OpenSwathBase.h File Reference

#include <OpenMS/APPLICATIONS/OpenMS_CLIConfig.h>
#include <memory>
#include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>
#include <OpenMS/FORMAT/DATAACCESS/MSDataSqlConsumer.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/FORMAT/SwathFile.h>
#include <OpenMS/ANALYSIS/OPENSWATH/SwathWindowLoader.h>
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionTSVFile.h>
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionPQPFile.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathLibraryIDNormalizer.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/DataAccessHelper.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SimpleOpenMSSpectraAccessFactory.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/ANALYSIS/OPENSWATH/OpenSwathWorkflow.h>
#include <cassert>
#include <limits>
#include <OpenMS/APPLICATIONS/TOPPBase.h>

Go to the source code of this file.

Classes
class	TOPPOpenSwathBase
	Shared TOPPBase scaffolding for OpenSWATH-family CLI tools (currently OpenSwathWorkflow). More...
struct	TOPPOpenSwathBase::CalibrationResult
	Per-run outputs of the RT / m/z / IM calibration step. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::TOPPOpenSwathBase::CalibrationResult

struct OpenMS::TOPPOpenSwathBase::CalibrationResult

Per-run outputs of the RT / m/z / IM calibration step.

Populated by the consuming tool (via CalibrationWorkflow) and consumed later during the analytical extraction phase. Window fields default to -1.0 meaning "not computed" — callers must check before using them as extraction windows.

Class Members
double	ms1_im_window { -1.0 }	MS1 ion mobility extraction window (full width, native IM units). -1 if not computed/applicable.
double	ms1_mz_window_ppm { -1.0 }	MS1 m/z extraction window (full width, ppm). -1 if not computed.
double	ms2_im_window { -1.0 }	MS2 ion mobility extraction window (full width, native IM units). -1 if not computed/applicable.
double	ms2_mz_window_ppm { -1.0 }	MS2 m/z extraction window (full width, ppm). -1 if not computed.
TransformationDescription	rt_trafo	RT normalization transformation (fitted Trafo)