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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