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_CHEMISTRY_ENZYMATICDIGESTION_H 00028 #define OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H 00029 00030 #include <OpenMS/CONCEPT/Types.h> 00031 #include <OpenMS/CHEMISTRY/AASequence.h> 00032 00033 #include <string> 00034 #include <vector> 00035 00036 namespace OpenMS 00037 { 00043 class EnzymaticDigestion 00044 { 00045 public: 00047 enum Enzyme 00048 { 00049 TRYPSIN, 00050 SIZE_OF_ENZYMES 00051 }; 00052 00054 static const std::string NamesOfEnzymes[SIZE_OF_ENZYMES]; 00055 00057 EnzymaticDigestion(); 00058 00060 UInt getMissedCleavages() const; 00061 00063 void setMissedCleavages(UInt missed_cleavages); 00064 00066 Enzyme getEnzyme() const; 00067 00069 void setEnzyme(Enzyme enzyme); 00070 00072 void digest(const AASequence& protein, std::vector<AASequence>& output); 00073 00075 UInt peptideCount(const AASequence& protein); 00076 00077 protected: 00079 UInt missed_cleavages_; 00081 Enzyme enzyme_; 00082 00084 void nextCleavageSite_(const AASequence& sequence, AASequence::ConstIterator& iterator); 00085 }; 00086 00087 } // namespace OpenMS 00088 00089 #endif // OPENMS_CHEMISTRY_ENZYMATICDIGESTION_H
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