SpectrumAnnotator#

class pyopenms.SpectrumAnnotator#

Bases: object

Cython implementation of _SpectrumAnnotator

Original C++ documentation is available here: – Inherits from [‘DefaultParamHandler’]

__init__()#

Overload:

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

Overload:

Methods

`__init__`
`addIonMatchStatistics`(self, pi, spec, tg, sa)	Adds ion match statistics to pi PeptideIdentifcation
`addPeakAnnotationsToPeptideHit`(self, ph, ...)	Adds peak annotations to the ph PeptideHit
`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

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

Adds peak annotations to the ph PeptideHit

Parameters:

ph – A PeptideHit whose PeakAnnotations vector will be filled with the ion matches
spec – A PeakSpectrum containing the peaks from which the ph 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
include_unmatched_peaks – If true, all spectrum peaks will be included in the PeakAnnotations vector. Unmatched peaks will have empty annotation strings. If false, only matched peaks are included.

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