MzIdentMLFile

class pyopenms.MzIdentMLFile

Bases: object

Cython implementation of _MzIdentMLFile

Original C++ documentation is available here

– Inherits from [‘ProgressLogger’]

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: MzIdentMLFile) → None

Methods

__init__	Overload:
endProgress(self)	Ends the progress display
getLogType(self)	Returns the type of progress log being used
isSemanticallyValid(self, filename, errors, ...)	Checks if a file is valid with respect to the mapping file and the controlled vocabulary
load(self, filename, poid, peid)	Loads the identifications from a MzIdentML file
nextProgress(self)	Increment progress by 1 (according to range begin-end)
setLogType(self, in_0)	Sets the progress log that should be used.
setProgress(self, value)	Sets the current progress
startProgress(self, begin, end, label)
store(self, filename, poid, peid)	Stores the identifications in a MzIdentML file

endProgress(self) → None

Ends the progress display

getLogType(self) → int

Returns the type of progress log being used

isSemanticallyValid(self, filename: bytes | str | String, errors: List[bytes], warnings: List[bytes]) → bool

Checks if a file is valid with respect to the mapping file and the controlled vocabulary

Parameters:

• filename – File name of the file to be checked

• errors – Errors during the validation are returned in this output parameter

• warnings – Warnings during the validation are returned in this output parameter

Raises:

Exception: FileNotFound is thrown if the file could not be opened

load(self, filename: bytes | str | String, poid: List[ProteinIdentification], peid: List[PeptideIdentification]) → None

Loads the identifications from a MzIdentML file

Parameters:

filename – File name of the file to be checked

Raises:

Exception: FileNotFound is thrown if the file could not be opened

Raises:

Exception: ParseError is thrown if an error occurs during parsin

nextProgress(self) → None

Increment progress by 1 (according to range begin-end)

setLogType(self, in_0: int) → None

Sets the progress log that should be used. The default type is NONE!

setProgress(self, value: int) → None

Sets the current progress

startProgress(self, begin: int, end: int, label: bytes | str | String) → None

store(self, filename: bytes | str | String, poid: List[ProteinIdentification], peid: List[PeptideIdentification]) → None

Stores the identifications in a MzIdentML file

Raises:

Exception: UnableToCreateFile is thrown if the file could not be created