SpectrumLookup

class pyopenms.SpectrumLookup

Bases: object

Cython implementation of _SpectrumLookup

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1SpectrumLookup.html

__init__()

Cython signature: void SpectrumLookup()

Methods

__init__	Cython signature: void SpectrumLookup()
addReferenceFormat	Cython signature: void addReferenceFormat(String regexp)
empty	Cython signature: bool empty() Check if any spectra were set
extractScanNumber	Cython signature: int extractScanNumber(const String & native_id, const String & native_id_type_accession)
findByIndex	Cython signature: size_t findByIndex(size_t index, bool count_from_one)
findByNativeID	Cython signature: size_t findByNativeID(String native_id)
findByRT	Cython signature: size_t findByRT(double rt)
findByReference	Cython signature: size_t findByReference(String spectrum_ref)
findByScanNumber	Cython signature: size_t findByScanNumber(size_t scan_number)
readSpectra	Cython signature: void readSpectra(MSExperiment spectra, String scan_regexp)

Attributes

rt_tolerance

addReferenceFormat()

Cython signature: void addReferenceFormat(String regexp)

Parameters

regexp – Regular expression defining the format

empty()

Cython signature: bool empty() Check if any spectra were set

extractScanNumber()

Cython signature: int extractScanNumber(const String & native_id, const String & native_id_type_accession)

findByIndex()

Cython signature: size_t findByIndex(size_t index, bool count_from_one)

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()

Cython signature: size_t findByNativeID(String native_id)

Parameters

native_id – Native ID to look up

Returns

Index of the spectrum that matched

findByRT()

Cython signature: size_t findByRT(double rt)

Parameters

rt – Retention time to look up

Returns

Index of the spectrum that matched

findByReference()

Cython signature: size_t findByReference(String spectrum_ref)

Parameters

spectrum_ref – Spectrum reference to parse

Returns

Index of the spectrum that matched

findByScanNumber()

Cython signature: size_t findByScanNumber(size_t scan_number)

Parameters

scan_number – Scan number to look up

Returns

Index of the spectrum that matched

readSpectra()

Cython signature: void readSpectra(MSExperiment spectra, String scan_regexp)

Parameters

• spectra – Container of spectra

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

rt_tolerance