MzMLSqliteSwathHandler.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 2002-2020.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest
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#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
 
// forward declarations
struct sqlite3;
 
namespace OpenMS
{
 
  namespace Internal
  {
 
    class OPENMS_DLLAPI MzMLSqliteSwathHandler
    {
 
public:
 
      MzMLSqliteSwathHandler(const String& filename) :
        filename_(filename)
      {}
 
      std::vector<OpenSwath::SwathMap> readSwathWindows();
 
      std::vector<int> readMS1Spectra();
 
      std::vector<int> readSpectraForWindow(const OpenSwath::SwathMap & swath_map);
 
protected:
 
      String filename_;
 
      /*
       * These are spectra and chromatogram ids that are global for a specific
       * database file. Keeping track of them allows us to append spectra and
       * chromatograms multiple times to a database.
      */
      Int spec_id_;
      Int chrom_id_;
 
    };
 
 
  }   // namespace Internal
} // namespace OpenMS