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 2002-2017.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest
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#pragma once

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/FORMAT/Base64.h>
#include <OpenMS/FORMAT/MSNumpressCoder.h>

#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>

// forward declarations
struct sqlite3;

namespace OpenMS
{
  class ProgressLogger;

  namespace Internal
  {

    class OPENMS_DLLAPI MzMLSqliteSwathHandler
    {

public:

      MzMLSqliteSwathHandler(String filename) :
        filename_(filename)
      {}

      std::vector<OpenSwath::SwathMap> readSwathWindows();

      std::vector<int> readMS1Spectra();

      std::vector<int> readSpectraForWindow(OpenSwath::SwathMap swath_map);

protected:

      sqlite3* openDB();

      String filename_;

      Base64 base64coder_;
      MSNumpressCoder numpress_coder_;

      /*
       * 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