MzMLFile

class pyopenms.MzMLFile

Bases: object

Cython implementation of _MzMLFile

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1MzMLFile.html

– Inherits from [‘ProgressLogger’]

Provides methods to load and store MzML files. PeakFileOptions allow to load a reduced subset of the data into an MSExperiment. —– See help(MSExperiment) how data is stored after loading. See help(PeakFileOptions) for available options. —– Usage:

exp = MSExperiment() MzMLFile().load(“test.mzML”, exp) spec = [] for s in exp.getSpectra():

if s.getMSLevel() != 1:

spec.append(s)

exp.setSpectra(spec) MzMLFile().store(“filtered.mzML”, exp)

__init__()

  • Cython signature: void MzMLFile()

  • Cython signature: void MzMLFile(MzMLFile &)

Methods

__init__

  • Cython signature: void MzMLFile()

endProgress

Cython signature: void endProgress() Ends the progress display

getLogType

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

getOptions

Cython signature: PeakFileOptions getOptions()

isSemanticallyValid

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

load

Cython signature: void load(const String & filename, MSExperiment &) Loads from an MzML file.

loadBuffer

Cython signature: void loadBuffer(const String & input, MSExperiment & exp)

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.

setOptions

Cython signature: void setOptions(PeakFileOptions) Set PeakFileOptions to perform filtering during loading.

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(const String & filename, MSExperiment &) Stores a MSExperiment in an MzML file

storeBuffer

Cython signature: void storeBuffer(String & output, MSExperiment exp)

transform

endProgress()

Cython signature: void endProgress() Ends the progress display

getLogType()

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

getOptions()

Cython signature: PeakFileOptions getOptions()

isSemanticallyValid()

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

load()

Cython signature: void load(const String & filename, MSExperiment &) Loads from an MzML file. Spectra and chromatograms are sorted by default (this can be disabled using PeakFileOptions)

loadBuffer()

Cython signature: void loadBuffer(const String & input, MSExperiment & exp)

Parameters

  • buffer – The buffer with the data (i.e. string with content of an mzML file)

  • exp – Is an MSExperiment

Raises

Exception: ParseError is thrown if an error occurs during parsing

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!

setOptions()

Cython signature: void setOptions(PeakFileOptions) Set PeakFileOptions to perform filtering during loading. E.g., to load only MS1 spectra or meta data only

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(const String & filename, MSExperiment &) Stores a MSExperiment in an MzML file

storeBuffer()

Cython signature: void storeBuffer(String & output, MSExperiment exp)

Parameters

  • output – An empty string to store the result

  • exp – Has to be an MSExperiment

transform()