MRMScoring.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 2002-2022.
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// $Maintainer: Hannes Roest $a
// $Authors: Hannes Roest $
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#pragma once

#include <string>

#include <OpenMS/DATASTRUCTURES/Matrix.h>
#include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>

#include "OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h"
#include "OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h"
#include "OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h"
#include "OpenMS/OPENSWATHALGO/ALGO/StatsHelpers.h"
#include "OpenMS/OPENSWATHALGO/ALGO/Scoring.h"

namespace OpenSwath
{

    class OPENMS_DLLAPI MRMScoring
    {

    public:

        typedef OpenSwath::Scoring::XCorrArrayType XCorrArrayType;
        typedef OpenMS::Matrix<XCorrArrayType> XCorrMatrixType;

        typedef OpenSwath::SpectrumPtr SpectrumType;
        typedef OpenSwath::LightTransition TransitionType;
        typedef OpenSwath::LightCompound PeptideType;
        typedef OpenSwath::LightProtein ProteinType;

        typedef boost::shared_ptr<OpenSwath::IFeature> FeatureType;

        const XCorrMatrixType& getXCorrMatrix() const;

        const XCorrMatrixType& getXCorrContrastMatrix() const;

        const XCorrMatrixType& getXCorrPrecursorContrastMatrix() const;

        const XCorrMatrixType& getXCorrPrecursorCombinedMatrix() const;

      
        void initializeXCorrMatrix(const std::vector< std::vector< double > >& data);

        void initializeXCorrMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& native_ids);

        void initializeXCorrContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& native_ids_set1, const std::vector<std::string>& native_ids_set2);

        void initializeXCorrPrecursorMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids);

        void initializeXCorrPrecursorContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids, const std::vector<std::string>& native_ids);

        void initializeXCorrPrecursorContrastMatrix(const std::vector< std::vector< double > >& data_precursor, const std::vector< std::vector< double > >& data_fragments);

        void initializeXCorrPrecursorCombinedMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids, const std::vector<std::string>& native_ids);

        double calcXcorrCoelutionScore();

        double calcXcorrCoelutionWeightedScore(const std::vector<double>& normalized_library_intensity);

        double calcXcorrContrastCoelutionScore();

        std::vector<double> calcSeparateXcorrContrastCoelutionScore();

        double calcXcorrPrecursorCoelutionScore();

        double calcXcorrPrecursorContrastCoelutionScore();

        double calcXcorrPrecursorContrastSumFragCoelutionScore();

        double calcXcorrPrecursorCombinedCoelutionScore();

        double calcXcorrShapeScore();

        double calcXcorrShapeWeightedScore(const std::vector<double>& normalized_library_intensity);

        double calcXcorrContrastShapeScore();

        std::vector<double> calcSeparateXcorrContrastShapeScore();

        double calcXcorrPrecursorShapeScore();

        double calcXcorrPrecursorContrastShapeScore();

        double calcXcorrPrecursorContrastSumFragShapeScore();

        double calcXcorrPrecursorCombinedShapeScore();

        static void calcLibraryScore(OpenSwath::IMRMFeature* mrmfeature,
                                     const std::vector<TransitionType>& transitions, double& correlation,
                                     double& norm_manhattan, double& manhattan, double& dotprod,
                                     double& spectral_angle, double& rmsd);

        static double calcRTScore(const PeptideType& peptide, double normalized_experimental_rt);

        //  using a vector of SignalToNoiseEstimatorMedian that were calculated for
        //  each chromatogram of the transition_group.
        static double calcSNScore(OpenSwath::IMRMFeature* mrmfeature,
                                  std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);

        static std::vector<double> calcSeparateSNScore(OpenSwath::IMRMFeature* mrmfeature,
                                                       std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators);

        const OpenMS::Matrix<double> & getMIMatrix() const;

        const OpenMS::Matrix<double> & getMIContrastMatrix() const;

        const OpenMS::Matrix<double> & getMIPrecursorContrastMatrix() const;

        const OpenMS::Matrix<double> & getMIPrecursorCombinedMatrix() const;

        void initializeMIMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& native_ids);

        void initializeMIContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& native_ids_set1, const std::vector<std::string>& native_ids_set2);

        void initializeMIPrecursorMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids);

        void initializeMIPrecursorContrastMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids, const std::vector<std::string>& native_ids);

        void initializeMIPrecursorCombinedMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<std::string>& precursor_ids, const std::vector<std::string>& native_ids);

        double calcMIScore();
        double calcMIWeightedScore(const std::vector<double>& normalized_library_intensity);
        double calcMIPrecursorScore();
        double calcMIPrecursorContrastScore();
        double calcMIPrecursorCombinedScore();
        std::vector<double> calcSeparateMIContrastScore();


    private:
        XCorrMatrixType xcorr_matrix_;

        OpenMS::Matrix<int> xcorr_matrix_max_peak_;
        OpenMS::Matrix<double> xcorr_matrix_max_peak_sec_;

        XCorrMatrixType xcorr_contrast_matrix_;

        OpenMS::Matrix<double > xcorr_contrast_matrix_max_peak_sec_;

        XCorrMatrixType xcorr_precursor_matrix_;

        XCorrMatrixType xcorr_precursor_contrast_matrix_;

        XCorrMatrixType xcorr_precursor_combined_matrix_;


        OpenMS::Matrix<double> mi_matrix_;
        OpenMS::Matrix<double> mi_contrast_matrix_;

        OpenMS::Matrix<double> mi_precursor_matrix_;

        OpenMS::Matrix<double> mi_precursor_contrast_matrix_;

        OpenMS::Matrix<double> mi_precursor_combined_matrix_;
    };
}