text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2016.
  //
  // 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: Andreas Bertsch $
  // $Authors: Andreas Bertsch $
  // --------------------------------------------------------------------------
  
  #ifndef OPENMS_FORMAT_XTANDEMXMLFILE_H
  #define OPENMS_FORMAT_XTANDEMXMLFILE_H
  
  #include <OpenMS/METADATA/PeptideIdentification.h>
  #include <OpenMS/FORMAT/XMLFile.h>
  #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
  #include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
  
  #include <vector>
  
  namespace OpenMS
  {
    class String;
    class ProteinIdentification;
  
    /**
      @brief Used to load XTandemXML files
  
      This class is used to load documents that implement
      the schema of XTandemXML files.
  
      @ingroup FileIO
    */
    class OPENMS_DLLAPI XTandemXMLFile :
      protected Internal::XMLHandler,
      public Internal::XMLFile
    {
  public:
  
      /// Default constructor
      XTandemXMLFile();
  
      /// Destructor
      virtual ~XTandemXMLFile();
      /**
        @brief loads data from a XTandemXML file
  
        @param filename the file to be loaded
        @param protein_identification protein identifications belonging to the whole experiment
        @param id_data the identifications with m/z and RT
  
        This class serves to read in a XTandemXML file. The information can be
        retrieved via the load function.
  
        @ingroup FileIO
      */
      void load(const String & filename, ProteinIdentification & protein_identification, std::vector<PeptideIdentification> & id_data);
  
  
      /// sets the valid modifications
      void setModificationDefinitionsSet(const ModificationDefinitionsSet & rhs);
  
  protected:
  
      // Docu in base class
      void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);
  
      // Docu in base class
      void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);
  
      // Docu in base class
      void characters(const XMLCh * const chars, const XMLSize_t /*length*/);
  
      XTandemXMLFile(const XTandemXMLFile & rhs);
  
      XTandemXMLFile & operator=(const XTandemXMLFile & rhs);
  
  private:
  
      ProteinIdentification * protein_identification_;
  
      // used to indicate that an protein tag is open
      bool protein_open_;
  
      // true if actual
      bool is_description_;
  
      // peptide hits of one spectrum
      Map<UInt, std::vector<PeptideHit> > peptide_hits_;
  
      // protein hits, sorted by the id
      Map<String, ProteinHit> protein_hits_;
  
      // id of the actual protein
      String actual_protein_id_;
  
      // charge of actual peptide
      Int actual_charge_;
  
      // id of actual peptide
      Int actual_id_;
  
      // tag
      String tag_;
  
      // actual start position of peptide in protein sequence
      UInt actual_start_;
  
      // actual stop position of peptide in protein sequence
      UInt actual_stop_;
  
      // modification definitions
      ModificationDefinitionsSet mod_def_set_;
  
    };
  
  } // namespace OpenMS
  
  #endif // OPENMS_FORMAT_XTANDEMXMLFILE_H
  