ThermoRawFileMetadata.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: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
#pragma once
 
#include <OpenMS/OpenMSConfig.h>
 
#include <cstddef>
#include <map>
#include <optional>
#include <string>
#include <string_view>
#include <vector>
 
namespace OpenMS::Internal
{
struct OPENMS_DLLAPI ThermoTrailerEntry
{
  std::string label; 
  std::string value; 
};
 
struct OPENMS_DLLAPI ThermoReaction
{
  std::optional<double> precursor_mass;   
  std::optional<double> isolation_width;  
  std::optional<double> isolation_offset; 
  std::string activation;                 
  std::optional<double> collision_energy; 
  bool collision_energy_valid = false;    
};
 
struct OPENMS_DLLAPI ThermoScan
{
  int scan_number = 0;                     
  int ms_level = 0;                        
  std::string filter;                      
  std::string native_id;                   
  std::vector<ThermoTrailerEntry> trailer; 
  std::vector<ThermoReaction> reactions;   
};
 
class OPENMS_DLLAPI ThermoTrailerIndex
{
public:
  using Key = std::size_t;
 
  Key add(const std::string& label);
 
  const std::string* find(const ThermoScan& scan, Key key);
 
  const std::string& value(const ThermoScan& scan, Key key);
 
private:
  static constexpr std::size_t npos_ = static_cast<std::size_t>(-1);
  std::vector<std::string> labels_;      
  std::vector<std::size_t> positions_;   
};
 
struct OPENMS_DLLAPI ThermoPrecursor
{
  double target_mz = 0.0;         
  double selected_mz = 0.0;       
  std::optional<int> charge;      
  std::optional<double> width;    
  double lower_offset = 0.0;      
  double upper_offset = 0.0;      
  int parent_scan = 0;            
  bool estimate_intensity = true; 
  std::string spectrum_ref;       
  ThermoReaction activation;      
  std::optional<ThermoReaction> supplemental; 
};
 
class OPENMS_DLLAPI ThermoRawFileMetadata
{
public:
  ThermoRawFileMetadata();
 
  static std::string trailer(const ThermoScan& scan, const std::string& label);
 
  static std::optional<double> number(std::string_view value);
 
  static std::string filterKey(const std::string& filter);
 
  static double selectedIon(double target, std::optional<double> mono, double width);
 
  std::vector<ThermoPrecursor> precursors(const ThermoScan& scan);
 
private:
  struct State
  {
    int level = 1;             
    int parent = 0;            
    std::size_t reactions = 0; 
    std::string native_id;     
    std::vector<ThermoPrecursor> own; 
  };
  std::map<int, State> scans_;         
  std::map<std::string, int> filters_; 
  ThermoTrailerIndex trailer_;         
  ThermoTrailerIndex::Key master_key_, charge_key_, mono_key_, sps_masses_key_;
  std::vector<ThermoTrailerIndex::Key> width_keys_; 
 
  static bool supplemental_(const ThermoReaction& first, const ThermoReaction& second);
  static std::size_t lastReaction_(const std::vector<ThermoReaction>& reactions);
  int parentFromFilter_(const std::string& key) const;
  std::vector<double> spsMasses_(const ThermoScan& scan);
  static bool isLegacySpsLabel_(const std::string& label);
  static bool isModernSpsLabel_(const std::string& label);
};
} // namespace OpenMS::Internal