SwathFile#
- class pyopenms.SwathFile#
Bases:
object
Cython implementation of _SwathFile
- Original C++ documentation is available here
– Inherits from [‘ProgressLogger’]
Methods
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_: bytes | str | String, tmp: bytes | str | String, exp_meta: ExperimentalSettings, readoptions: 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_: bytes | str | String, tmp: bytes | str | String, exp_meta: ExperimentalSettings, readoptions: bytes | str | String) List[SwathMap] #
Loads a Swath run from a single mzXML file
- loadSplit(self, file_list: List[bytes], tmp: bytes | str | String, exp_meta: ExperimentalSettings, readoptions: 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