PeakShape Struct Reference

Internal representation of a peak shape (used by the PeakPickerCWT). More...

#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakShape.h>

List of all members.

Classes
class	PositionLess
	Comparison of mz_positions. More...
Public Types
enum	Type { LORENTZ_PEAK, SECH_PEAK, UNDEFINED }
	Peak shape type (asymmetric lorentzian or asymmetric hyperbolic secans squared). More...
typedef MSSpectrum::const_iterator	PeakIterator
	Iterator to the raw data vector.
Public Member Functions
	PeakShape ()
	Default constructor.
	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_)
	Constructor that sets most of the members.
	PeakShape (const PeakShape &rhs)
	Copy constructor.
virtual	~PeakShape ()
	Destructor.
PeakShape &	operator= (const PeakShape &rhs)
	Assignment operator.
bool	operator== (const PeakShape &rhs) const
bool	operator!= (const PeakShape &rhs) const
DoubleReal	operator() (DoubleReal x) const
	Compute the intensity of the peaks shape at position x.
DoubleReal	getSymmetricMeasure () const
	Computes symmetry measure of the peak shape, which is corresponds to th ratio of the left and right width parameters.
DoubleReal	getFWHM () const
	Estimates the full width at half maximum.
bool	iteratorsSet () const
	Check if endpoint iterators.
PeakIterator	getLeftEndpoint () const
void	setLeftEndpoint (PeakIterator left_endpoint)
PeakIterator	getRightEndpoint () const
void	setRightEndpoint (PeakIterator right_endpoint)
Public Attributes
DoubleReal	height
	Maximum intensity of the peak shape.
DoubleReal	mz_position
	Centroid position.
DoubleReal	left_width
	Left width parameter.
DoubleReal	right_width
	Right width parameter.
DoubleReal	area
	Area of the peak shape.
DoubleReal	r_value
	Correlation coefficient.
DoubleReal	signal_to_noise
	The signal to noise ratio at the mz_position.
Type	type
	peak shape type
Protected Attributes
PeakIterator	left_endpoint_
	Left peak endpoint in the data.
PeakIterator	right_endpoint_
	Right peak endpoint in the data.
MSSpectrum	exp_
	Needed for initialisation of endpoint iterators.
bool	left_iterator_set_
	flag if left endpoint iterator differs from default value
bool	right_iterator_set_
	flag if left endpoint iterator differs from default value

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Detailed Description

Internal representation of a peak shape (used by the PeakPickerCWT).

It defines an asymmetric lorentzian and asymmetric hyperbolic squared secan function.

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Member Typedef Documentation

typedef MSSpectrum ::const_iterator PeakIterator

Iterator to the raw data vector.

---

Member Enumeration Documentation

enum Type

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)

Enumerator:

LORENTZ_PEAK
SECH_PEAK
UNDEFINED

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Constructor & Destructor Documentation

PeakShape

(

)

[inline]

Default constructor.

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_
	)

Constructor that sets most of the members.

PeakShape

(

const PeakShape &

rhs

)

Copy constructor.

virtual ~PeakShape

(

)

[inline, virtual]

Destructor.

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Member Function Documentation

DoubleReal getFWHM

(

)

const

Estimates the full width at half maximum.

PeakIterator getLeftEndpoint

(

)

const

PeakIterator getRightEndpoint

(

)

const

DoubleReal getSymmetricMeasure

(

)

const

Computes symmetry measure of the peak shape, which is corresponds to th ratio of the left and right width parameters.

bool iteratorsSet

(

)

const

Check if endpoint iterators.

bool operator!=

(

const PeakShape &

rhs

)

const

DoubleReal operator()

(

DoubleReal

x

)

const

Compute the intensity of the peaks shape at position x.

PeakShape& operator=

(

const PeakShape &

rhs

)

Assignment operator.

bool operator==

(

const PeakShape &

rhs

)

const

void setLeftEndpoint

(

PeakIterator

left_endpoint

)

void setRightEndpoint

(

PeakIterator

right_endpoint

)

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Member Data Documentation

DoubleReal area

Area of the peak shape.

MSSpectrum exp_ [protected]

Needed for initialisation of endpoint iterators.

DoubleReal height

Maximum intensity of the peak shape.

Referenced by TwoDOptimization::optimizeRegionsScanwise_().

PeakIterator left_endpoint_ [protected]

Left peak endpoint in the data.

bool left_iterator_set_ [protected]

flag if left endpoint iterator differs from default value

DoubleReal left_width

Left width parameter.

Referenced by TwoDOptimization::optimizeRegionsScanwise_().

DoubleReal mz_position

Centroid position.

Referenced by PeakShape::PositionLess::operator()(), and TwoDOptimization::optimizeRegionsScanwise_().

DoubleReal r_value

Correlation coefficient.

It represents the squared pearson correlation coefficient with the original data (0 <= r_value <= 1).

PeakIterator right_endpoint_ [protected]

Right peak endpoint in the data.

bool right_iterator_set_ [protected]

flag if left endpoint iterator differs from default value

DoubleReal right_width

Right width parameter.

Referenced by TwoDOptimization::optimizeRegionsScanwise_().

DoubleReal signal_to_noise

The signal to noise ratio at the mz_position.

Type type

peak shape type