ExtendedIsotopeModel.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Timo Sachsenberg $
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#pragma once

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>

namespace OpenMS
{
  class OPENMS_DLLAPI ExtendedIsotopeModel :
    public InterpolationModel
  {

public:
    typedef InterpolationModel::CoordinateType CoordinateType;
    typedef InterpolationModel::CoordinateType IntensityType;

    enum Averagines {C = 0, H, N, O, S, AVERAGINE_NUM};

    ExtendedIsotopeModel();

    ExtendedIsotopeModel(const ExtendedIsotopeModel & source);

    ~ExtendedIsotopeModel() override;

    virtual ExtendedIsotopeModel & operator=(const ExtendedIsotopeModel & source);

    UInt getCharge();

    static BaseModel<1> * create()
    {
      return new ExtendedIsotopeModel();
    }

    static const String getProductName()
    {
      return "ExtendedIsotopeModel";
    }

    void setOffset(CoordinateType offset) override;

    CoordinateType getOffset();

    void setSamples() override;

    CoordinateType getCenter() const override;

protected:
    CoordinateType isotope_stdev_;
    UInt charge_;
    CoordinateType monoisotopic_mz_;
    double averagine_[AVERAGINE_NUM];
    Int max_isotope_;
    double trim_right_cutoff_;
    double isotope_distance_;

    void updateMembers_() override;
  };
}