| OpenMS 2.5.0

Classes | Namespaces
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>`

Go to the source code of 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.

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.