SpectrumAnnotator

class pyopenms.SpectrumAnnotator

Bases: object

Cython implementation of _SpectrumAnnotator

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1SpectrumAnnotator.html

– Inherits from [‘DefaultParamHandler’]

__init__()

• Cython signature: void SpectrumAnnotator()

Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options

• Cython signature: void SpectrumAnnotator(SpectrumAnnotator &)

Methods

__init__	Cython signature: void SpectrumAnnotator()
addIonMatchStatistics	Cython signature: void addIonMatchStatistics(PeptideIdentification & pi, MSSpectrum & spec, TheoreticalSpectrumGenerator & tg, SpectrumAlignment & sa)
annotateMatches	Cython signature: void annotateMatches(MSSpectrum & spec, PeptideHit & ph, TheoreticalSpectrumGenerator & tg, SpectrumAlignment & sa)
getDefaults	Cython signature: Param getDefaults() Returns the default parameters
getName	Cython signature: String getName() Returns the name
getParameters	Cython signature: Param getParameters() Returns the parameters
getSubsections	Cython signature: libcpp_vector[String] getSubsections()
setName	Cython signature: void setName(const String &) Sets the name
setParameters	Cython signature: void setParameters(Param & param) Sets the parameters

addIonMatchStatistics()

Cython signature: void addIonMatchStatistics(PeptideIdentification & pi, MSSpectrum & spec, TheoreticalSpectrumGenerator & tg, SpectrumAlignment & sa)

Parameters

• pi – A spectrum identifications to be annotated, looking up matches from a spectrum and the theoretical spectrum inferred from the identifications sequence

• spec – A PeakSpectrum containing the peaks from which the pi identifications are made

• tg – A TheoreticalSpectrumGenerator to infer the theoretical spectrum. Its own parameters define which ion types are referred

• sa – A SpectrumAlignment to match the theoretical spectrum with the measured. Its own parameters define the match tolerance

annotateMatches()

Cython signature: void annotateMatches(MSSpectrum & spec, PeptideHit & ph, TheoreticalSpectrumGenerator & tg, SpectrumAlignment & sa)

Parameters

• spec – A PeakSpectrum containing the peaks from which the pi identifications are made

• ph – A spectrum identifications to be used for the annotation, looking up matches from a spectrum and the theoretical spectrum inferred from the identifications sequence

• tg – A TheoreticalSpectrumGenerator to infer the theoretical spectrum. Its own parameters define which ion types are referred

• sa – A SpectrumAlignment to match the theoretical spectrum with the measured. Its own parameters define the match tolerance

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getName()

Cython signature: String getName() Returns the name

getParameters()

Cython signature: Param getParameters() Returns the parameters

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

setName()

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

setParameters()

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