IsotopeModel.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Clemens Groepl, Chris Bielow $
// --------------------------------------------------------------------------
 
 
#pragma once
 
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
 
namespace OpenMS
{
  class EmpiricalFormula;
 
  class OPENMS_DLLAPI IsotopeModel :
    public InterpolationModel
  {
 
public:
    typedef InterpolationModel::CoordinateType CoordinateType;
    typedef InterpolationModel::CoordinateType IntensityType;
 
    enum Averagines {C = 0, H, N, O, S, AVERAGINE_NUM};
 
    IsotopeModel();
 
    IsotopeModel(const IsotopeModel & source);
 
    ~IsotopeModel() override;
 
    virtual IsotopeModel & operator=(const IsotopeModel & source);
 
    UInt getCharge() const;
 
    static BaseModel<1> * create()
    {
      return new IsotopeModel();
    }
 
    static const String getProductName()
    {
      return "IsotopeModel";
    }
 
    void setOffset(CoordinateType offset) override;
 
    CoordinateType getOffset();
 
    EmpiricalFormula getFormula();
 
    virtual void setSamples(const EmpiricalFormula & formula);
 
    using InterpolationModel::setSamples;
 
    CoordinateType getCenter() const override;
 
    const IsotopeDistribution & getIsotopeDistribution() const;
 
 
protected:
    CoordinateType isotope_stdev_;
    CoordinateType isotope_lorentz_fwhm_;
 
    UInt charge_;
    CoordinateType mean_;
    CoordinateType monoisotopic_mz_;
    double averagine_[AVERAGINE_NUM];
    Int max_isotope_;
    double trim_right_cutoff_;
    double isotope_distance_;
    IsotopeDistribution isotope_distribution_;
 
    void updateMembers_() override;
 
  };
}