| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Public Attributes | Protected Attributes | List of all members
PeakShape Class 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 (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