ThermoRawScanReader.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: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FORMAT/ThermoRawFile.h>
 
#include <functional>
#include <memory>
#include <string>
#include <vector>
 
namespace OpenMS
{
  class DataProcessing;
  class ExperimentalSettings;
  class MSChromatogram;
  class MSSpectrum;
 
namespace Internal
{
  class OPENMS_DLLAPI ThermoRawScanReader
  {
  public:
    using Options = ThermoRawFile::Options;
 
    struct ScanInfo
    {
      int scan = 0;          
      int ms_level = 0;      
      double rt = 0.0;       
      double tic = 0.0;      
      double precursor_mz = 0.0; 
    };
 
    using ParentLookup = std::function<const MSSpectrum*(int scan)>;
 
    ThermoRawScanReader(const std::string& path, const Options& options);
    ~ThermoRawScanReader();
    ThermoRawScanReader(const ThermoRawScanReader&) = delete;
    ThermoRawScanReader& operator=(const ThermoRawScanReader&) = delete;
 
    bool hasMSData() const;
    int firstScan() const;
    int lastScan() const;
 
    void fillSettings(ExperimentalSettings& settings) const;
 
    const ScanInfo& header(int scan, bool with_peaks = false);
 
    void readAhead(int last_scan, int peaks_from);
 
    void scanHeaders(int first, int last, bool precursors, const std::function<bool(const ScanInfo&)>& visit);
 
    void convert(MSSpectrum& spectrum, ExperimentalSettings& settings, const ParentLookup& parent, bool peaks);
 
    void addInstrumentConfigurations(ExperimentalSettings& settings);
 
    std::shared_ptr<DataProcessing> dataProcessing() const;
 
    MSChromatogram ticChromatogram() const;
 
    void readDetectors(std::vector<MSChromatogram>& chromatograms, std::vector<MSSpectrum>& spectra);
 
  private:
    struct Impl;
    std::unique_ptr<Impl> impl_;
  };
} // namespace Internal
} // namespace OpenMS