PeakShape Class Reference

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

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

Collaboration diagram for PeakShape:

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. More...

Public Member Functions
	PeakShape ()
	Default constructor. More...
	PeakShape (double height_, double mz_position_, double left_width_, double right_width_, double area_, PeakIterator left_, PeakIterator right_, Type type_)
	Constructor that sets most of the members. More...
	PeakShape (double height_, double mz_position_, double left_width_, double right_width_, double area_, Type type_)
	Constructor that sets most of the members. More...
	PeakShape (const PeakShape &rhs)
	Copy constructor. More...
virtual	~PeakShape ()
	Destructor. More...
PeakShape &	operator= (const PeakShape &rhs)
	Assignment operator. More...
bool	operator== (const PeakShape &rhs) const
bool	operator!= (const PeakShape &rhs) const
double	operator() (double x) const
	Compute the intensity of the peaks shape at position x. More...
double	getSymmetricMeasure () const
	Computes symmetry measure of the peak shape, which is corresponds to the ratio of the left and right width parameters. More...
double	getFWHM () const
	Estimates the full width at half maximum. More...
bool	iteratorsSet () const
	Check if endpoint iterators are provided. More...
PeakIterator	getLeftEndpoint () const
void	setLeftEndpoint (PeakIterator left_endpoint)
PeakIterator	getRightEndpoint () const
void	setRightEndpoint (PeakIterator right_endpoint)

Public Attributes
double	height
	Maximum intensity of the peak shape. More...
double	mz_position
	Centroid position. More...
double	left_width
	Left width parameter. More...
double	right_width
	Right width parameter. More...
double	area
	Area of the peak shape. More...
double	r_value
	Correlation coefficient. More...
double	signal_to_noise
	The signal to noise ratio at the mz_position. More...
Type	type
	peak shape type More...

Protected Attributes
PeakIterator	left_endpoint_
	Left peak endpoint in the data. More...
PeakIterator	right_endpoint_
	Right peak endpoint in the data. More...
MSSpectrum	exp_
	Needed for initialization of endpoint iterators. More...
bool	left_iterator_set_
	flag if left endpoint iterator differs from default value More...
bool	right_iterator_set_
	flag if left endpoint iterator differs from default value More...

Detailed Description

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

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

Member Typedef Documentation

PeakIterator

typedef MSSpectrum::const_iterator PeakIterator

Iterator to the raw data vector.

Member Enumeration Documentation

Type

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

Constructor & Destructor Documentation

PeakShape() [1/4]

PeakShape

(

)

Default constructor.

PeakShape() [2/4]

PeakShape	(	double	height_,
		double	mz_position_,
		double	left_width_,
		double	right_width_,
		double	area_,
		PeakIterator	left_,
		PeakIterator	right_,
		Type	type_
	)

Constructor that sets most of the members.

PeakShape() [3/4]

PeakShape	(	double	height_,
		double	mz_position_,
		double	left_width_,
		double	right_width_,
		double	area_,
		Type	type_
	)

Constructor that sets most of the members.

PeakShape() [4/4]

PeakShape

(

const PeakShape &

rhs

)

Copy constructor.

~PeakShape()

virtual ~PeakShape ( )

virtual

Destructor.

Member Function Documentation

getFWHM()

double getFWHM

(

)

const

Estimates the full width at half maximum.

getLeftEndpoint()

PeakIterator getLeftEndpoint

(

)

const

getRightEndpoint()

PeakIterator getRightEndpoint

(

)

const

getSymmetricMeasure()

double getSymmetricMeasure

(

)

const

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

iteratorsSet()

bool iteratorsSet

(

)

const

Check if endpoint iterators are provided.

operator!=()

bool operator!=

(

const PeakShape &

rhs

)

const

operator()()

double operator()

(

double

x

)

const

Compute the intensity of the peaks shape at position x.

operator=()

PeakShape& operator=

(

const PeakShape &

rhs

)

Assignment operator.

operator==()

bool operator==

(

const PeakShape &

rhs

)

const

setLeftEndpoint()

void setLeftEndpoint

(

PeakIterator

left_endpoint

)

setRightEndpoint()

void setRightEndpoint

(

PeakIterator

right_endpoint

)

Member Data Documentation

area

double area

Area of the peak shape.

exp_

MSSpectrum exp_

protected

Needed for initialization of endpoint iterators.

height

double height

Maximum intensity of the peak shape.

Referenced by TwoDOptimization::optimizeRegionsScanwise_().

left_endpoint_

PeakIterator left_endpoint_

protected

Left peak endpoint in the data.

left_iterator_set_

bool left_iterator_set_

protected

flag if left endpoint iterator differs from default value

left_width

double left_width

Left width parameter.

Referenced by TwoDOptimization::optimizeRegionsScanwise_().

mz_position

double mz_position

Centroid position.

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

r_value

double r_value

Correlation coefficient.

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

right_endpoint_

PeakIterator right_endpoint_

protected

Right peak endpoint in the data.

right_iterator_set_

bool right_iterator_set_

protected

flag if left endpoint iterator differs from default value

right_width

double right_width

Right width parameter.

Referenced by TwoDOptimization::optimizeRegionsScanwise_().

signal_to_noise

double signal_to_noise

The signal to noise ratio at the mz_position.

type

Type type

peak shape type