SpectrumLookup

class pyopenms.SpectrumLookup

Bases: object

Cython implementation of _SpectrumLookup

Original C++ documentation is available here

__init__(self) → None

Methods

__init__(self)
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)
readSpectra(self, spectra, scan_regexp)	Read and index spectra for later look-up

Attributes

rt_tolerance

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

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+)”).

rt_tolerance