text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2021.
  //
  // 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,
  // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
  // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
  // 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: Chris Bielow $
  // $Authors: Marc Sturm, Chris Bielow, Clemens Groepl $
  // --------------------------------------------------------------------------
  
  #pragma once
  
  #include <OpenMS/FORMAT/OPTIONS/FeatureFileOptions.h>
  #include <OpenMS/FORMAT/XMLFile.h>
  #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
  #include <OpenMS/CONCEPT/ProgressLogger.h>
  #include <OpenMS/METADATA/ProteinIdentification.h>
  #include <OpenMS/METADATA/PeptideIdentification.h>
  #include <OpenMS/DATASTRUCTURES/ConvexHull2D.h>
  #include <OpenMS/DATASTRUCTURES/Param.h>
  #include <OpenMS/DATASTRUCTURES/Map.h>
  
  #include <iosfwd>
  
  namespace OpenMS
  {
    class Feature;
    class FeatureMap;
  
    namespace Internal
    {
  
    /**
      @brief This class provides Input/Output functionality for feature maps
  
      A documented schema for this format can be found at https://github.com/OpenMS/OpenMS/tree/develop/share/OpenMS/SCHEMAS
  
      @todo Take care that unique ids are assigned properly by TOPP tools before
      calling FeatureXMLFile::store().  There will be a message on OPENMS_LOG_INFO but
      we will make no attempt to fix the problem in this class.  (all developers)
  
      @note This format will eventually be replaced by the HUPO-PSI AnalysisXML
      (mzIdentML and mzQuantML) formats!
  
      @ingroup FileIO
    */
    class OPENMS_DLLAPI FeatureXMLHandler :
      public Internal::XMLHandler,
      public ProgressLogger
    {
  
  public:
  
      /** @name Constructors and Destructor */
      //@{
      ///Default constructor
      FeatureXMLHandler(FeatureMap& map, const String& filename);
      FeatureXMLHandler(const FeatureMap& map, const String& filename);
      ///Destructor
      ~FeatureXMLHandler() override;
      //@}
  
  
      /// Docu in base class XMLHandler::writeTo
      void writeTo(std::ostream& os) override;
  
      /// Mutable access to the options for loading/storing
      FeatureFileOptions& getOptions();
  
      /// Non-mutable access to the options for loading/storing
      const FeatureFileOptions& getOptions() const;
  
      /// setter for options for loading/storing
      void setOptions(const FeatureFileOptions&);
  
      void setSizeOnly(const bool size_only)
      {
        size_only_ = size_only;
      }
  
      Size getSize() const
      {
        return expected_size_;
      }
  
  protected:
  
      // restore default state for next load/store operation
      void resetMembers_();
  
      // Docu in base class
      void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
  
      // Docu in base class
      void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
  
      // Docu in base class
      void characters(const XMLCh* const chars, const XMLSize_t length) override;
  
      /// Writes a feature to a stream
      void writeFeature_(const String& filename, std::ostream& os, const Feature& feat, const String& identifier_prefix, UInt64 identifier, UInt indentation_level);
  
      /// Writes a peptide identification to a stream (for assigned/unassigned peptide identifications)
      void writePeptideIdentification_(const String& filename, std::ostream& os, const PeptideIdentification& id, const String& tag_name, UInt indentation_level);
  
      /**
          @brief update the pointer to the current feature
  
          @param create If true, a new (empty) Feature is added at the appropriate subordinate_feature_level_
      */
      void updateCurrentFeature_(bool create);
  
      /// allows for early return in parsing functions when certain sections should be ignored
      /// <=0 - parsing ON
      ///  >0 - this number of tags have been entered that forbid parsing and need to be exited before parsing continues
      Int disable_parsing_;
  
      /// points to the last open &lt;feature&gt; tag (possibly a subordinate feature)
      Feature* current_feature_;
      /// Feature map pointer for writing
      FeatureMap* map_;
      /// Feature map pointer for reading
      const FeatureMap* cmap_;
      /// Options that can be set
      FeatureFileOptions options_;
      /// only parse until "count" tag is reached (used in loadSize())
      bool size_only_;
      /// holds the putative size given in count
      Size expected_size_;
  
      /**@name temporary data structures to hold parsed data */
      //@{
      Param param_;
      ConvexHull2D::PointArrayType current_chull_;
      DPosition<2> hull_position_;
      //@}
  
      /// current dimension of the feature position, quality, or convex hull point
      UInt dim_;
  
      /// for downward compatibility, all tags in the old description must be ignored
      bool in_description_;
  
      /// level in Feature stack during parsing
      Int subordinate_feature_level_;
  
      /// Pointer to last read object as a MetaInfoInterface, or null.
      MetaInfoInterface* last_meta_;
  
      /// Temporary protein ProteinIdentification
      ProteinIdentification prot_id_;
      /// Temporary peptide ProteinIdentification
      PeptideIdentification pep_id_;
      /// Temporary protein hit
      ProteinHit prot_hit_;
      /// Temporary peptide hit
      PeptideHit pep_hit_;
      /// Map from protein id to accession
      Map<String, String> proteinid_to_accession_;
      /// Map from search identifier concatenated with protein accession to id
      Map<String, Size> accession_to_id_;
      /// Map from identification run identifier to file xs:id (for linking peptide identifications to the corresponding run)
      Map<String, String> identifier_id_;
      /// Map from file xs:id to identification run identifier (for linking peptide identifications to the corresponding run)
      Map<String, String> id_identifier_;
      /// Temporary search parameters file
      ProteinIdentification::SearchParameters search_param_;
  
    };
  
  } // namespace Internal
  } // namespace OpenMS
  
  