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 2002-2018.
//
// This software is released under a three-clause BSD license:
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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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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest$
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#pragma once

#include <string>
#include <boost/math/special_functions/fpclassify.hpp> // for isnan
#include <boost/numeric/conversion/cast.hpp>

#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"
//#include "OpenMS/OPENSWATHALGO/ALGO/DIAHelpers.h"

namespace OpenSwath
{

  class OPENSWATHALGO_DLLAPI MRMScoring
  {

public:


    typedef OpenSwath::Scoring::XCorrArrayType XCorrArrayType;
    typedef std::vector<std::vector<XCorrArrayType> > XCorrMatrixType;

    typedef std::string String;

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

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

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

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

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

    double calcXcorrCoelutionScore();

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

    double calcXcorrContrastCoelutionScore();

    std::string calcSeparateXcorrContrastCoelutionScore();

    double calcXcorrPrecursorCoelutionScore();

    double calcXcorrPrecursorContrastCoelutionScore();

    double calcXcorrPrecursorCombinedCoelutionScore();

    double calcXcorrShapeScore();

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

    double calcXcorrContrastShapeScore();

    std::string calcSeparateXcorrContrastShapeScore();

    double calcXcorrPrecursorShapeScore();

    double calcXcorrPrecursorContrastShapeScore();

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

    const std::vector< std::vector<double> > & getMIMatrix() const;

    const std::vector< std::vector<double> > & getMIContrastMatrix() const;

    const std::vector< std::vector<double> > & getMIPrecursorContrastMatrix() const;

    const std::vector< std::vector<double> > & getMIPrecursorCombinedMatrix() const;

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

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

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

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

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

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


private:

    XCorrMatrixType xcorr_matrix_;

    XCorrMatrixType xcorr_contrast_matrix_;

    XCorrMatrixType xcorr_precursor_matrix_;

    XCorrMatrixType xcorr_precursor_contrast_matrix_;

    XCorrMatrixType xcorr_precursor_combined_matrix_;

    std::vector< std::vector<double> > mi_matrix_;

    std::vector< std::vector<double> > mi_contrast_matrix_;

    std::vector< std::vector<double> > mi_precursor_matrix_;

    std::vector< std::vector<double> > mi_precursor_contrast_matrix_;

    std::vector< std::vector<double> > mi_precursor_combined_matrix_;

  };
}