OpenSwathWorkflow.h File Reference

#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
#include <OpenMS/INTERFACES/IMSDataConsumer.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathHelper.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SimpleOpenMSSpectraAccessFactory.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathTSVWriter.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMRTNormalizer.h>
#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMTransitionGroupPicker.h>
#include <OpenMS/ANALYSIS/OPENSWATH/SwathMapMassCorrection.h>
#include <OpenMS/FILTERING/TRANSFORMERS/LinearResamplerAlign.h>
#include <cassert>
#include <limits>

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Classes
struct	ChromExtractParams
	ChromatogramExtractor parameters. More...
class	OpenSwathWorkflowBase
class	OpenSwathCalibrationWorkflow
	Execute all steps for retention time and m/z calibration of SWATH-MS data. More...
class	OpenSwathWorkflow
	Execute all steps in an OpenSwath analysis. More...
class	OpenSwathWorkflowSonar
	Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data) More...

Namespaces
	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::ChromExtractParams

struct OpenMS::ChromExtractParams

ChromatogramExtractor parameters.

A small helper struct to pass the parameters for the chromatogram extraction through to the actual algorithm.

Collaboration diagram for ChromExtractParams:

Class Members
double	extra_rt_extract	Whether to extract some extra in the retention time (can be useful if one wants to look at the chromatogram outside the window)
String	extraction_function	The extraction function in mass space.
double	im_extraction_window	Extraction window in ion mobility.
double	min_upper_edge_dist	Whether to not extract anything closer than this (in Da) from the upper edge.
double	mz_extraction_window	Extraction window in Da or ppm (e.g. 50ppm means extraction +/- 25ppm)
bool	ppm	Whether the extraction window is given in ppm or Da.
double	rt_extraction_window	The retention time extraction window.