OpenMS
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#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/PROCESSING/ID/IDFilter.h>
#include <OpenMS/FORMAT/CsvFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/FORMAT/PepXMLFile.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/SYSTEM/JavaInfo.h>
#include <QProcessEnvironment>
#include <cstddef>
#include <fstream>
#include <map>