SwathFile.h

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// Copyright (c) 2002-2023, The OpenMS Team -- 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/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/KERNEL/StandardTypes.h>
 
#include <vector>
#include <boost/shared_ptr.hpp>
 
namespace OpenMS
{
  class ExperimentalSettings;
  namespace Interfaces
  {
    class IMSDataConsumer;
  }
  
 
  class OPENMS_DLLAPI SwathFile :
    public ProgressLogger
  {
public:
 
    std::vector<OpenSwath::SwathMap> loadSplit(StringList file_list,
                                               const String& tmp,
                                               boost::shared_ptr<ExperimentalSettings>& exp_meta, 
                                               const String& readoptions = "normal");
 
    std::vector<OpenSwath::SwathMap> loadMzML(const String& file, 
                                              const String& tmp,
                                              boost::shared_ptr<ExperimentalSettings>& exp_meta,
                                              const String& readoptions = "normal",
                                              Interfaces::IMSDataConsumer* plugin_consumer = nullptr);
 
    std::vector<OpenSwath::SwathMap> loadMzXML(const String& file, 
                                               const String& tmp,
                                               boost::shared_ptr<ExperimentalSettings>& exp_meta,
                                               const String& readoptions = "normal");
 
    std::vector<OpenSwath::SwathMap> loadSqMass(const String& file, boost::shared_ptr<ExperimentalSettings>& /* exp_meta */);
 
protected:
 
    OpenSwath::SpectrumAccessPtr doCacheFile_(const String& in, const String& tmp, const String& tmp_fname,
                                              const boost::shared_ptr<PeakMap >& experiment_metadata);
 
    boost::shared_ptr< PeakMap > populateMetaData_(const 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);
 
  };
}