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BaseModel.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 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_H
00028 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_H
00029 
00030 #include <OpenMS/CONCEPT/FactoryProduct.h>
00031 #include <OpenMS/KERNEL/DPeak.h>
00032 #include <OpenMS/KERNEL/Peak1D.h>
00033 #include <OpenMS/KERNEL/DPeakArray.h>
00034 
00035 namespace OpenMS
00036 {
00045   template <UInt D>
00046     class BaseModel
00047     : public FactoryProduct
00048     {
00049 
00050       public:
00051         typedef int Flag;
00052         typedef std::vector<Flag> Flags;
00053 
00054         typedef typename DPeak<D>::IntensityType IntensityType;
00055         typedef typename DPeak<D>::CoordinateType CoordinateType;
00056         typedef DPosition<D> PositionType;
00057         typedef DPeak<D> PeakType;
00058         typedef DPeakArray<DPeak<D> > SamplesType;
00059 
00060 
00062         BaseModel()
00063         : FactoryProduct("BaseModel")
00064         {
00065           defaults_.setValue("cutoff",0.0,"Low intensity cutoff of the model.  Peaks below this intensity are not considered part of the model.");
00066         }
00067 
00069         BaseModel(const BaseModel& source)
00070         : FactoryProduct(source),
00071           cut_off_(source.cut_off_)
00072         {
00073         }
00074 
00076         virtual ~BaseModel()
00077         {
00078         }
00079 
00081         virtual BaseModel& operator = (const BaseModel& source)
00082         {
00083           if (&source == this) return *this;
00084 
00085           FactoryProduct::operator = (source);
00086           cut_off_ = source.cut_off_;
00087 
00088           return *this;
00089         }
00090 
00092         static void registerChildren();
00093 
00095         virtual IntensityType getIntensity(const PositionType& pos) const=0;
00096 
00098         virtual bool isContained(const PositionType& pos) const
00099         {
00100           return getIntensity(pos) >= cut_off_;
00101         }
00102 
00104         virtual void  fillIntensity(PeakType& peak) const
00105         {
00106           peak.setIntensity( getIntensity(peak.getPosition()) );
00107         }
00108 
00110         template <class PeakIterator>
00111         void  fillIntensities(PeakIterator beg, PeakIterator end) const
00112         {
00113           for (PeakIterator it=beg; it!=end; it++)
00114           {
00115             fillIntensity(*it);
00116           }
00117         }
00118 
00120         virtual IntensityType getCutOff() const
00121         {
00122           return cut_off_;
00123         }
00124 
00126         virtual void setCutOff(IntensityType cut_off)
00127         {
00128           cut_off_ = cut_off;
00129           param_.setValue("cutoff",cut_off_);
00130         }
00131 
00133         virtual void getSamples(SamplesType& cont) const =0;
00134 
00136         virtual void getSamples(std::ostream& os)
00137         {
00138           SamplesType samples;
00139           getSamples(samples);
00140           for (typename SamplesType::ConstIterator it=samples.begin();it!=samples.end(); ++it)
00141           {
00142             os << *it << std::endl;
00143           }
00144         }
00145 
00146       protected:
00147         IntensityType cut_off_;
00148 
00149         virtual void updateMembers_()
00150         {
00151           cut_off_ = (double)param_.getValue("cutoff");
00152         }
00153   };
00154 }
00155 
00156 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_H

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