DIAScoring.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest, Witold Wolski $
// --------------------------------------------------------------------------

#pragma once

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

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

namespace OpenMS
{
  class TheoreticalSpectrumGenerator;

  class OPENMS_DLLAPI DIAScoring :
    public DefaultParamHandler
  {

    typedef OpenSwath::SpectrumPtr SpectrumPtrType;
    typedef OpenSwath::LightTransition TransitionType;

public:


    DIAScoring();

    ~DIAScoring() override;

    // DIA / SWATH scoring


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

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

    bool dia_ms1_massdiff_score(double precursor_mz, SpectrumPtrType spectrum,
                                double& ppm_score);

    void dia_ms1_isotope_scores(double precursor_mz, SpectrumPtrType spectrum, size_t charge_state, 
                                double& isotope_corr, double& isotope_overlap, std::string sum_formula = "");

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

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

private:

    DIAScoring(const DIAScoring& rhs);

    DIAScoring& operator=(const DIAScoring& rhs);

    void updateMembers_() override;

    void diaIsotopeScoresSub_(const std::vector<TransitionType>& transitions,
                                SpectrumPtrType 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:

    void largePeaksBeforeFirstIsotope_(SpectrumPtrType spectrum, double mono_mz, double mono_int, int& nr_occurrences, double& max_ratio);

    double scoreIsotopePattern_(double product_mz, const std::vector<double>& isotopes_int, 
                                int putative_fragment_charge, std::string sum_formula = "");

    // 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_;
    double peak_before_mono_max_ppm_diff_;
    bool dia_extraction_ppm_;

    TheoreticalSpectrumGenerator * generator;
  };
}