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
//    without specific prior written permission.
// 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"
//#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 std::vector< std::vector<double> > & getMIMatrix() const;

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

    void initializeMS1XCorr(OpenSwath::IMRMFeature* mrmfeature, const std::vector<String>& native_ids, const std::string& precursor_id);

    void initializeXCorrIdMatrix(OpenSwath::IMRMFeature* mrmfeature, const std::vector<String>& native_ids_identification, const std::vector<String>& native_ids_detection);

    double calcXcorrCoelutionScore();
    std::string calcIndXcorrIdCoelutionScore();

    double calcXcorrShape_score();
    std::string calcIndXcorrIdShape_score();

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

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

    double calcMS1XcorrCoelutionScore();

    double calcMS1XcorrShape_score();

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

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

    void initializeMS1MI(OpenSwath::IMRMFeature* mrmfeature, std::vector<String> native_ids, std::string precursor_id);

    void initializeMIIdMatrix(OpenSwath::IMRMFeature* mrmfeature, std::vector<String> native_ids_identification, std::vector<String> native_ids_detection);

    double calcMIScore();
    double calcMIScore_weighted(const std::vector<double>& normalized_library_intensity);
    double calcMS1MIScore();
    std::string calcIndMIIdScore();


private:

    XCorrMatrixType xcorr_matrix_;

    std::vector<XCorrArrayType> ms1_xcorr_vector_;

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

    std::vector<double> ms1_mi_vector_;

  };
}