MRMFeatureFinderScoring

class pyopenms.MRMFeatureFinderScoring

Bases: object

Cython implementation of _MRMFeatureFinderScoring

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1MRMFeatureFinderScoring.html

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

__init__()

Cython signature: void MRMFeatureFinderScoring()

Methods

__init__	Cython signature: void MRMFeatureFinderScoring()
endProgress	Cython signature: void endProgress() Ends the progress display
getDefaults	Cython signature: Param getDefaults() Returns the default parameters
getLogType	Cython signature: LogType getLogType() Returns the type of progress log being used
getName	Cython signature: String getName() Returns the name
getParameters	Cython signature: Param getParameters() Returns the parameters
getSubsections	Cython signature: libcpp_vector[String] getSubsections()
nextProgress	Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)
pickExperiment	Cython signature: void pickExperiment(MSExperiment & chromatograms, FeatureMap & output, TargetedExperiment & transition_exp_, TransformationDescription trafo, MSExperiment & swath_map)
prepareProteinPeptideMaps_	Cython signature: void prepareProteinPeptideMaps_(LightTargetedExperiment & transition_exp)
scorePeakgroups	Cython signature: void scorePeakgroups(LightMRMTransitionGroupCP transition_group, TransformationDescription trafo, libcpp_vector[SwathMap] swath_maps, FeatureMap & output, bool ms1only)
setLogType	Cython signature: void setLogType(LogType) Sets the progress log that should be used.
setMS1Map	Cython signature: void setMS1Map(shared_ptr[SpectrumAccessOpenMS] ms1_map)
setName	Cython signature: void setName(const String &) Sets the name
setParameters	Cython signature: void setParameters(Param & param) Sets the parameters
setProgress	Cython signature: void setProgress(ptrdiff_t value) Sets the current progress
setStrictFlag	Cython signature: void setStrictFlag(bool flag)
startProgress	Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)

endProgress()

Cython signature: void endProgress() Ends the progress display

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getLogType()

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

getName()

Cython signature: String getName() Returns the name

getParameters()

Cython signature: Param getParameters() Returns the parameters

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

nextProgress()

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

pickExperiment()

Cython signature: void pickExperiment(MSExperiment & chromatograms, FeatureMap & output, TargetedExperiment & transition_exp_, TransformationDescription trafo, MSExperiment & swath_map)

Parameters

• chromatograms – The input chromatograms

• output – The output features with corresponding scores

• transition_exp – The transition list describing the experiment

• trafo – Optional transformation of the experimental retention time to the normalized retention time space used in the transition list

• swath_map – Optional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted

prepareProteinPeptideMaps_()

Cython signature: void prepareProteinPeptideMaps_(LightTargetedExperiment & transition_exp)

Parameters

transition_exp – The transition list describing the experiment

scorePeakgroups()

Cython signature: void scorePeakgroups(LightMRMTransitionGroupCP transition_group, TransformationDescription trafo, libcpp_vector[SwathMap] swath_maps, FeatureMap & output, bool ms1only)

Parameters

• transition_group – The MRMTransitionGroup to be scored (input)

• trafo – Optional transformation of the experimental retention time to the normalized retention time space used in the transition list

• swath_maps – Optional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted. Use empty map if no data is available

• output – The output features with corresponding scores (the found features will be added to this FeatureMap)

• ms1only – Whether to only do MS1 scoring and skip all MS2 scoring

setLogType()

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

setMS1Map()

• Cython signature: void setMS1Map(shared_ptr[SpectrumAccessOpenMS] ms1_map)

• Cython signature: void setMS1Map(shared_ptr[SpectrumAccessOpenMSCached] ms1_map)

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters

setProgress()

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

setStrictFlag()

Cython signature: void setStrictFlag(bool flag)

startProgress()

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