MzMLSpectrumDecoder

class pyopenms.MzMLSpectrumDecoder

Bases: object

Cython implementation of _MzMLSpectrumDecoder

Original C++ documentation is available here

A class to decode input strings that contain an mzML chromatogram or spectrum tag

It uses xercesc to parse a string containing either a exactly one mzML spectrum or chromatogram (from <chromatogram> to </chromatogram> or <spectrum> to </spectrum> tag). It returns the data contained in the binaryDataArray for Intensity / mass-to-charge or Intensity / time

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: MzMLSpectrumDecoder) → None

Methods

__init__	Overload:
domParseChromatogram(self, in_, cptr)	Extract data from a string which contains a full mzML chromatogram
domParseSpectrum(self, in_, cptr)	Extract data from a string which contains a full mzML spectrum
setSkipXMLChecks(self, only)	Whether to skip some XML checks (e.g.

domParseChromatogram(self, in_: bytes | str | String, cptr: _Interfaces_Chromatogram) → None

Extract data from a string which contains a full mzML chromatogram

Extracts data from the input string which is expected to contain exactly one <chromatogram> tag (from <chromatogram> to </chromatogram>). This function will extract the contained binaryDataArray and provide the result as Chromatogram

Parameters:

• in – Input string containing the raw XML

• cptr – Resulting chromatogram

domParseSpectrum(self, in_: bytes | str | String, cptr: _Interfaces_Spectrum) → None

Extract data from a string which contains a full mzML spectrum

Extracts data from the input string which is expected to contain exactly one <spectrum> tag (from <spectrum> to </spectrum>). This function will extract the contained binaryDataArray and provide the result as Spectrum

Parameters:

• in – Input string containing the raw XML

• cptr – Resulting spectrum

setSkipXMLChecks(self, only: bool) → None

Whether to skip some XML checks (e.g. removing whitespace inside base64 arrays) and be fast instead