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 2002-2012.
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// $Maintainer: Clemens Groepl $
// $Authors: Clemens Groepl, Chris Bielow $
// --------------------------------------------------------------------------


#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_ISOTOPEMODEL_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_ISOTOPEMODEL_H

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>
#include <OpenMS/CHEMISTRY/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);

    virtual ~IsotopeModel();

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

    UInt getCharge();

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

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

    void setOffset(CoordinateType offset);

    CoordinateType getOffset();

    EmpiricalFormula getFormula();

    void setSamples(const EmpiricalFormula & formula);

    CoordinateType getCenter() const;

    const IsotopeDistribution & getIsotopeDistribution() const;


protected:
    CoordinateType isotope_stdev_;
    CoordinateType isotope_lorentz_fwhm_;

    UInt charge_;
    CoordinateType mean_;
    CoordinateType monoisotopic_mz_;
    DoubleReal averagine_[AVERAGINE_NUM];
    Int max_isotope_;
    DoubleReal trim_right_cutoff_;
    DoubleReal isotope_distance_;
    IsotopeDistribution isotope_distribution_;

    void updateMembers_();

  };
}

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_ISOTOPEMODEL_H