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Viewing changes to include/OpenMS/TRANSFORMATIONS/FEATUREFINDER/Fitter1D.h

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2012-11-12 15:58:12 UTC
  • Revision ID: package-import@ubuntu.com-20121112155812-vr15wtg9b50cuesg
Tags: upstream-1.9.0
Import upstream version 1.9.0

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include/OpenMS/TRANSFORMATIONS/FEATUREFINDER/Fitter1D.h
 
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// -*- mode: C++; tab-width: 2; -*-
 
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// vi: set ts=2:
 
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//
 
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// --------------------------------------------------------------------------
 
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//                   OpenMS Mass Spectrometry Framework
 
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// --------------------------------------------------------------------------
 
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//  Copyright (C) 2003-2011 -- Oliver Kohlbacher, Knut Reinert
 
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//
 
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//  This library is free software; you can redistribute it and/or
 
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//  modify it under the terms of the GNU Lesser General Public
 
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//  License as published by the Free Software Foundation; either
 
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//  version 2.1 of the License, or (at your option) any later version.
 
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//
 
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//  This library is distributed in the hope that it will be useful,
 
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//  but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
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//  Lesser General Public License for more details.
 
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//
 
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//  You should have received a copy of the GNU Lesser General Public
 
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//  License along with this library; if not, write to the Free Software
 
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//  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
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//
 
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// --------------------------------------------------------------------------
 
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// $Maintainer: Clemens Groepl $
 
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// $Authors: $
 
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// --------------------------------------------------------------------------
 
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#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FITTER1D_H
 
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#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FITTER1D_H
 
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#include <OpenMS/DATASTRUCTURES/IsotopeCluster.h>
 
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#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
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#include <OpenMS/CONCEPT/Exception.h>
 
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#include <OpenMS/KERNEL/Feature.h>
 
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#include <OpenMS/MATH/STATISTICS/BasicStatistics.h>
 
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#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderDefs.h>
 
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namespace OpenMS
 
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{
 
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        class InterpolationModel;
 
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        /**
 
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        @brief Abstract base class for all 1D-dimensional model fitter.
 
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        Every derived class has to implement the static functions
 
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        "T* create()" and "const String getProductName()" (see DefaultParamHandler for details)
 
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        @htmlinclude OpenMS_Fitter1D.parameters
 
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        @ingroup FeatureFinder
 
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        */
 
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        class OPENMS_DLLAPI Fitter1D
 
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    : public DefaultParamHandler,
 
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      public FeatureFinderDefs
 
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        {
 
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         public:
 
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                /// IndexSet
 
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                typedef IsotopeCluster::IndexSet IndexSet;
 
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                /// IndexSet with charge information
 
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                typedef IsotopeCluster::ChargedIndexSet ChargedIndexSet;
 
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                /// Single coordinate
 
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                typedef Feature::CoordinateType CoordinateType;
 
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                /// Quality of a feature
 
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                typedef Feature::QualityType QualityType;
 
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                /// Raw data point type
 
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                typedef Peak1D PeakType;
 
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                /// Raw data container type using for the temporary storage of the input data
 
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                typedef std::vector<PeakType > RawDataArrayType;
 
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                /// Raw data iterator
 
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                typedef RawDataArrayType::iterator PeakIterator;
 
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                /// Default constructor.
 
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                Fitter1D();
 
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                /// copy constructor
 
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                Fitter1D(const Fitter1D& source);
 
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                /// destructor
 
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                virtual ~Fitter1D()
 
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                {
 
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                }
 
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                /// assignment operator
 
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                virtual Fitter1D& operator = (const Fitter1D& source);
 
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                /// return interpolation model
 
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                virtual QualityType fit1d(const RawDataArrayType& /* range */, InterpolationModel*& /* model */)
 
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                {
 
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                        throw Exception::NotImplemented(__FILE__,__LINE__,__PRETTY_FUNCTION__);
 
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                }
 
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                /// register all derived classes here
 
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                static void registerChildren();
 
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         protected:
 
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                /// standard derivation in bounding box         
 
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                CoordinateType tolerance_stdev_box_;
 
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                /// minimum of the bounding box
 
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                CoordinateType min_;
 
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                /// maximum of the bounding box
 
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                CoordinateType max_;
 
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                /// standard derivation
 
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                CoordinateType stdev1_; 
 
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                /// standard derivation            
 
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                CoordinateType stdev2_;
 
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                /// basic statistics           
 
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                Math::BasicStatistics<> statistics_;
 
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                /// interpolation step size
 
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                CoordinateType interpolation_step_;
 
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                virtual void updateMembers_();
 
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        };
 
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}
 
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#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FITTER1D_H