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 2002-2020.
//
// 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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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#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"
 
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(const std::vector< std::vector< double > >& data);
 
    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 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<String>& precursor_ids, const std::vector<String>& native_ids);
 
    /*
       @brief Calculate the cross-correlation coelution score
 
       The score is a distance where zero indicates perfect coelution.
    */
    double calcXcorrCoelutionScore();
 
    /*
       @brief Calculate the weighted cross-correlation coelution score
 
       The score is a distance where zero indicates perfect coelution. The
       score is weighted by the transition intensities, non-perfect coelution
       in low-intensity transitions should thus become less important.
    */
    double calcXcorrCoelutionWeightedScore(const std::vector<double>& normalized_library_intensity);
 
    double calcXcorrContrastCoelutionScore();
 
    std::vector<double> calcSeparateXcorrContrastCoelutionScore();
 
    double calcXcorrPrecursorCoelutionScore();
 
    /*
       @brief Calculate the precursor cross-correlation contrast score against the transitions
 
       The score is a distance where zero indicates perfect coelution.
    */
    double calcXcorrPrecursorContrastCoelutionScore();
 
    double calcXcorrPrecursorCombinedCoelutionScore();
 
    /*
       @brief Calculate the cross-correlation shape score
 
       The score is a correlation measure where 1 indicates perfect correlation
       and 0 means no correlation.
    */
    double calcXcorrShapeScore();
 
    /*
       @brief Calculate the weighted cross-correlation shape score
 
       The score is a correlation measure where 1 indicates perfect correlation
       and 0 means no correlation. The score is weighted by the transition
       intensities, non-perfect coelution in low-intensity transitions should
       thus become less important.
    */
    double calcXcorrShapeWeightedScore(const std::vector<double>& normalized_library_intensity);
 
    double calcXcorrContrastShapeScore();
 
    std::vector<double> 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::vector<double> 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::vector<double> 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_;
 
  };
}