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_ANALYSIS_MAPMATCHING_PAIRMATCHER_H 00028 #define OPENMS_ANALYSIS_MAPMATCHING_PAIRMATCHER_H 00029 00030 #include <OpenMS/ANALYSIS/MAPMATCHING/ElementPair.h> 00031 #include <OpenMS/KERNEL/FeatureMap.h> 00032 #include <OpenMS/CONCEPT/FactoryProduct.h> 00033 00034 #include <cmath> 00035 00036 namespace OpenMS 00037 { 00045 class PairMatcher 00046 : public FactoryProduct 00047 { 00048 public: 00049 00053 00054 typedef Feature FeatureType; 00055 typedef FeatureMap<> FeatureMapType; 00056 typedef ElementPair<> PairType; 00057 typedef std::vector< PairType > PairVectorType; 00059 00061 PairMatcher(FeatureMapType& features); 00062 00064 PairMatcher(const PairMatcher& source); 00065 00067 virtual PairMatcher& operator = (const PairMatcher& source); 00068 00070 virtual ~PairMatcher(); 00071 00076 const PairVectorType& run(); 00077 00082 const PairVectorType& getBestPairs(); 00083 00089 static void printInfo(std::ostream& out, const PairVectorType& pairs); 00090 00091 static const String getProductName() 00092 { 00093 return "PairMatcher"; 00094 } 00095 00096 protected: 00098 static const double sqrt2_; 00099 00101 FeatureMapType& features_; 00102 00104 PairVectorType pairs_; 00105 00107 PairVectorType best_pairs_; 00108 00110 struct Comparator 00111 { 00112 bool operator()(const PairType& a, const PairType& b) 00113 { 00114 return a.getQuality() > b.getQuality(); 00115 } 00116 }; 00117 00120 inline double PValue_(double x, double m, double sig1, double sig2) 00121 { 00122 if (m<x) 00123 { 00124 return 1-erf((x-m)/sig2/sqrt2_); 00125 } 00126 else 00127 { 00128 return 1-erf((m-x)/sig1/sqrt2_); 00129 } 00130 } 00131 00132 }; // end of class PairMatcher 00133 00134 } // end of namespace OpenMS 00135 00136 #endif // OPENMS_ANALYSIS_MAPMATCHER_PAIRMATCHER_H
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