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PeakShape Struct Reference

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

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

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 (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. More...
 
 PeakShape (DoubleReal height_, DoubleReal mz_position_, DoubleReal left_width_, DoubleReal right_width_, DoubleReal area_, Type type_)
 Constructor that sets most of the members. More...
 
 PeakShape (const PeakShape &rhs)
 Copy constructor. More...
 
virtual ~PeakShape ()
 Destructor. More...
 
PeakShapeoperator= (const PeakShape &rhs)
 Assignment operator. More...
 
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. More...
 
DoubleReal getSymmetricMeasure () const
 Computes symmetry measure of the peak shape, which is corresponds to th ratio of the left and right width parameters. More...
 
DoubleReal getFWHM () const
 Estimates the full width at half maximum. More...
 
bool iteratorsSet () const
 Check if endpoint iterators. More...
 
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. More...
 
DoubleReal mz_position
 Centroid position. More...
 
DoubleReal left_width
 Left width parameter. More...
 
DoubleReal right_width
 Right width parameter. More...
 
DoubleReal area
 Area of the peak shape. More...
 
DoubleReal r_value
 Correlation coefficient. More...
 
DoubleReal 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 initialisation 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

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 

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 ( )
inlinevirtual

Destructor.

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)

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
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


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:35 using doxygen 1.8.5