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SuffixArrayPeptideFinder.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_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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