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EnzymaticDigestion.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_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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