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InspectInfile.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_INSPECTINFILE_H
00028 #define OPENMS_FORMAT_INSPECTINFILE_H
00029 
00030 #include <OpenMS/DATASTRUCTURES/String.h>
00031 #include <OpenMS/CONCEPT/Exception.h>
00032 
00033 #include <map>
00034 
00035 
00036 namespace OpenMS
00037 {
00045   class InspectInfile
00046   {
00047     public:
00048       
00050       InspectInfile();
00051 
00053       InspectInfile(const InspectInfile& inspect_infile);
00054 
00056       virtual ~InspectInfile();
00057 
00059       InspectInfile& operator=(const InspectInfile& inspect_infile);
00060 
00062       bool operator==(const InspectInfile& inspect_infile) const;
00063 
00065       void store(const String& filename) throw (Exception::UnableToCreateFile);
00066 
00068       void handlePTMs(const String& modification_line, const String& modifications_filename, const bool monoisotopic) throw (Exception::FileNotReadable, Exception::FileNotFound, Exception::ParseError);
00069       
00075       const std::string& getSpectra() const;
00076       void setSpectra(const std::string& spectra);
00077       
00083       const String& getDb() const;
00084       void setDb(const String& db);
00085       
00087       const String& getEnzyme() const;
00088       void setEnzyme(const String& enzyme);
00089       
00091       Int getModificationsPerPeptide() const;
00092       void setModificationsPerPeptide(Int modifications_per_peptide);
00093       
00099       UInt getBlind() const;
00100       void setBlind(UInt blind);
00101       
00107       const Real getMaxPTMsize() const;
00108       void setMaxPTMsize(Real maxptmsize);
00109       
00115       const Real getPrecursorMassTolerance() const;
00116       void setPrecursorMassTolerance(Real precursor_mass_tolerance);
00117       
00123       const Real getPeakMassTolerance() const;
00124       void setPeakMassTolerance(Real peak_mass_tolerance);
00125       
00127       UInt getMulticharge() const;
00128       void setMulticharge(UInt multicharge);
00129       
00131       const String& getInstrument() const;
00132       void setInstrument(const String& instrument);
00133       
00135       Int getTagCount() const;
00136       void setTagCount(Int TagCount);
00137 
00139       const std::map< String, std::vector< String > >& getModifications() const;
00140       
00141     private:
00142       
00143       String spectra_; 
00144 
00145       String db_; 
00146 
00147       String enzyme_; 
00148 
00149       Int modifications_per_peptide_; 
00150 
00151       UInt blind_; 
00152 
00153 
00154       Real maxptmsize_; 
00155 
00156       Real precursor_mass_tolerance_; 
00157 
00158       Real peak_mass_tolerance_; 
00159       
00160       UInt multicharge_; 
00161 
00162 
00163       String instrument_; 
00164 
00165       Int tag_count_; 
00166       
00167       std::map< String, std::vector< String > > PTMname_residues_mass_type_;
00168     
00169   };
00170 
00171 } // namespace OpenMS
00172 
00173 #endif // OPENMS_FORMAT_INSPECTINFILE_H

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