FeatureFinder

class pyopenms.FeatureFinder

Bases: object

Cython implementation of _FeatureFinder

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1FeatureFinder.html: – Inherits from [‘ProgressLogger’]

__init__()

Cython signature: void FeatureFinder()
Cython signature: void FeatureFinder(FeatureFinder &)

Methods

`__init__`	Cython signature: void FeatureFinder()
`endProgress`	Cython signature: void endProgress() Ends the progress display
`getLogType`	Cython signature: LogType getLogType() Returns the type of progress log being used
`getParameters`	Cython signature: Param getParameters(String algorithm_name) Returns the default parameters for the algorithm with name algorithm_name
`nextProgress`	Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)
`run`	Cython signature: void run(String algorithm_name, MSExperiment & input_map, FeatureMap & feats, Param & param, FeatureMap & seeds)
`setLogType`	Cython signature: void setLogType(LogType) Sets the progress log that should be used.
`setProgress`	Cython signature: void setProgress(ptrdiff_t value) Sets the current progress
`startProgress`	Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)

endProgress(): Cython signature: void endProgress() Ends the progress display

getLogType(): Cython signature: LogType getLogType() Returns the type of progress log being used

getParameters(): Cython signature: Param getParameters(String algorithm_name) Returns the default parameters for the algorithm with name algorithm_name

nextProgress(): Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)

run()

Cython signature: void run(String algorithm_name, MSExperiment & input_map, FeatureMap & feats, Param & param, FeatureMap & seeds)

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 —– :param algorithm_name: Name of the feature finding algorithm to use :param input_map: Input peak map :param features: Output feature map :param param: Algorithm parameters :param seeds: List of seeds to use

setLogType(): Cython signature: void setLogType(LogType) Sets the progress log that should be used. The default type is NONE!

setProgress(): Cython signature: void setProgress(ptrdiff_t value) Sets the current progress

startProgress(): Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)