#include <OpenMS/ANALYSIS/OPENSWATH/MRMAssay.h>
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionTSVFile.h>
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionPQPFile.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/FORMAT/TraMLFile.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/ANALYSIS/OPENSWATH/SwathWindowLoader.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <iostream>