| OpenMS 2.5.0

Public Member Functions | Private Member Functions | Private Attributes | List of all members
PeakPickerIterative Class Reference
Analysis » PeakPicking

This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data). More...

`#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerIterative.h>`

Inheritance diagram for PeakPickerIterative:

## Public Member Functions

| PeakPickerIterative ()
| Constructor. More...
void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. More...
| ~PeakPickerIterative () override
| Destructor. More...
void | pick (const MSSpectrum &input, MSSpectrum &output)
void | pickExperiment (const PeakMap &input, PeakMap &output)
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (const ProgressLogger &other)
| Assignment Operator. More...
void | setLogType (LogType type) const
| Sets the progress log that should be used. The default type is NONE! More...
LogType | getLogType () const
| Returns the type of progress log being used. More...
void | startProgress (SignedSize begin, SignedSize end, const String &label) const
| Initializes the progress display. More...
void | setProgress (SignedSize value) const
| Sets the current progress. More...
void | endProgress () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Private Member Functions

void | pickRecenterPeaks_ (const MSSpectrum &input, std::vector< PeakCandidate > &PeakCandidates, SignalToNoiseEstimatorMedian< MSSpectrum > &snt)

## Private Attributes

double | signal_to_noise_
double | peak_width_
double | spacing_difference_
int | sn_bin_count_
int | nr_iterations_
double | sn_win_len_
bool | check_width_internally_

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...
Static Protected Member Functions inherited from ProgressLogger
static String | logTypeToFactoryName_ (LogType type)
| Return the name of the factory product used for this log type. More...
Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data).

This peak-picking algorithm detects ion signals in profile data and reconstructs the corresponding peak shape by identifying the left and right borders of the peak. It reports the area under the peak as intensity and the weighted m/z values as the m/z value as well as left/right border. Furthermore, it next tries to improve the peak positioning iteratively using the m/z center computed in the last iteration. This allows for refinement in the peak boundaries and more accurate determination of peak center and borders.

Its approach is similar to the PeakPickerHiRes but additionally uses an iterative approach to find and re-center peaks.

- First, it uses the PeakPickerHiRes to find seeds or candidate peaks.
- Next it uses n iterations to re-center those peaks and compute left/right borders for each peak.
- Finally it removes peaks that are within the borders of other peaks.

So far, this peak picker was mainly tested on high resolution TOF-MS data.

Note
  The peaks must be sorted according to ascending m/z!

## Constructor & Destructor Documentation

## ◆ PeakPickerIterative()

PeakPickerIterative | ( |  | ) |

inline

Constructor.

## ◆ ~PeakPickerIterative()

~PeakPickerIterative | ( |  | ) |

inline override

Destructor.

## Member Function Documentation

## ◆ pick()

void pick | ( | const MSSpectrum & | input,
|  | MSSpectrum & | output
| ) |  |

inline

References SpectrumSettings::CENTROID, MSSpectrum::clear(), DefaultParamHandler::getDefaults(), MSSpectrum::getFloatDataArrays(), MSSpectrum::getMSLevel(), MSSpectrum::getName(), MSSpectrum::getRT(), OpenMS::Constants::k, OPENMS_LOG_DEBUG, PeakPickerHiRes::pick(), Peak1D::setIntensity(), MSSpectrum::setMSLevel(), Peak1D::setMZ(), MSSpectrum::setName(), DefaultParamHandler::setParameters(), MSSpectrum::setRT(), SpectrumSettings::setType(), Param::setValue(), OpenMS::sort_peaks_by_intensity(), and MSSpectrum::sortByPosition().

## ◆ pickExperiment()

void pickExperiment | ( | const PeakMap & | input,
|  | PeakMap & | output
| ) |  |

inline

References MSExperiment::clear(), MSExperiment::resize(), and MSExperiment::size().

## ◆ pickRecenterPeaks_()

void pickRecenterPeaks_ | ( | const MSSpectrum & | input,
|  | std::vector< PeakCandidate > & | PeakCandidates,
|  | SignalToNoiseEstimatorMedian< MSSpectrum > & | snt
| ) |  |

inline private

References SignalToNoiseEstimator< Container >::getSignalToNoise(), and OpenMS::Constants::k.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

inline override virtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ check_width_internally_

bool check_width_internally_

private

## ◆ nr_iterations_

int nr_iterations_

private

## ◆ peak_width_

double peak_width_

private

## ◆ signal_to_noise_

double signal_to_noise_

private

## ◆ sn_bin_count_

int sn_bin_count_

private

## ◆ sn_win_len_

double sn_win_len_

private

## ◆ spacing_difference_

double spacing_difference_

private