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ExtendedIsotopeModel.h (Maintainer: Marcel Grunert)

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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: Marcel Grunert $
00025 // --------------------------------------------------------------------------
00026 
00027 
00028 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_EXTENDEDISOTOPEMODEL_H
00029 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_EXTENDEDISOTOPEMODEL_H
00030 
00031 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>
00032 
00033 namespace OpenMS
00034 {
00042   class ExtendedIsotopeModel
00043   : public InterpolationModel
00044   {
00045 
00046     public:
00047     typedef InterpolationModel::CoordinateType CoordinateType;
00048     typedef InterpolationModel::CoordinateType IntensityType;
00049 
00050     enum Averagines{C=0,H,N,O,S,AVERAGINE_NUM};
00051 
00053     ExtendedIsotopeModel();
00054 
00056     ExtendedIsotopeModel(const ExtendedIsotopeModel& source);
00057 
00059     virtual ~ExtendedIsotopeModel();
00060 
00062     virtual ExtendedIsotopeModel& operator = (const ExtendedIsotopeModel& source);
00063 
00064     UInt getCharge();
00065 
00067     static BaseModel<1>* create()
00068     {
00069        return new ExtendedIsotopeModel();
00070     }
00071 
00073     static const String getProductName()
00074     {
00075        return "ExtendedIsotopeModel";
00076     }
00077 
00085     void setOffset(CoordinateType offset);
00086 
00087     CoordinateType getOffset();
00088 
00090     void setSamples();
00091 
00094     CoordinateType getCenter() const;
00095 
00096     protected:
00097       CoordinateType isotope_stdev_;
00098       UInt charge_;
00099       CoordinateType monoisotopic_mz_;
00100       DoubleReal averagine_[AVERAGINE_NUM];
00101       Int max_isotope_;
00102       DoubleReal trim_right_cutoff_;
00103       DoubleReal isotope_distance_;
00104 
00105       void updateMembers_();
00106   };
00107 }
00108 
00109 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_EXTENDEDISOTOPEMODEL_H

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