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FeatureFinder.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_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_H
00028 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_H
00029 
00030 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderDefs.h>
00031 
00032 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>
00033 #include <OpenMS/CONCEPT/ProgressLogger.h>
00034 
00035 namespace OpenMS
00036 {
00037 
00048   class FeatureFinder :
00049     public ProgressLogger,
00050     public FeatureFinderDefs
00051   {
00052 
00053     public:
00055       FeatureFinder();
00056 
00058       virtual ~FeatureFinder();
00059 
00074       template<class PeakType, class FeatureType>
00075       void run(const String& algorithm_name, MSExperiment<PeakType> const & input_map, FeatureMap<FeatureType> & features, const Param& param);
00076 
00078       const Flag& getPeakFlag(const IndexPair& index) const
00079       {
00080         return flags_[index.first][index.second];
00081       }
00082 
00084       Flag& getPeakFlag(const IndexPair& index) 
00085       { 
00086         return flags_[index.first][index.second];
00087       }
00088 
00090       Param getParameters(const String& algorithm_name) const;
00091 
00092     protected:
00093 
00095       std::vector< std::vector<Flag> > flags_;
00096 
00097   }; // class FeatureFinder
00098 
00099 } // namespace OpenMS
00100 
00101 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_H

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