PeakPickerHiRes

class pyopenms.PeakPickerHiRes

Bases: object

Cython implementation of _PeakPickerHiRes

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’, ‘ProgressLogger’]

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: PeakPickerHiRes) → None

Methods

__init__	Overload:
endProgress(self)	Ends the progress display
getDefaults(self)	Returns the default parameters
getLogType(self)	Returns the type of progress log being used
getName(self)	Returns the name
getParameters(self)	Returns the parameters
getSubsections(self)
nextProgress(self)	Increment progress by 1 (according to range begin-end)
pick	Overload:
pickExperiment	Overload:
setLogType(self, in_0)	Sets the progress log that should be used.
setName(self, in_0)	Sets the name
setParameters(self, param)	Sets the parameters
setProgress(self, value)	Sets the current progress
startProgress(self, begin, end, label)

endProgress(self) → None

Ends the progress display

getDefaults(self) → Param

Returns the default parameters

getLogType(self) → int

Returns the type of progress log being used

getName(self) → Union[bytes, str, String]

Returns the name

getParameters(self) → Param

Returns the parameters

getSubsections(self) → List[bytes]

nextProgress(self) → None

Increment progress by 1 (according to range begin-end)

pick()

Overload:

pick(self, input: MSSpectrum, output: MSSpectrum) → None

Overload:

pick(self, input: MSChromatogram, output: MSChromatogram) → None

pickExperiment()

Overload:

pickExperiment(self, input: MSExperiment, output: MSExperiment, check_spectrum_type: bool) → None

Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map

Parameters

• input – Input map in profile mode

• output – Output map with picked peaks

• check_spectrum_type – If set, checks spectrum type and throws an exception if a centroided spectrum is passed

Overload:

pickExperiment(self, input: MSExperiment, output: MSExperiment, boundaries_spec: List[List[PeakBoundary]], boundaries_chrom: List[List[PeakBoundary]], check_spectrum_type: bool) → None

setLogType(self, in_0: int) → None

Sets the progress log that should be used. The default type is NONE!

setName(self, in_0: Union[bytes, str, String]) → None

Sets the name

setParameters(self, param: Param) → None

Sets the parameters

setProgress(self, value: int) → None

Sets the current progress

startProgress(self, begin: int, end: int, label: Union[bytes, str, String]) → None