text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2017.
  //
  // 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: George Rosenberger $
  // $Authors: George Rosenberger $
  // --------------------------------------------------------------------------
  
  #ifndef OPENMS_FORMAT_OSWFILE_H
  #define OPENMS_FORMAT_OSWFILE_H
  
  #include <OpenMS/CONCEPT/Exception.h>
  #include <OpenMS/DATASTRUCTURES/String.h>
  #include <OpenMS/KERNEL/StandardTypes.h>
  #include <sqlite3.h>
  
  #include <map>
  
  namespace OpenMS
  {
    /**
      @brief This class serves for reading in and writing OpenSWATH OSW files.
  
      The reader and writer returns data in a format suitable for PercolatorAdapter.
      OSW files have a flexible data structure. They contain all peptide query
      parameters of TraML/PQP files with the detected and quantified features of
      OpenSwathWorkflow (feature, feature_ms1, feature_ms2 & feature_transition).
  
      The OSWFile reader extracts the feature information from the OSW file for
      each level (MS1, MS2 & transition) separately and generates Percolator input
      files. For each of the three Percolator reports, OSWFile writer adds a table
      (score_ms1, score_ms2, score_transition) with the respective confidence metrics.
      These tables can be mapped to the corresponding feature tables, are very similar
      to PyProphet results and can thus be used interchangeably.
      
    */
    class OPENMS_DLLAPI OSWFile
    {
  public:
      /// Default constructor
      OSWFile();
  
      /// Destructor
      virtual ~OSWFile();
  
      /**
        @brief Reads an OSW SQLite file and returns the data on MS1-, MS2- or transition-level
        as stringstream TXT input for PercolatorAdapter.
      */
      void read(const std::string& in_osw, const std::string& osw_level, std::stringstream& pin_output, const double& ipf_max_peakgroup_pep, const double& ipf_max_transition_isotope_overlap, const double& ipf_min_transition_sn);
  
      /**
      @brief Updates an OpenSWATH OSW SQLite files with the MS1-, MS2- or transition-level results of Percolator.
      */
      void write(const std::string& in_osw, const std::string& osw_level, const std::map< std::string, std::vector<double> >& features);
  
  private:
      /**
      @brief Helper function for writing OSW SQLite files
      */
      static int callback(void * /* NotUsed */, int argc, char **argv, char **azColName);
  
    };
  
  } // namespace OpenMS
  
  #endif // OPENMS_FORMAT_OSWFILE_H
  