FLASHHelperClasses.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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/FEATUREFINDER/MassTraceDetection.h>
#include <boost/dynamic_bitset.hpp>
 
namespace OpenMS
{
  struct OPENMS_DLLAPI FLASHHelperClasses
  {
    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<double> snr_mul_factor_;
      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, double decoy_iso_distance = -1);
 
      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;
 
      double getSNRMultiplicationFactor(double mass) const;
    };
 
    struct OPENMS_DLLAPI MassFeature
    {
    public:
      uint index;
      MassTrace mt;
      std::vector<float> per_charge_intensity;
      std::vector<float> per_isotope_intensity;
      int iso_offset;
      int scan_number, min_scan_number, max_scan_number, rep_charge;
      double avg_mass;
      int min_charge, max_charge, charge_count;
      double isotope_score, qscore;
      double rep_mz;
      bool is_decoy;
      uint ms_level;
      bool operator<(const MassFeature& a) const
      {
        return avg_mass < a.avg_mass;
      }
      bool operator>(const MassFeature& a) const
      {
        return avg_mass > a.avg_mass;
      }
      bool operator==(const MassFeature& other) const
      {
        return avg_mass == other.avg_mass;
      }
    };
 
    struct OPENMS_DLLAPI IsobaricQuantities
    {
    public:
      int scan;
      double rt;
      double precursor_mz;
      double precursor_mass;
      std::vector<double> quantities;
      std::vector<double> merged_quantities;
      bool empty() const;
    };
 
    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() const;
 
      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);
  };
} // namespace OpenMS