OpenMS
2.6.0
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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... | |
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 | |
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LORENTZ_PEAK | |
SECH_PEAK | |
UNDEFINED |
PeakShape | ( | ) |
Default constructor.
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 | ( | double | height_, |
double | mz_position_, | ||
double | left_width_, | ||
double | right_width_, | ||
double | area_, | ||
Type | type_ | ||
) |
Constructor that sets most of the members.
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virtual |
Destructor.
double getFWHM | ( | ) | const |
Estimates the full width at half maximum.
PeakIterator getLeftEndpoint | ( | ) | const |
PeakIterator getRightEndpoint | ( | ) | const |
double getSymmetricMeasure | ( | ) | const |
Computes symmetry measure of the peak shape, which is corresponds to the ratio of the left and right width parameters.
bool iteratorsSet | ( | ) | const |
Check if endpoint iterators are provided.
bool operator!= | ( | const PeakShape & | rhs | ) | const |
bool operator== | ( | const PeakShape & | rhs | ) | const |
void setLeftEndpoint | ( | PeakIterator | left_endpoint | ) |
void setRightEndpoint | ( | PeakIterator | right_endpoint | ) |
double area |
Area of the peak shape.
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protected |
Needed for initialization of endpoint iterators.
double height |
Maximum intensity of the peak shape.
Referenced by TwoDOptimization::optimizeRegionsScanwise_().
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protected |
Left peak endpoint in the data.
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protected |
flag if left endpoint iterator differs from default value
double left_width |
Left width parameter.
Referenced by TwoDOptimization::optimizeRegionsScanwise_().
double mz_position |
Centroid position.
Referenced by PeakShape::PositionLess::operator()(), and TwoDOptimization::optimizeRegionsScanwise_().
double r_value |
Correlation coefficient.
It represents the squared Pearson correlation coefficient with the original data (0 <= r_value <= 1).
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protected |
Right peak endpoint in the data.
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protected |
flag if left endpoint iterator differs from default value
double right_width |
Right width parameter.
Referenced by TwoDOptimization::optimizeRegionsScanwise_().
double signal_to_noise |
The signal to noise ratio at the mz_position.
Type type |
peak shape type