MascotXMLHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Nico Pfeifer $
// $Authors: Nico Pfeifer, Chris Bielow $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
#define OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H

#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/DATASTRUCTURES/Map.h>

#include <vector>

namespace OpenMS
{
  namespace Internal
  {
    class OPENMS_DLLAPI MascotXMLHandler :
      public XMLHandler
    {
public:

      typedef Map<String, Real> RTMapping;

      MascotXMLHandler(ProteinIdentification & protein_identification,
                       std::vector<PeptideIdentification> & identifications,
                       const String & filename,
                       std::map<String, std::vector<AASequence> > & peptides,
                       const RTMapping & rt_mapping = RTMapping());

      virtual ~MascotXMLHandler();

      // Docu in base class
      virtual void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);

      // Docu in base class
      virtual void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);

      // Docu in base class
      virtual void characters(const XMLCh * const chars, const XMLSize_t /*length*/);

private:

      ProteinIdentification & protein_identification_;  
      std::vector<PeptideIdentification> & id_data_;     
      ProteinHit actual_protein_hit_;
      PeptideHit actual_peptide_hit_;
      UInt peptide_identification_index_;
      String tag_;
      DateTime date_;
      String date_time_string_;
      UInt actual_query_;
      ProteinIdentification::SearchParameters search_parameters_;
      String identifier_;
      String actual_title_;
      std::map<String, std::vector<AASequence> > & modified_peptides_;
      String warning_msg_;

      StringList tags_open_;       
      String major_version_;
      String minor_version_;

      const RTMapping & rt_mapping_; 


    };

  }   // namespace Internal
} // namespace OpenMS

#endif // OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H