#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/FileHandler.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/PROCESSING/RESAMPLING/LinearResamplerAlign.h>
#include <cassert>
#include <limits>

Include dependency graph for OpenSwathWorkflow.h:

This graph shows which files directly or indirectly include this file:

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.

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:

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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.

Classes

Namespaces

Class Documentation

◆ OpenMS::ChromExtractParams