SpectrumMetaDataLookup

class pyopenms.SpectrumMetaDataLookup

Bases: object

Cython implementation of _SpectrumMetaDataLookup

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1SpectrumMetaDataLookup.html

– Inherits from [‘SpectrumLookup’]

__init__()

Cython signature: void SpectrumMetaDataLookup()

Methods

__init__	Cython signature: void SpectrumMetaDataLookup()
addMissingRTsToPeptideIDs	Cython signature: bool addMissingRTsToPeptideIDs(libcpp_vector[PeptideIdentification], String filename, bool stop_on_error)
addMissingSpectrumReferences	Cython signature: bool addMissingSpectrumReferences(libcpp_vector[PeptideIdentification], String filename, bool stop_on_error, bool override_spectra_data, bool override_spectra_references, libcpp_vector[ProteinIdentification] proteins)
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)
getSpectrumMetaData	Cython signature: void getSpectrumMetaData(MSSpectrum spectrum, SpectrumMetaData & meta)
readSpectra	Cython signature: void readSpectra(MSExperiment spectra, String scan_regexp, bool get_precursor_rt)
setSpectraDataRef	Cython signature: void setSpectraDataRef(const String & spectra_data)

addMissingRTsToPeptideIDs()

Cython signature: bool addMissingRTsToPeptideIDs(libcpp_vector[PeptideIdentification], String filename, bool stop_on_error)

addMissingSpectrumReferences()

Cython signature: bool addMissingSpectrumReferences(libcpp_vector[PeptideIdentification], String filename, bool stop_on_error, bool override_spectra_data, bool override_spectra_references, libcpp_vector[ProteinIdentification] proteins)

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

getSpectrumMetaData()

Cython signature: void getSpectrumMetaData(MSSpectrum spectrum, SpectrumMetaData & meta)

readSpectra()

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

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.) - 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>”)

setSpectraDataRef()

Cython signature: void setSpectraDataRef(const String & spectra_data)