#include <OpenMS/APPLICATIONS/TOPPExternalToolBase.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/PROCESSING/ID/IDFilter.h>
#include <OpenMS/FORMAT/CsvFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/FORMAT/PepXMLFile.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/SYSTEM/TempFiles.h>
#include <OpenMS/SYSTEM/JavaInfo.h>
#include <OpenMS/ANALYSIS/ID/IDScoreSwitcherAlgorithm.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <cstddef>
#include <fstream>
#include <map>