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)__static_SpectrumMetaDataLookup_addMissingRTsToPeptideIDs(in_0: List[PeptideIdentification] , filename: Union[bytes, str, String] , stop_on_error: bool ) -> bool
__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)
__static_SpectrumMetaDataLookup_getSpectrumMetaData(spectrum: MSSpectrum , meta: SpectrumMetaData ) -> None
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: 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: bytes | str | String, native_id_type_accession: 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: 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: 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: 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: 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+)”).