MzMLSqliteHandler.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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#ifndef OPENMS_FORMAT_HANDLERS_MZMLSQLITEHANDLER_H
#define OPENMS_FORMAT_HANDLERS_MZMLSQLITEHANDLER_H

#include <OpenMS/KERNEL/MSExperiment.h>

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

// forward declarations
struct sqlite3;

namespace OpenMS
{
  class ProgressLogger;

  namespace Internal
  {

    class OPENMS_DLLAPI MzMLSqliteHandler
    {

public:

      MzMLSqliteHandler(String filename);


      void readExperiment(MSExperiment & exp, bool meta_only = false);

protected:

      void populateChromatogramsWithData_(sqlite3 *db, std::vector<MSChromatogram >& chromatograms);

      void populateSpectraWithData_(sqlite3 *db, std::vector<MSSpectrum>& spectra);

      void prepareChroms_(sqlite3 *db, std::vector<MSChromatogram >& chromatograms);

      void prepareSpectra_(sqlite3 *db, std::vector<MSSpectrum>& spectra);

public:


      void writeExperiment(const MSExperiment & exp);

      void createTables();

      void writeSpectra(const std::vector<MSSpectrum>& spectra);

      void writeChromatograms(const std::vector<MSChromatogram >& chroms);

protected:

      void executeBlobBind_(sqlite3 *db, String& prepare_statement, std::vector<String>& data);

      void executeSql_(sqlite3 *db, const std::stringstream& statement);

      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

#endif // OPENMS_FORMAT_HANDLERS_MZMLSQLITEHANDLER_H