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
Generated Tue Apr 1 15:36:38 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |