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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