MzIdentMLFile

class pyopenms.MzIdentMLFile

Bases: object

Cython implementation of _MzIdentMLFile

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1MzIdentMLFile.html

– Inherits from [‘ProgressLogger’]

__init__()

  • Cython signature: void MzIdentMLFile()

  • Cython signature: void MzIdentMLFile(MzIdentMLFile &)

Methods

__init__

  • Cython signature: void MzIdentMLFile()

endProgress

Cython signature: void endProgress() Ends the progress display

getLogType

Cython signature: LogType getLogType() Returns the type of progress log being used

isSemanticallyValid

Cython signature: bool isSemanticallyValid(String filename, StringList errors, StringList warnings)

load

Cython signature: void load(String filename, libcpp_vector[ProteinIdentification] & poid, libcpp_vector[PeptideIdentification] & peid)

nextProgress

Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)

setLogType

Cython signature: void setLogType(LogType) Sets the progress log that should be used.

setProgress

Cython signature: void setProgress(ptrdiff_t value) Sets the current progress

startProgress

Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)

store

Cython signature: void store(String filename, libcpp_vector[ProteinIdentification] & poid, libcpp_vector[PeptideIdentification] & peid)
endProgress()

Cython signature: void endProgress() Ends the progress display

getLogType()

Cython signature: LogType getLogType() Returns the type of progress log being used

isSemanticallyValid()

Cython signature: bool isSemanticallyValid(String filename, StringList errors, StringList warnings)

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()

Cython signature: void load(String filename, libcpp_vector[ProteinIdentification] & poid, libcpp_vector[PeptideIdentification] & peid)

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()

Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)

setLogType()

Cython signature: void setLogType(LogType) Sets the progress log that should be used. The default type is NONE!

setProgress()

Cython signature: void setProgress(ptrdiff_t value) Sets the current progress

startProgress()

Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)

store()

Cython signature: void store(String filename, libcpp_vector[ProteinIdentification] & poid, libcpp_vector[PeptideIdentification] & peid)

Raises

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