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IsotopeDiffFilter.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_ISOTOPEDIFFFILTER_H
00028 #define OPENMS_FILTERING_TRANSFORMERS_ISOTOPEDIFFFILTER_H
00029 
00030 #include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
00031 
00032 #include <map>
00033 #include <string>
00034 #include <cmath>
00035 
00036 namespace OpenMS
00037 {
00045   class IsotopeDiffFilter : public FilterFunctor
00046   {
00047   
00048   public:
00049   
00050     // @name Constructors and Destrutors
00051     // @{
00053     IsotopeDiffFilter();
00054 
00056     IsotopeDiffFilter(const IsotopeDiffFilter& source);
00057 
00059     virtual ~IsotopeDiffFilter();
00060     // @}
00061 
00062     // @name Operators
00063     // @{
00065     IsotopeDiffFilter& operator = (const IsotopeDiffFilter& source);
00066     // @}
00067 
00068     // @name Accessors
00069     // @{
00071     static FilterFunctor* create() { return new IsotopeDiffFilter(); }
00072 
00074     template <typename SpectrumType> double apply(SpectrumType& spectrum)
00075     {
00076       double tolerance = (double)param_.getValue("tolerance");
00077       double isodiff = 0;
00078       
00079       //iterate over all peaks
00080       for (int i = 0; i < (int)spectrum.size(); ++i)
00081       {
00082         for (uint j = 1; i + j < spectrum.size(); ++j)
00083         {
00084           double pos_ij = spectrum.getContainer()[i+j].getPosition()[0];
00085           double pos_i = spectrum.getContainer()[i].getPosition()[0];
00086           if (std::fabs(pos_ij - pos_i + 1) < tolerance)
00087           {
00088             isodiff += spectrum.getContainer()[i].getIntensity() + spectrum.getContainer()[i+j].getIntensity();
00089           }
00090           else 
00091           {
00092             if (std::fabs(spectrum.getContainer()[i+j].getPosition()[0] - spectrum.getContainer()[i].getPosition()[0]) > 1 + tolerance)
00093             {
00094               break;
00095             }
00096           }
00097         }
00098       }
00099       return isodiff;
00100     }
00101 
00103     static const String getProductName()
00104     {
00105       return "IsotopeDiffFilter";
00106     }
00107     // @}
00108 
00109   private:
00110   };
00111 }
00112 #endif // OPENMS_FILTERING_TRANSFORMERS_ISOTOPEDIFFFILTER_H

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