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... | |
| PeakShape & | operator= (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... | |
Internal representation of a peak shape (used by the PeakPickerCWT)
It defines an asymmetric lorentzian and asymmetric hyperbolic squared secan function.
| typedef MSSpectrum ::const_iterator PeakIterator |
Iterator to the raw data vector.
| 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 | |
|
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.
|
inlinevirtual |
Destructor.
| 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.
| bool operator== | ( | const PeakShape & | rhs | ) | const |
| void setLeftEndpoint | ( | PeakIterator | left_endpoint | ) |
| void setRightEndpoint | ( | PeakIterator | right_endpoint | ) |
| DoubleReal area |
Area of the peak shape.
|
protected |
Needed for initialisation of endpoint iterators.
| DoubleReal height |
Maximum intensity of the peak shape.
Referenced by TwoDOptimization::optimizeRegionsScanwise_().
|
protected |
Left peak endpoint in the data.
|
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).
|
protected |
Right peak endpoint in the data.
|
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 |