PrecursorPurity.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 2002-2018.
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// $Maintainer: Eugen Netz $
// $Authors: Eugen Netz $
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#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <vector>


namespace OpenMS
{
  class OPENMS_DLLAPI PrecursorPurity
  {

  public:

    struct PurityScores
    {
      double total_intensity = 0.0;
      double target_intensity = 0.0;
      double residual_intensity = 0.0;
      double signal_proportion = 0.0;
      Size target_peak_count = 0;
      Size residual_peak_count = 0;
    };

    /* @brief compute precursor purity metrics for each MS2 spectrum in a PeakMap
       This is the main function of this class. See class description.

     * @param spectra A PeakMap containing MS1 and MS2 spectra in order of acquisition or measurement. The first spectrum must be an MS1.
     * @param precursor_mass_tolerance The precursor tolerance. Is used for determining the targeted peak and deisotoping.
     * @param precursor_mass_tolerance_unit_ppm The unit of the precursor tolerance
    */
    static std::vector<PurityScores> computePrecursorPurities(const PeakMap& spectra, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm);

    /* @brief compute precursor purity metrics for one MS2 precursor

       @note This function is implemented in a general way and can also be used for e.g. MS3 precursor isolation windows in MS2 spectra

     * @param ms1 The Spectrum containing the isolation window
     * @param pre The precursor containing the definition the isolation window
     * @param precursor_mass_tolerance The precursor tolerance. Is used for determining the targeted peak and deisotoping.
     * @param precursor_mass_tolerance_unit_ppm The unit of the precursor tolerance
    */
    static PurityScores computePrecursorPurity(const PeakSpectrum& ms1, const Precursor& pre, const double precursor_mass_tolerance, const bool precursor_mass_tolerance_unit_ppm);


  private:
    // simple helper to combine the metrics contained in two PurityScores
    static PurityScores combinePrecursorPurities(const PrecursorPurity::PurityScores& score1, const PrecursorPurity::PurityScores& score2);

  };
}