FLASHDeconvHelperStructs.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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//  * Redistributions in binary form must reproduce the above copyright
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// $Maintainer: Kyowon Jeong, Jihyung Kim $
// $Authors: Kyowon Jeong, Jihyung Kim $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.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 const mass) const;
    public:
      PrecalculatedAveragine() = default;
 
      PrecalculatedAveragine(const double min_mass,
                             const double max_mass,
                             const double delta,
                             CoarseIsotopePatternGenerator *generator,
                             const bool use_RNA_averagine);
 
      IsotopeDistribution get(const double mass) const;
 
      int getMaxIsotopeIndex() const;
 
      void setMaxIsotopeIndex(const int index);
 
      Size getLeftCountFromApex(const double mass) const;
 
      Size getRightCountFromApex(const double mass) const;
 
      Size getApexIndex(const double mass) const;
 
      Size getLastIndex(const double mass) const;
 
      double getAverageMassDelta(const double mass) const;
 
      double getMostAbundantMassDelta(const double mass) const;
    };
 
    struct OPENMS_DLLAPI TopPicItem
    {
    public:
      TopPicItem() = default;
 
      explicit TopPicItem(String in);
 
      String str;
      int prsm_id;
      int spec_id;
      int scan;
      double rt;
      int peak_count;
      int charge;
      double precursor_mass;
      double adj_precursor_mass;
      int proteform_id = -1;
      String protein_acc = "";
      int first_residue;
      int last_residue;
      std::vector<double> unexp_mod;
      int matched_peaks;
      int matched_frags;
      double e_value;
      double spec_q_value;
      double proteofrom_q_value;
      double intensity;
 
      bool operator<(const TopPicItem& a) const;
 
      bool operator>(const TopPicItem& a) const;
 
      bool operator==(const TopPicItem& other) 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;
      double 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, const 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(const double mz, const bool positive);
 
    static double getChargeMass(const bool positive);
 
  };
}