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MarkerMower.h (Maintainer: Andreas Bertsch)

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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: Andreas Bertsch $
00025 // --------------------------------------------------------------------------
00026 //
00027 #ifndef OPENMS_FILTERING_TRANSFORMERS_MARKERMOWER_H
00028 #define OPENMS_FILTERING_TRANSFORMERS_MARKERMOWER_H
00029 
00030 #include <OpenMS/FILTERING/TRANSFORMERS/PreprocessingFunctor.h>
00031 #include <OpenMS/FILTERING/TRANSFORMERS/PeakMarker.h>
00032 
00033 #include <vector>
00034 #include <map>
00035 
00036 namespace OpenMS
00037 {
00043   class MarkerMower : public PreprocessingFunctor
00044   {
00045   public:
00046 
00047     // @name Constructors and Destructors
00048     // @{
00050     MarkerMower();
00051 
00053     MarkerMower(const MarkerMower& source);
00054 
00056     virtual ~MarkerMower();
00057     // @}
00058 
00059     // @name Operators
00060     // @{
00062     MarkerMower& operator = (const MarkerMower& source);
00063     // @}
00064 
00065     // @name Accessors
00066     // @{
00068     static PreprocessingFunctor* create() { return new MarkerMower(); }
00069 
00071     template <typename SpectrumType> void filterSpectrum(SpectrumType& spectrum)
00072     {
00073       typedef typename SpectrumType::Iterator Iterator;
00074     
00075       std::map<double, int> marks;
00076       for (std::vector<PeakMarker*>::const_iterator cvit = markers_.begin(); cvit != markers_.end(); ++cvit)
00077       {
00078         std::map<double, bool> marked;
00079         (*cvit)->apply(marked, spectrum);
00080         for (std::map<double, bool>::const_iterator cmit = marked.begin(); cmit != marked.end(); ++cmit)
00081         {
00082           if (cmit->second) 
00083           {
00084             marks[cmit->first]++;
00085           }
00086         }
00087       }
00088 
00089       for (Iterator it = spectrum.begin(); it != spectrum.end(); )
00090       {
00091         if (marks[it->getMZ()] > 0)
00092         {
00093           ++it;
00094         }
00095         else
00096         {
00097           it = spectrum.getContainer().erase(it);
00098         }
00099       }
00100     }
00101 
00102     void filterPeakSpectrum(PeakSpectrum& spectrum);
00103 
00104     void filterPeakMap(PeakMap& exp);
00105     
00106     static const String getProductName()
00107     {
00108       return "MarkerMower";
00109     }
00110 
00112     void insertmarker(PeakMarker* peak_marker);
00113     // @}
00114   
00115   private: 
00116   
00118     std::vector<PeakMarker*> markers_;
00119   };
00120 }
00121 #endif // OPENMS_COMPARISON_CLUSTERING_MARKERMOWER_H

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