FLASHDeconvHelperStructs.h

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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Kyowon Jeong, Jihyung Kim $
// $Authors: Kyowon Jeong, Jihyung Kim $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h>

namespace OpenMS
{
  struct OPENMS_DLLAPI FLASHDeconvHelperStructs
  {
    class OPENMS_DLLAPI PrecalculatedAveragine
    {
    private:
      std::vector<IsotopeDistribution> isotopes_;
      std::vector<double> norms_;
      std::vector<double> average_mono_mass_difference_;
      std::vector<double> abundant_mono_mass_difference_;
      std::vector<int> left_count_from_apex_;
      std::vector<int> right_count_from_apex_;
      std::vector<Size> apex_index_;

      Size max_isotope_index_;
      double mass_interval_;
      double min_mass_;
      Size massToIndex_(double mass) const;
    public:
      PrecalculatedAveragine() = default;

      PrecalculatedAveragine(double min_mass,
                             double max_mass,
                             double delta,
                             CoarseIsotopePatternGenerator &generator,
                             bool use_RNA_averagine);


      PrecalculatedAveragine(const PrecalculatedAveragine& ) = default;

      PrecalculatedAveragine(PrecalculatedAveragine&& other) noexcept = default;

      PrecalculatedAveragine& operator=(const PrecalculatedAveragine& pc) = default;

      PrecalculatedAveragine& operator=(PrecalculatedAveragine&& pc) noexcept = default;

      ~PrecalculatedAveragine() = default ;


      IsotopeDistribution get(double mass) const;

      size_t getMaxIsotopeIndex() const;

      void setMaxIsotopeIndex(int index);

      Size getLeftCountFromApex(double mass) const;

      Size getRightCountFromApex(double mass) const;

      Size getApexIndex(double mass) const;

      Size getLastIndex(double mass) const;

      double getAverageMassDelta(double mass) const;

      double getMostAbundantMassDelta(double mass) const;
    };

    struct OPENMS_DLLAPI MassFeature
    {
    public:
      MassTrace mt;
      std::vector<float> per_charge_intensity;
      std::vector<float> per_isotope_intensity;
      int iso_offset;
      int scan_number, rep_charge;
      double avg_mass;
      int min_charge, max_charge, charge_count;
      double isotope_score, qscore;
      double rep_mz;
    };

    class OPENMS_DLLAPI LogMzPeak
    {
    public:
      double mz = 0;
      float intensity = 0;
      double logMz = -1000;
      double mass = .0;
      int abs_charge = 0;
      bool is_positive = true;
      int isotopeIndex = -1;

      LogMzPeak() = default;

      explicit LogMzPeak(const Peak1D& peak, bool positive);

      LogMzPeak(const LogMzPeak& ) = default;

      ~LogMzPeak() = default;

      double getUnchargedMass();

      bool operator<(const LogMzPeak& a) const;
      bool operator>(const LogMzPeak& a) const;
      bool operator==(const LogMzPeak& other) const;
    };

    static double getLogMz(double mz, bool positive);

    static float getChargeMass(bool positive_ioniziation_mode);
  };
}