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NeutralLossDiffFilter.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_NEUTRALLOSSDIFFFILTER_H
00028 #define OPENMS_FILTERING_TRANSFORMERS_NEUTRALLOSSDIFFFILTER_H
00029 
00030 #include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
00031 
00032 #include <map>
00033 #include <cmath>
00034 
00035 namespace OpenMS
00036 {
00044   class NeutralLossDiffFilter : public FilterFunctor
00045   {
00046   public:
00047 
00048     // @name Constructors and Destructors
00049     // @{
00051     NeutralLossDiffFilter();
00052 
00054     NeutralLossDiffFilter(const NeutralLossDiffFilter& source);
00055 
00057     virtual ~NeutralLossDiffFilter();
00058     // @}
00059 
00060     // @name Operators
00061     // @{
00063     NeutralLossDiffFilter& operator = (const NeutralLossDiffFilter& source);
00064     // @}
00065 
00066     // @name Accessors
00067     // @{
00069     static FilterFunctor* create() { return new NeutralLossDiffFilter(); }
00070 
00072     template <typename SpectrumType> double apply(SpectrumType& spectrum)
00073     {
00074       double tolerance = (double)param_.getValue("tolerance");
00075       double isodiff = 0;
00076       //iterate over all peaks
00077       for (int i = 0; i < (int)spectrum.size(); ++i)
00078       {
00079         for (int j = 1; i - j >= 0; ++j)
00080         {
00081           double pos_diff = std::fabs(spectrum.getContainer()[i-j].getPosition()[0] - spectrum.getContainer()[i].getPosition()[0]);
00082           if (std::fabs(pos_diff - 18) < tolerance || std::fabs(pos_diff - 17) < tolerance) // water and ammonium
00083           {
00084             isodiff += spectrum.getContainer()[i-j].getIntensity() + spectrum.getContainer()[i].getIntensity();
00085           }
00086           else 
00087           {
00088             if (pos_diff > 18 + tolerance)
00089             {
00090               break;
00091             }
00092           }
00093         }
00094       }
00095 
00096       return isodiff;
00097     }
00098 
00100     static const String getProductName()
00101     {
00102       return "NeutralLossDiffFilter";
00103     }
00104     // @}
00105 
00106   };
00107 }
00108 #endif // OPENMS_FILTERING_TRANSFORMERS_NEUTRALLOSSDIFFFILTER_H

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