libopenms-dev 1.11.1-5 / usr / include / OpenMS / TRANSFORMATIONS / RAW2PEAK / PeakShape.h

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// $Maintainer: Alexandra Zerck $
// $Authors: Eva Lange $
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#ifndef OPENMS_TRANSFORMATIONS_RAW2PEAK_PEAKSHAPE_H
#define OPENMS_TRANSFORMATIONS_RAW2PEAK_PEAKSHAPE_H

#include <cmath>

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/KERNEL/MSSpectrum.h>

namespace OpenMS
{
  /**
    @brief Internal representation of a peak shape (used by the PeakPickerCWT)

    It defines an asymmetric lorentzian and asymmetric hyperbolic squared secan function.
  */
  struct OPENMS_DLLAPI PeakShape
  {
    /**
      @brief Peak shape type (asymmetric lorentzian or asymmetric hyperbolic secans squared).

      The peak shape can represent an asymmetric lorentzian function, given by

      l(x) = height/(1.+pow(left_width*(x - mz_position), 2)) (x<=mz_position)

      l(x) = height/(1.+pow(right_width*(x - mz_position), 2)) (x>mz_position)

      or an asymmetric hyperbolic secans squared function

      s(x) = height/pow(cosh(left_width*(x-mz_position)), 2) (x<=mz_position)

      s(x) = height/pow(cosh(right_width*(x-mz_position)), 2) (x>mz_position)
    */
    enum Type
    {
      LORENTZ_PEAK,
      SECH_PEAK,
      UNDEFINED
    };

    /// Iterator to the raw data vector
    typedef MSSpectrum<>::const_iterator PeakIterator;

    /// Default constructor
    PeakShape() :
      height(0),
      mz_position(0),
      left_width(0),
      right_width(0),
      area(0),
      r_value(0),
      signal_to_noise(0.),
      type(UNDEFINED)
    {
      left_endpoint_ = exp_.end();
      right_endpoint_ = exp_.end();
    }

    /// Constructor that sets most of the members
    PeakShape(DoubleReal height_, DoubleReal mz_position_, DoubleReal left_width_, DoubleReal right_width_, DoubleReal area_, PeakIterator left_, PeakIterator right_, Type type_);

    /// Constructor that sets most of the members
    PeakShape(DoubleReal height_, DoubleReal mz_position_, DoubleReal left_width_, DoubleReal right_width_, DoubleReal area_, Type type_);


    /// Copy constructor
    PeakShape(const PeakShape & rhs);

    /// Destructor
    virtual ~PeakShape()
    {
    }

    /// Assignment operator
    PeakShape & operator=(const PeakShape & rhs);

    //Equality operator
    bool operator==(const PeakShape & rhs) const;
    //Equality operator
    bool operator!=(const PeakShape & rhs) const;

    /// Compute the intensity of the peaks shape at position x
    DoubleReal operator()(DoubleReal x) const;
    /// Computes symmetry measure of the peak shape, which is corresponds to th ratio of the left and right width parameters.
    DoubleReal getSymmetricMeasure() const;
    /// Estimates the full width at half maximum.
    DoubleReal getFWHM() const;
    /// Check if endpoint iterators
    bool iteratorsSet() const;

    PeakIterator getLeftEndpoint() const;
    void setLeftEndpoint(PeakIterator left_endpoint);

    PeakIterator getRightEndpoint() const;
    void setRightEndpoint(PeakIterator right_endpoint);
    /// Maximum intensity of the peak shape
    DoubleReal height;
    /// Centroid position
    DoubleReal mz_position;
    /// Left width parameter
    DoubleReal left_width;
    /// Right width parameter
    DoubleReal right_width;
    /// Area of the peak shape
    DoubleReal area;
    /** @brief Correlation coefficient.

      It represents the squared pearson correlation coefficient with the original data (0 <= r_value <= 1).
    */
    DoubleReal r_value;
    /// The signal to noise ratio at the mz_position
    DoubleReal signal_to_noise;

    ///peak shape type
    Type type;

    /**
         @brief  Comparison of mz_positions.
    */
    class OPENMS_DLLAPI PositionLess
    {
public:

      inline bool operator()(const PeakShape & a, const PeakShape & b)
      {
        return a.mz_position < b.mz_position;
      }

    };
protected:
    /// Left peak endpoint in the data
    PeakIterator left_endpoint_;
    /// Right peak endpoint in the data
    PeakIterator right_endpoint_;
    /// Needed for initialisation of endpoint iterators
    MSSpectrum<> exp_;
    /// flag if left endpoint iterator differs from default value
    bool left_iterator_set_;
    /// flag if left endpoint iterator differs from default value
    bool right_iterator_set_;
  };
} // namespace OpenMS

#endif