ThermoRawFile.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/KERNEL/MSExperiment.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
 
#include <limits>
#include <vector>
 
namespace OpenMS
{
  namespace Interfaces
  {
    class IMSDataConsumer;
  }
 
  class OPENMS_DLLAPI ThermoRawFile : public ProgressLogger
  {
  public:
    struct Options
    {
      bool centroid = false; 
      bool charge_data = false; 
      bool noise_data = false; 
      bool all_detectors = false; 
      bool preserve_trailers = true; 
      bool instrument_methods = true; 
      bool checksum = true; 
 
      int first_scan = 0; 
      int last_scan = 0; 
      double rt_min = -std::numeric_limits<double>::infinity(); 
      double rt_max = std::numeric_limits<double>::infinity(); 
      std::vector<int> ms_levels; 
      double precursor_mz_min = -std::numeric_limits<double>::infinity();
      double precursor_mz_max = std::numeric_limits<double>::infinity(); 
 
      bool metadata_only = false;
      bool skip_chromatograms = false; 
    };
 
    const Options& getOptions() const { return options_; }
    void setOptions(const Options& options) { options_ = options; }
    void load(const std::string& path, MSExperiment& exp);
 
    void transform(const std::string& path, Interfaces::IMSDataConsumer* consumer);
 
  private:
    Options options_;
  };
 
} // namespace OpenMS
 
#endif // WITH_THERMO_RAW