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_SUFFIXARRAYPEPTIDEFINDER_H 00029 #define OPENMS_DATASTRUCTURES_SUFFIXARRAYPEPTIDEFINDER_H 00030 00031 #include <vector> 00032 #include <OpenMS/CONCEPT/Exception.h> 00033 #include <OpenMS/DATASTRUCTURES/BigString.h> 00034 00035 namespace OpenMS 00036 { 00037 class String; 00038 class SuffixArray; 00042 class SuffixArrayPeptideFinder 00043 { 00044 00045 public: 00046 00050 typedef std::pair <String, String> FASTAEntry; 00051 00056 SuffixArrayPeptideFinder(const String & fFile, const String & method) throw (Exception::FileNotFound,Exception::ParseError,Exception::InvalidValue); 00057 00061 SuffixArrayPeptideFinder(const SuffixArrayPeptideFinder & source); 00062 00066 virtual ~SuffixArrayPeptideFinder(); 00067 00074 void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String > > >& candidates, const std::vector<double> & spec); 00075 00083 void getCandidates(std::vector<std::vector<std::pair<FASTAEntry, String > > >& candidates, const String & DTA_file) throw (Exception::FileNotFound,Exception::ParseError); 00084 00089 void setTolerance(const float t); 00090 00095 float getTolerance() const; 00096 00101 void setNumberOfModifications(UInt number_of_mods) const; 00102 00107 UInt getNumberOfModifications() const; 00108 00114 void setTags(const std::vector<OpenMS::String> & tags) throw (OpenMS::Exception::InvalidValue); 00115 00120 const std::vector<OpenMS::String> & getTags(); 00121 00126 void setUseTags(bool use_tags); 00127 00132 bool getUseTags(); 00133 00138 void setModificationOutputMethod(const String & s) throw (OpenMS::Exception::InvalidValue); 00139 00144 String getModificationOutputMethod(); 00145 00146 protected: 00147 00148 String vToString_(std::vector<String> v); 00149 00150 BigString big_string_; 00151 00152 SuffixArray* sa_; 00153 00154 String modification_output_method_; 00155 00156 }; 00157 00158 } 00159 00160 #endif //OPENMS_EXAMPLES_SuffixArrayPeptideFinder_H
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