DIAScoring.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest, Witold Wolski $
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#ifndef OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H
#define OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H

#include <boost/math/special_functions/fpclassify.hpp> // for isnan
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ITransition.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>

namespace OpenMS
{
  class OPENMS_DLLAPI DIAScoring :
    public DefaultParamHandler
  {


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

public:



    DIAScoring();

    virtual ~DIAScoring() {}



    void set_dia_parameters(double dia_extract_window, double dia_centroided,
                            double dia_byseries_intensity_min, double dia_byseries_ppm_diff, double dia_nr_isotopes, double dia_nr_charges);

    // DIA / SWATH scoring



    void dia_isotope_scores(const std::vector<TransitionType>& transitions,
                            SpectrumType spectrum, OpenSwath::IMRMFeature* mrmfeature, double& isotope_corr,
                            double& isotope_overlap);

    void dia_massdiff_score(const std::vector<TransitionType>& transitions,
                            SpectrumType spectrum, const std::vector<double>& normalized_library_intensity,
                            double& ppm_score, double& ppm_score_weighted);

    void dia_by_ion_score(SpectrumType spectrum, AASequence& sequence,
                          int charge, double& bseries_score, double& yseries_score);

    void score_with_isotopes(SpectrumType spectrum, const std::vector<TransitionType>& transitions,
                             double& dotprod, double& manhattan);

private:

    DIAScoring(const DIAScoring& rhs);

    DIAScoring& operator=(const DIAScoring& rhs);

    void updateMembers_();

    void diaIsotopeScoresSub_(const std::vector<TransitionType>& transitions,
                                SpectrumType spectrum, std::map<std::string, double>& intensities,
                                double& isotope_corr, double& isotope_overlap);

    void getFirstIsotopeRelativeIntensities_(const std::vector<TransitionType>& transitions,
                                            OpenSwath::IMRMFeature* mrmfeature,
                                            std::map<std::string, double>& intensities //experimental intensities of transitions
                                            );

private:

    DoubleReal largePeaksBeforeFirstIsotope_(double product_mz,
                                            SpectrumType& spectrum, double max_ppm_diff, double main_peak);

    DoubleReal scoreIsotopePattern_(double product_mz,
                                   const std::vector<double>& isotopes_int, int putative_fragment_charge);

    // Parameters
    double dia_extract_window_;
    double dia_centroided_;
    double dia_byseries_intensity_min_;
    double dia_byseries_ppm_diff_;
    double dia_nr_isotopes_;
    double dia_nr_charges_;

  };
}

#endif