MRMScoring.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// 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
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// 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 $a
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#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_;
    };
}