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SuffixArray.h (Maintainer: Chris Bauer)

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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 // $Maintainer: Chris Bauer$
00025 // --------------------------------------------------------------------------
00026 
00027 
00028 #ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAY_H
00029 #define OPENMS_DATASTRUCTURES_SUFFIXARRAY_H
00030 
00031 #include <vector>
00032 #include <OpenMS/CONCEPT/Exception.h>
00033 
00034 
00035 namespace OpenMS 
00036 {
00037   class String;
00038 
00043 class SuffixArray 
00044 {
00045   
00046 public:
00047 
00055   SuffixArray(const String & st, const String & sa_file_name) throw (Exception::InvalidValue, Exception::FileNotFound);
00056 
00060   SuffixArray(const SuffixArray & sa);
00061 
00065   virtual ~SuffixArray() = 0;
00066 
00070   virtual String toString() = 0;
00071 
00079   virtual void findSpec(std::vector<std::vector<std::pair<std::pair<int, int>,float > > >& candidates, const std::vector<double> & spec) throw (Exception::InvalidValue) = 0;
00080 
00087   virtual bool save(const String & file_name) throw (Exception::UnableToCreateFile) = 0;
00094   virtual bool open(const String & file_name) throw (Exception::FileNotFound) = 0;
00095 
00101   virtual void setTolerance (double t) throw (Exception::InvalidValue) = 0;
00102 
00107   virtual double getTolerance () const  = 0;
00108 
00115   virtual bool isDigestingEnd(const char aa1, const char aa2) const = 0;
00116 
00122   virtual void setTags(const std::vector<String>& tags) throw (Exception::InvalidValue) = 0;
00123 
00128   virtual const std::vector<String>& getTags () = 0;
00129 
00134   virtual void setUseTags(bool use_tags) = 0;
00135 
00140   virtual bool getUseTags() = 0;
00141 
00146   virtual void setNumberOfModifications(unsigned int number_of_mods) = 0;
00147 
00152   virtual unsigned int getNumberOfModifications () = 0;
00153 
00157   virtual void printStatistic() = 0;
00158 
00162   SuffixArray (); 
00163 
00164   
00165 };
00166 }
00167 
00168 #endif //OPENMS_DATASTRUCTURES_SUFARRAY_H

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