MzMLSqliteHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/ExperimentalSettings.h>

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

// forward declarations
struct sqlite3;
struct sqlite3_stmt;

namespace OpenMS
{
  class ProgressLogger;

  namespace Internal
  {

    class OPENMS_DLLAPI MzMLSqliteHandler
    {

public:

      MzMLSqliteHandler(String filename);


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

      void readSpectra(std::vector<MSSpectrum> & exp, const std::vector<int> & indices, bool meta_only = false) const;

      void readChromatograms(std::vector<MSChromatogram> & exp, const std::vector<int> & indices, bool meta_only = false) const;

      Size getNrSpectra() const;

      Size getNrChromatograms() const;

      void setConfig(bool write_full_meta, bool use_lossy_compression, double linear_abs_mass_acc, int sql_batch_size = 500) 
      {
        write_full_meta_ = write_full_meta;
        use_lossy_compression_ = use_lossy_compression;
        linear_abs_mass_acc_ = linear_abs_mass_acc; 
        sql_batch_size_ = sql_batch_size; 
      }

      std::vector<size_t> getSpectraIndicesbyRT(double RT, double deltaRT, const std::vector<int> & indices) const;

protected:

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

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

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

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

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

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

public:


      void writeExperiment(const MSExperiment & exp);

      void createTables();
      void createIndices();

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

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

      void writeRunLevelInformation(const MSExperiment & exp, bool write_full_meta, int run_id);

protected:

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

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

      sqlite3* openDB() const;

      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.
       *
       * However, currently they are initialized to zero when opening a new
       * file, so appending to an existing file won't work.
      */
      Int spec_id_;
      Int chrom_id_;
      Int run_id_;

      bool use_lossy_compression_;
      double linear_abs_mass_acc_; 
      double write_full_meta_; 
      int sql_batch_size_; 
    };


  } // namespace Internal
} // namespace OpenMS