ChromatogramExtractorAlgorithm

class pyopenms.ChromatogramExtractorAlgorithm

Bases: object

Cython implementation of _ChromatogramExtractorAlgorithm

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1ChromatogramExtractorAlgorithm.html: – Inherits from [‘ProgressLogger’]

__init__()

Cython signature: void ChromatogramExtractorAlgorithm()
Cython signature: void ChromatogramExtractorAlgorithm(ChromatogramExtractorAlgorithm &)

Methods

`__init__`	Cython signature: void ChromatogramExtractorAlgorithm()
`endProgress`	Cython signature: void endProgress() Ends the progress display
`extractChromatograms`	Cython signature: void extractChromatograms(shared_ptr[SpectrumAccessOpenMS] input, libcpp_vector[shared_ptr[OSChromatogram]] & output, libcpp_vector[ExtractionCoordinates] extraction_coordinates, double mz_extraction_window, bool ppm, double im_extraction_window, String filter)
`getLogType`	Cython signature: LogType getLogType() Returns the type of progress log being used
`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

extractChromatograms()

Cython signature: void extractChromatograms(shared_ptr[SpectrumAccessOpenMS] input, libcpp_vector[shared_ptr[OSChromatogram]] & output, libcpp_vector[ExtractionCoordinates] extraction_coordinates, double mz_extraction_window, bool ppm, double im_extraction_window, String filter)

Param

input Input spectral map

Parameters

output – Output chromatograms (XICs)
extraction_coordinates – Extracts around these coordinates (from rt_start to rt_end in seconds - extracts the whole chromatogram if rt_end - rt_start < 0).
mz_extraction_window – Extracts a window of this size in m/z

dimension in Th or ppm (e.g. a window of 50 ppm means an extraction of 25 ppm on either side) :param ppm: Whether mz_extraction_window is in ppm or in Th :param filter: Which function to apply in m/z space (currently “tophat” only)

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

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)