SwathFile

class pyopenms.SwathFile

Bases: object

Cython implementation of _SwathFile

Original C++ documentation is available here

– Inherits from [‘ProgressLogger’]

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: SwathFile) → None

Methods

__init__

Overload:

endProgress(self)

Ends the progress display

getLogType(self)

Returns the type of progress log being used

loadMzML(self, file_, tmp, exp_meta, readoptions)

Loads a Swath run from a single mzML file

loadMzXML(self, file_, tmp, exp_meta, ...)

Loads a Swath run from a single mzXML file

loadSplit(self, file_list, tmp, exp_meta, ...)

Loads a Swath run from a list of split mzML files

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)

endProgress(self) → None

Ends the progress display

getLogType(self) → int

Returns the type of progress log being used

loadMzML(self, file_: Union[bytes, str, String], tmp: Union[bytes, str, String], exp_meta: ExperimentalSettings, readoptions: Union[bytes, str, String]) → List[SwathMap]

Loads a Swath run from a single mzML file

Using the plugin_consumer, you can provide a custom consumer which will be chained into the process of loading the data and making it available (depending on readoptions). This is useful if you want to modify the data a priori or extract some other information using MSDataTransformingConsumer (for example). Make sure it leaves the data intact, such that the returned SwathMaps are actually useful

Parameters

  • file – Input filename

  • tmp – Temporary directory (for cached data)

  • exp_meta – Experimental metadata from mzML file

  • readoptions – How are spectra accessed after reading - tradeoff between memory usage and time (disk caching)

  • plugin_consumer – An intermediate custom consumer

Returns

Swath maps for MS2 and MS1 (unless readoptions == split, which returns no data)

loadMzXML(self, file_: Union[bytes, str, String], tmp: Union[bytes, str, String], exp_meta: ExperimentalSettings, readoptions: Union[bytes, str, String]) → List[SwathMap]

Loads a Swath run from a single mzXML file

loadSplit(self, file_list: List[bytes], tmp: Union[bytes, str, String], exp_meta: ExperimentalSettings, readoptions: Union[bytes, str, String]) → List[SwathMap]

Loads a Swath run from a list of split mzML files

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: Union[bytes, str, String]) → None