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PepNovoOutfile.h (Maintainer: Martin Langwisch)

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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: Martin Langwisch $
00025 // --------------------------------------------------------------------------
00026 
00027 #ifndef OPENMS_FORMAT_PEPNOVOOUTFILE_H
00028 #define OPENMS_FORMAT_PEPNOVOOUTFILE_H
00029 
00030 #include <OpenMS/CONCEPT/Exception.h>
00031 #include <OpenMS/DATASTRUCTURES/String.h>
00032 #include <OpenMS/METADATA/PeptideIdentification.h>
00033 #include <OpenMS/METADATA/PeptideHit.h>
00034 #include <OpenMS/METADATA/ProteinHit.h>
00035 #include <OpenMS/METADATA/ProteinIdentification.h>
00036 
00037 #include <vector>
00038 #include <map>
00039 
00040 namespace OpenMS
00041 {
00050   class PepNovoOutfile
00051   {
00052     public:
00054       PepNovoOutfile();
00055 
00057       PepNovoOutfile(const PepNovoOutfile& pepnovo_outfile);
00058 
00060       virtual ~PepNovoOutfile();
00061 
00063       PepNovoOutfile& operator=(const PepNovoOutfile& pepnovo_outfile);
00064 
00066       bool operator==(const PepNovoOutfile& pepnovo_outfile) const;
00067 
00080       void load(const std::string& result_filename, std::vector< PeptideIdentification >& peptide_identifications, ProteinIdentification& protein_identification, const Real& p_value_threshold, const std::map< String, Real >& dta_filenames_and_precursor_retention_times) throw (Exception::FileNotFound, Exception::ParseError);
00081 
00083       void getSearchEngineAndVersion(const String& pepnovo_output_without_parameters_filename, ProteinIdentification& protein_identification) throw (Exception::FileNotFound);
00084 
00085   };
00086 
00087 } //namespace OpenMS
00088 
00089 #endif // OPENMS_FORMAT_PEPNOVOOUTFILE_H
00090 

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