SwathFile.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: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/config.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/DATASTRUCTURES/TypeAliases.h>
#include <OpenMS/KERNEL/StandardTypes.h>
 
#include <vector>
#include <memory>
#include <limits>
 
namespace OpenMS
{
  class ExperimentalSettings;
 
  struct OPENMS_DLLAPI FAIMSSwathMapGroup
  {
    double faims_cv{std::numeric_limits<double>::quiet_NaN()};
    std::vector<OpenSwath::SwathMap> swath_maps;
  };
 
  namespace Interfaces
  {
    class IMSDataConsumer;
  }
  
 
  class OPENMS_DLLAPI SwathFile :
    public ProgressLogger
  {
public:
 
    std::vector<OpenSwath::SwathMap> loadSplit(StringList file_list,
                                               const std::string& tmp,
                                               std::shared_ptr<ExperimentalSettings>& exp_meta, 
                                               const std::string& readoptions = "normal");
 
    std::vector<OpenSwath::SwathMap> loadMzML(const std::string& file, 
                                              const std::string& tmp,
                                              std::shared_ptr<ExperimentalSettings>& exp_meta,
                                              const std::string& readoptions = "normal",
                                              Interfaces::IMSDataConsumer* plugin_consumer = nullptr);
 
    std::vector<OpenSwath::SwathMap> loadFromMSExperiment(const std::shared_ptr<PeakMap>& exp,
                                                          const std::string& tmp,
                                                          std::shared_ptr<ExperimentalSettings>& exp_meta,
                                                          const std::string& readoptions = "normal");
 
    std::vector<FAIMSSwathMapGroup> loadFromMSExperimentByFAIMSCV(
      PeakMap&& exp,
      const std::string& tmp,
      std::shared_ptr<ExperimentalSettings>& exp_meta,
      const std::string& readoptions = "normal");
 
    std::vector<OpenSwath::SwathMap> loadMzXML(const std::string& file,
                                               const std::string& tmp,
                                               std::shared_ptr<ExperimentalSettings>& exp_meta,
                                               const std::string& readoptions = "normal");
 
    std::vector<OpenSwath::SwathMap> loadSqMass(const std::string& file, std::shared_ptr<ExperimentalSettings>& /* exp_meta */);
 
#ifdef WITH_OPENTIMS
    std::vector<OpenSwath::SwathMap> loadBrukerTdf(const std::string& file,
                                                    const std::string& tmp,
                                                    std::shared_ptr<ExperimentalSettings>& exp_meta,
                                                    const std::string& readoptions);
 
    std::vector<OpenSwath::SwathMap> loadBrukerTdf(const std::string& file,
                                                    std::shared_ptr<ExperimentalSettings>& exp_meta);
#endif
 
protected:
 
    OpenSwath::SpectrumAccessPtr doCacheFile_(const std::string& in, const std::string& tmp, const std::string& tmp_fname,
                                              const std::shared_ptr<PeakMap >& experiment_metadata);
 
    std::shared_ptr< PeakMap > populateMetaData_(const std::string& file);
 
    void countScansInSwath_(const std::vector<MSSpectrum>& exp,
                            std::vector<int>& swath_counter, int& nr_ms1_spectra, 
                            std::vector<OpenSwath::SwathMap>& known_window_boundaries,
                            double TOLERANCE=1e-6);
 
  };
}