FLASHDeconvAlgorithm#

class pyopenms.FLASHDeconvAlgorithm#

Bases: object

Cython implementation of _FLASHDeconvAlgorithm

Original C++ documentation is available here: – Inherits from [‘DefaultParamHandler’, ‘ProgressLogger’]

FLASHDeconv algorithm: ultrafast mass deconvolution algorithm for top down mass spectrometry dataset. From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps:

decharging and select candidate masses - speed up via binning

collecting isotopes from the candidate masses and deisotoping - peak groups are defined here

scoring and filter out low scoring masses (i.e., peak groups)

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: FLASHDeconvAlgorithm) → None

Methods

`__init__`
`endProgress`(self)	Ends the progress display
`getAveragine`(self)
`getDecoyAveragine`(self)
`getDefaults`(self)	Returns the default parameters
`getLogType`(self)	Returns the type of progress log being used
`getName`(self)	Returns the name
`getNoiseDecoyWeight`(self)
`getParameters`(self)	Returns the parameters
`getScanNumber`	__static_FLASHDeconvAlgorithm_getScanNumber(exp: MSExperiment , index: int ) -> int
`getSubsections`(self)
`getTolerances`(self)
`nextProgress`(self)	Increment progress by 1 (according to range begin-end)
`run`(self, input_map, deconvolved_spectra, ...)	Run FLASHDeconv algorithm for input_map and store deconvolved_spectra and deconvolved_features.
`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

getAveragine(self) → PrecalAveragine#

getDecoyAveragine(self) → PrecalAveragine#

getDefaults(self) → Param#: Returns the default parameters

getLogType(self) → int#: Returns the type of progress log being used

getName(self) → bytes | str | String#: Returns the name

getNoiseDecoyWeight(self) → float#

getParameters(self) → Param#: Returns the parameters

getScanNumber()#: __static_FLASHDeconvAlgorithm_getScanNumber(exp: MSExperiment , index: int ) -> int

getSubsections(self) → List[bytes]#

getTolerances(self) → List[float]#

nextProgress(self) → None#: Increment progress by 1 (according to range begin-end)

run(self, input_map: MSExperiment, deconvolved_spectra: List[DeconvolvedSpectrum], deconvolved_features: List[MassFeature_FDHS]) → None#: Run FLASHDeconv algorithm for input_map and store deconvolved_spectra and deconvolved_features. :param input_map: The input MSExperiment containing spectra to deconvolve :param deconvolved_spectra: Output vector to store deconvolved spectra :param deconvolved_features: Output vector to store mass features

setLogType(self, in_0: int) → None#: Sets the progress log that should be used. The default type is NONE!

setName(self, in_0: 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: bytes | str | String) → None#