SwathFile

class pyopenms.SwathFile

Bases: object

Cython implementation of _SwathFile

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1SwathFile.html: – Inherits from [‘ProgressLogger’]

__init__()

Cython signature: void SwathFile()
Cython signature: void SwathFile(SwathFile &)

Methods

`__init__`	Cython signature: void SwathFile()
`endProgress`	Cython signature: void endProgress() Ends the progress display
`getLogType`	Cython signature: LogType getLogType() Returns the type of progress log being used
`loadMzML`	Cython signature: libcpp_vector[SwathMap] loadMzML(String file_, String tmp, shared_ptr[ExperimentalSettings] exp_meta, String readoptions)
`loadMzXML`	Cython signature: libcpp_vector[SwathMap] loadMzXML(String file_, String tmp, shared_ptr[ExperimentalSettings] exp_meta, String readoptions) Loads a Swath run from a single mzXML file
`loadSplit`	Cython signature: libcpp_vector[SwathMap] loadSplit(StringList file_list, String tmp, shared_ptr[ExperimentalSettings] exp_meta, String readoptions) Loads a Swath run from a list of split mzML files
`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)

endProgress(): Cython signature: void endProgress() Ends the progress display

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

loadMzML()

Cython signature: libcpp_vector[SwathMap] loadMzML(String file_, String tmp, shared_ptr[ExperimentalSettings] exp_meta, String readoptions)

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 —– :param file: Input filename :param tmp: Temporary directory (for cached data) :param exp_meta: Experimental metadata from mzML file :param readoptions: How are spectra accessed after reading - tradeoff between memory usage and time (disk caching) :param plugin_consumer: An intermediate custom consumer :returns: Swath maps for MS2 and MS1 (unless readoptions == split, which returns no data)

loadMzXML(): Cython signature: libcpp_vector[SwathMap] loadMzXML(String file_, String tmp, shared_ptr[ExperimentalSettings] exp_meta, String readoptions) Loads a Swath run from a single mzXML file

loadSplit(): Cython signature: libcpp_vector[SwathMap] loadSplit(StringList file_list, String tmp, shared_ptr[ExperimentalSettings] exp_meta, String readoptions) Loads a Swath run from a list of split mzML files

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)