OnDiscThermoRawExperiment.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/config.h>
 
#ifdef WITH_THERMO_RAW
 
#include <OpenMS/FORMAT/ThermoRawFile.h>
#include <OpenMS/KERNEL/IMSExperimentRandomAccess.h>
 
#include <memory>
#include <string>
 
namespace OpenMS
{
  class OPENMS_DLLAPI OnDiscThermoRawExperiment :
    public IMSExperimentRandomAccess
  {
  public:
    using Options = ThermoRawFile::Options;
 
    OnDiscThermoRawExperiment();
 
    OnDiscThermoRawExperiment(const OnDiscThermoRawExperiment& source);
 
    OnDiscThermoRawExperiment(OnDiscThermoRawExperiment&& source) noexcept;
 
    OnDiscThermoRawExperiment& operator=(const OnDiscThermoRawExperiment& source);
 
    OnDiscThermoRawExperiment& operator=(OnDiscThermoRawExperiment&& source) noexcept;
 
    ~OnDiscThermoRawExperiment() override;
 
    void openFile(const std::string& path, const Options& options = Options());
 
    bool isOpen() const;
 
    const std::string& getFilename() const;
 
    const Options& getOptions() const;
 
    Size getNrSpectra() const override;
    Size getNrChromatograms() const override;
 
    MSSpectrum getSpectrum(Size index) override;
 
    MSSpectrum operator[](Size index)
    {
      return getSpectrum(index);
    }
 
    MSSpectrum getSpectrumMetadata(Size index) override;
 
    MSSpectrum getSpectrumPeaks(Size index) override;
 
    MSSpectrum getSpectrumByNativeId(const std::string& native_id);
 
    double getSpectrumRT(Size index) const override;
    UInt getSpectrumMSLevel(Size index) const override;
 
    const std::string& getSpectrumNativeID(Size index) const;
 
    int getScanNumber(Size index) const;
 
    Size getSpectrumIndexByScanNumber(int scan) const;
 
    bool isSortedByRT() const override;
    Size findFirstRT(double rt) const override;
 
    MSChromatogram getChromatogram(Size index) override;
 
    std::shared_ptr<const ExperimentalSettings> getExperimentalSettings() const override;
 
    std::unique_ptr<IMSExperimentRandomAccess> clone() const override;
 
  private:
    struct Index;
    struct Handle;
    void checkIndex_(Size index) const;
    std::shared_ptr<const Index> index_;
    std::unique_ptr<Handle> handle_;
  };
} // namespace OpenMS
 
#endif // WITH_THERMO_RAW