    double rt_normalization_factor_;
    int add_up_spectra_;
    double spacing_for_spectra_resampling_;
    OpenSwath_Scores_Usage su_;

  public:

    OpenSwathScoring();

    ~OpenSwathScoring();

    void initialize(double rt_normalization_factor,
                    int add_up_spectra,
                    double spacing_for_spectra_resampling,
                    const OpenSwath_Scores_Usage & su);

    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);

    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);

    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,
                            OpenSwath::SpectrumAccessPtr ms1_map,
                            OpenMS::DIAScoring& diascoring,
                            const CompoundType& compound,
                            OpenSwath_Scores& scores,
                            std::vector<double>& mzerror_ppm,
                            double drift_lower,
                            double drift_upper);

    void calculatePrecursorDIAScores(OpenSwath::SpectrumAccessPtr ms1_map, 
                                     OpenMS::DIAScoring& diascoring, 
                                     double precursor_mz, 
                                     double rt, 
                                     const CompoundType& compound, 
                                     OpenSwath_Scores& scores,
                                     double drift_lower,
                                     double drift_upper);

    void calculateDIAIdScores(OpenSwath::IMRMFeature* imrmfeature,
                              const TransitionType & transition,
                              const std::vector<OpenSwath::SwathMap> swath_maps,
                              OpenMS::DIAScoring & diascoring,
                              OpenSwath_Scores & scores,
                              double drift_lower,
                              double drift_upper);

    void getNormalized_library_intensities_(const std::vector<TransitionType> & transitions,
                                            std::vector<double>& normalized_library_intensity);

    OpenSwath::SpectrumPtr fetchSpectrumSwath(std::vector<OpenSwath::SwathMap> swath_maps,
                                              double RT,
                                              int nr_spectra_to_add,
                                              const double drift_lower,
                                              const double drift_upper);
    
    OpenSwath::SpectrumPtr fetchSpectrumSwath(OpenSwath::SpectrumAccessPtr swath_map,
                                              double RT,
                                              int nr_spectra_to_add,
                                              const double drift_lower,
                                              const double drift_upper);

  protected:

    OpenSwath::SpectrumPtr getAddedSpectra_(OpenSwath::SpectrumAccessPtr swath_map,
                                            double RT,
                                            int nr_spectra_to_add,
                                            const double drift_lower,
                                            const double drift_upper);

  };
}