#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentTransformer.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/CONCEPT/VersionInfo.h>
#include <OpenMS/DATASTRUCTURES/StringListUtils.h>
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <OpenMS/FORMAT/TraMLFile.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/FORMAT/TransformationXMLFile.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <boost/regex.hpp>