SpectrumAnnotator#

class pyopenms.SpectrumAnnotator#

Bases: object

Cython implementation of _SpectrumAnnotator

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’]

__init__()#

Overload:

__init__(self) → None

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

Overload:

__init__(self, in_0: SpectrumAnnotator) → None

Methods

__init__

Overload:

addIonMatchStatistics(self, pi, spec, tg, sa)

Adds ion match statistics to pi PeptideIdentifcation

annotateMatches(self, spec, ph, tg, sa)

Adds ion match annotation to the spec input spectrum

getDefaults(self)

Returns the default parameters

getName(self)

Returns the name

getParameters(self)

Returns the parameters

getSubsections(self)

setName(self, in_0)

Sets the name

setParameters(self, param)

Sets the parameters
addIonMatchStatistics(self, pi: PeptideIdentification, spec: MSSpectrum, tg: TheoreticalSpectrumGenerator, sa: SpectrumAlignment) → None#

Adds ion match statistics to pi PeptideIdentifcation

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(self, spec: MSSpectrum, ph: PeptideHit, tg: TheoreticalSpectrumGenerator, sa: SpectrumAlignment) → None#

Adds ion match annotation to the spec input spectrum

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(self) → Param#

Returns the default parameters

getName(self) → bytes | str | String#

Returns the name

getParameters(self) → Param#

Returns the parameters

getSubsections(self) → List[bytes]#
setName(self, in_0: bytes | str | String) → None#

Sets the name

setParameters(self, param: Param) → None#

Sets the parameters