OpenSwathWorkflow.h File Reference

#include <OpenMS/INTERFACES/IMSDataConsumer.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathHelper.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SimpleOpenMSSpectraAccessFactory.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.h>
#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMRTNormalizer.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:

Go to the source code of this file.

Classes
struct	ChromExtractParams
	ChromatogramExtractor parameters. More...
class	OpenSwathWorkflowBase
class	OpenSwathWorkflow
	Execute all steps in an OpenSwath analysis. More...

Namespaces
namespace	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:

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.