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Viewing changes to include/OpenMS/FORMAT/HANDLERS/MascotXMLHandler.h

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2012-11-12 15:58:12 UTC
  • Revision ID: package-import@ubuntu.com-20121112155812-vr15wtg9b50cuesg
Tags: upstream-1.9.0
Import upstream version 1.9.0

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include/OpenMS/FORMAT/HANDLERS/MascotXMLHandler.h
 
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// -*- mode: C++; tab-width: 2; -*-
 
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// vi: set ts=2:
 
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//
 
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// --------------------------------------------------------------------------
 
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//                   OpenMS Mass Spectrometry Framework
 
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// --------------------------------------------------------------------------
 
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//  Copyright (C) 2003-2011 -- Oliver Kohlbacher, Knut Reinert
 
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//
 
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//  This library is free software; you can redistribute it and/or
 
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//  modify it under the terms of the GNU Lesser General Public
 
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//  License as published by the Free Software Foundation; either
 
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//  version 2.1 of the License, or (at your option) any later version.
 
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// 
 
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//  This library is distributed in the hope that it will be useful,
 
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//  but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
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//  Lesser General Public License for more details.
 
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//
 
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//  You should have received a copy of the GNU Lesser General Public
 
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//  License along with this library; if not, write to the Free Software
 
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//  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
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//
 
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// --------------------------------------------------------------------------
 
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// $Maintainer: Nico Pfeifer $
 
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// $Authors: Nico Pfeifer, Chris Bielow $
 
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// --------------------------------------------------------------------------
 
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#ifndef OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
 
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#define OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H
 
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#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
 
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#include <OpenMS/CHEMISTRY/AASequence.h>
 
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#include <OpenMS/METADATA/ProteinIdentification.h>
 
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#include <OpenMS/METADATA/PeptideIdentification.h>
 
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#include <vector>
 
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namespace OpenMS
 
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{
 
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        namespace Internal
 
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        {
 
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  /**
 
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    @brief Handler that is used for parsing MascotXML data
 
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  */
 
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  class OPENMS_DLLAPI MascotXMLHandler:
 
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    public XMLHandler
 
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  {
 
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    public:
 
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      /// Constructor
 
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      MascotXMLHandler(ProteinIdentification& protein_identification, std::vector<PeptideIdentification>& identifications, const String& filename, std::map<String, std::vector<AASequence> >& peptides);
 
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      /// Destructor
 
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      virtual ~MascotXMLHandler();
 
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                        // Docu in base class
 
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      virtual void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname);
 
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                        // Docu in base class
 
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      virtual void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes);
 
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                        // Docu in base class
 
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      virtual void characters(const XMLCh* const chars, const XMLSize_t /*length*/);
 
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    private:
 
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        ProteinIdentification& protein_identification_; ///< the protein identifications
 
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      std::vector<PeptideIdentification>& id_data_;             ///< the identifications (storing the peptide hits)
 
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      ProteinHit actual_protein_hit_;                                                                                           
 
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      PeptideHit actual_peptide_hit_;
 
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                        UInt peptide_identification_index_;
 
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                        String tag_;
 
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                        DateTime date_;
 
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                        String date_time_string_;
 
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                        UInt actual_query_;
 
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                        ProteinIdentification::SearchParameters search_parameters_;
 
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                        String identifier_;
 
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                        String actual_title_;
 
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                        std::map<String, std::vector<AASequence> >& modified_peptides_;
 
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      String warning_msg_;
 
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                        StringList tags_open_; ///< tracking the current XML tree
 
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                        String major_version_;
 
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                        String minor_version_;
 
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  };
 
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        } // namespace Internal
 
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} // namespace OpenMS
 
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#endif // OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_H