#include <OpenMS/ANALYSIS/OPENSWATH/SwathQC.h>
#include <OpenMS/ANALYSIS/OPENSWATH/SwathWindowLoader.h>
#include <OpenMS/FORMAT/DATAACCESS/MSDataTransformingConsumer.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/SwathFile.h>
#include <OpenMS/METADATA/ExperimentalSettings.h>
#include <OpenMS/SYSTEM/File.h>
#include <QDir>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>