MzMLSqliteHandler.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// 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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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 std::vector<int> & indices = {}) const;
 
      void prepareSpectra_(sqlite3 *db, std::vector<MSSpectrum>& spectra, const std::vector<int> & indices = {}) const;
 
public:
 
 
      void writeExperiment(const MSExperiment & exp);
 
      void createTables();
 
      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 createIndices_();
 
      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