FeatureFinder

class pyopenms.FeatureFinder

Bases: object

Cython implementation of _FeatureFinder

Original C++ documentation is available here

– Inherits from [‘ProgressLogger’]

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: FeatureFinder) → None

Methods

__init__

Overload:

endProgress(self)

Ends the progress display

getLogType(self)

Returns the type of progress log being used

getParameters(self, algorithm_name)

Returns the default parameters for the algorithm with name algorithm_name

nextProgress(self)

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

run(self, algorithm_name, input_map, feats, ...)

Executes the FeatureFinder using the given algorithm

setLogType(self, in_0)

Sets the progress log that should be used.

setProgress(self, value)

Sets the current progress

startProgress(self, begin, end, label)

endProgress(self) → None

Ends the progress display

getLogType(self) → int

Returns the type of progress log being used

getParameters(self, algorithm_name: Union[bytes, str, String]) → Param

Returns the default parameters for the algorithm with name algorithm_name

nextProgress(self) → None

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

run(self, algorithm_name: Union[bytes, str, String], input_map: MSExperiment, feats: FeatureMap, param: Param, seeds: FeatureMap) → None

Executes the FeatureFinder using the given algorithm

There are several constraints for the input_map. They are tested before the algorithm starts. It must only contain MS 1 level scans and you have to call updateRanges() before passing it to this method The input map is sorted by RT & m/z if that’s not the case Furthermore we throw an Exception if the data contains negative m/z values, as this will disturb most algorithms

Parameters

  • algorithm_name – Name of the feature finding algorithm to use

  • input_map – Input peak map

  • features – Output feature map

  • param – Algorithm parameters

  • seeds – List of seeds to use

setLogType(self, in_0: int) → None

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

setProgress(self, value: int) → None

Sets the current progress

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