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IdXMLFile.h (Maintainer: Marc Sturm)

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00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 // --------------------------------------------------------------------------
00005 //                   OpenMS Mass Spectrometry Framework
00006 // --------------------------------------------------------------------------
00007 //  Copyright (C) 2003-2008 -- Oliver Kohlbacher, Knut Reinert
00008 //
00009 //  This library is free software; you can redistribute it and/or
00010 //  modify it under the terms of the GNU Lesser General Public
00011 //  License as published by the Free Software Foundation; either
00012 //  version 2.1 of the License, or (at your option) any later version.
00013 // 
00014 //  This library is distributed in the hope that it will be useful,
00015 //  but WITHOUT ANY WARRANTY; without even the implied warranty of
00016 //  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
00017 //  Lesser General Public License for more details.
00018 //
00019 //  You should have received a copy of the GNU Lesser General Public
00020 //  License along with this library; if not, write to the Free Software
00021 //  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
00022 //
00023 // --------------------------------------------------------------------------
00024 // $Maintainer: Marc Sturm $
00025 // --------------------------------------------------------------------------
00026 
00027 #ifndef OPENMS_FORMAT_IDXMLFILE_H
00028 #define OPENMS_FORMAT_IDXMLFILE_H
00029 
00030 #include <OpenMS/METADATA/ProteinIdentification.h>
00031 #include <OpenMS/METADATA/PeptideIdentification.h>
00032 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
00033 #include <OpenMS/FORMAT/XMLFile.h>
00034 
00035 #include <vector>
00036 
00037 namespace OpenMS 
00038 {
00055   class IdXMLFile
00056     : protected Internal::XMLHandler,
00057       public Internal::XMLFile
00058   {
00059     public:
00060     
00062       IdXMLFile();
00063       
00070       void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids) throw (Exception::FileNotFound, Exception::ParseError);
00071              
00077       void store(String filename, const std::vector<ProteinIdentification>& protein_ids, const std::vector<PeptideIdentification>& peptide_ids) throw (Exception::UnableToCreateFile); 
00078     
00079     protected:
00080       // Docu in base class
00081       virtual void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname);
00082       
00083       // Docu in base class
00084       virtual void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes);
00085       
00087 
00088 
00089       std::vector<ProteinIdentification>* prot_ids_;
00091       std::vector<PeptideIdentification>* pep_ids_;
00093       MetaInfoInterface* last_meta_;
00095       std::map<String,ProteinIdentification::SearchParameters> parameters_;
00097       ProteinIdentification::SearchParameters param_;
00099       String id_;
00101       ProteinIdentification prot_id_;
00103       PeptideIdentification pep_id_;
00105       ProteinHit prot_hit_;
00107       PeptideHit pep_hit_;
00109       std::map<String,String> proteinid_to_accession_;
00110       
00112   };
00113  
00114 } // namespace OpenMS
00115 
00116 #endif // OPENMS_FORMAT_IDXMLFILE_H

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