SwathFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#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,
                                               String tmp,
                                               boost::shared_ptr<ExperimentalSettings>& exp_meta, 
                                               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(String file, 
                                               String tmp,
                                               boost::shared_ptr<ExperimentalSettings>& exp_meta,
                                               String readoptions = "normal");

    std::vector<OpenSwath::SwathMap> loadSqMass(String file, boost::shared_ptr<ExperimentalSettings>& /* exp_meta */);

protected:

    OpenSwath::SpectrumAccessPtr doCacheFile_(const String& in, const String& tmp, const String& tmp_fname,
                                              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);

  };
}