SpectrumMetaDataLookup

class pyopenms.SpectrumMetaDataLookup

Bases: object

Cython implementation of _SpectrumMetaDataLookup

Original C++ documentation is available here

– Inherits from [‘SpectrumLookup’]

__init__(self) → None

Methods

__init__(self)
addMissingRTsToPeptideIDs	__static_SpectrumMetaDataLookup_addMissingRTsToPeptideIDs(in_0: List[PeptideIdentification] , filename: Union[bytes, str, String] , stop_on_error: bool ) -> bool
addMissingSpectrumReferences	__static_SpectrumMetaDataLookup_addMissingSpectrumReferences(in_0: List[PeptideIdentification] , filename: Union[bytes, str, String] , stop_on_error: bool , override_spectra_data: bool , override_spectra_references: bool , proteins: List[ProteinIdentification] ) -> bool
addReferenceFormat(self, regexp)	Register a possible format for a spectrum reference
empty(self)	Check if any spectra were set
extractScanNumber(self, native_id, ...)
findByIndex(self, index, count_from_one)	Look up spectrum by index (position in the vector of spectra)
findByNativeID(self, native_id)	Look up spectrum by native ID
findByRT(self, rt)	Look up spectrum by retention time (RT)
findByReference(self, spectrum_ref)	Look up spectrum by reference
findByScanNumber(self, scan_number)	Look up spectrum by scan number (extracted from the native ID)
getSpectrumMetaData	__static_SpectrumMetaDataLookup_getSpectrumMetaData(spectrum: MSSpectrum , meta: SpectrumMetaData ) -> None
readSpectra	Overload:
setSpectraDataRef(self, spectra_data)

addMissingRTsToPeptideIDs()

__static_SpectrumMetaDataLookup_addMissingRTsToPeptideIDs(in_0: List[PeptideIdentification] , filename: Union[bytes, str, String] , stop_on_error: bool ) -> bool

addMissingSpectrumReferences()

__static_SpectrumMetaDataLookup_addMissingSpectrumReferences(in_0: List[PeptideIdentification] , filename: Union[bytes, str, String] , stop_on_error: bool , override_spectra_data: bool , override_spectra_references: bool , proteins: List[ProteinIdentification] ) -> bool

addReferenceFormat(self, regexp: Union[bytes, str, String]) → None

Register a possible format for a spectrum reference

Parameters

regexp – Regular expression defining the format

empty(self) → bool

Check if any spectra were set

extractScanNumber(self, native_id: Union[bytes, str, String], native_id_type_accession: Union[bytes, str, String]) → int

findByIndex(self, index: int, count_from_one: bool) → int

Look up spectrum by index (position in the vector of spectra)

Parameters

• index – Index to look up

• count_from_one – Do indexes start counting at one (default zero)?

Returns

Index of the spectrum that matched

findByNativeID(self, native_id: Union[bytes, str, String]) → int

Look up spectrum by native ID

Parameters

native_id – Native ID to look up

Returns

Index of the spectrum that matched

findByRT(self, rt: float) → int

Look up spectrum by retention time (RT)

Parameters

rt – Retention time to look up

Returns

Index of the spectrum that matched

findByReference(self, spectrum_ref: Union[bytes, str, String]) → int

Look up spectrum by reference

Parameters

spectrum_ref – Spectrum reference to parse

Returns

Index of the spectrum that matched

findByScanNumber(self, scan_number: int) → int

Look up spectrum by scan number (extracted from the native ID)

Parameters

scan_number – Scan number to look up

Returns

Index of the spectrum that matched

getSpectrumMetaData()

__static_SpectrumMetaDataLookup_getSpectrumMetaData(spectrum: MSSpectrum , meta: SpectrumMetaData ) -> None

readSpectra()

Overload:

readSpectra(self, spectra: MSExperiment, scan_regexp: Union[bytes, str, String], get_precursor_rt: bool) → None

Read spectra and store their meta data

Parameters

• SpectrumContainer – Spectrum container class, must support size and operator[]

• spectra – Container of spectra

• scan_regexp – Regular expression for matching scan numbers in spectrum native IDs (must contain the named group “?<SCAN>”)

• get_precursor_rt – Assign precursor retention times? (This relies on all precursor spectra being present and in the right order.)

Overload:

readSpectra(self, spectra: MSExperiment, scan_regexp: Union[bytes, str, String]) → None

Read and index spectra for later look-up

Parameters

• spectra – Container of spectra

• scan_regexp – Regular expression for matching scan numbers in spectrum native IDs (must contain the named group “?<SCAN>”. For example, “scan=(?<SCAN>d+)”).

setSpectraDataRef(self, spectra_data: Union[bytes, str, String]) → None