#include <OpenMS/APPLICATIONS/SearchEngineBase.h>
#include <OpenMS/ANALYSIS/ID/PercolatorFeatureSetHelper.h>
#include <OpenMS/ANALYSIS/ID/PeptideIndexing.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/CHEMISTRY/ProteaseDB.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/FORMAT/CsvFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/SpectrumMetaDataLookup.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/SYSTEM/TempFiles.h>
#include <OpenMS/SYSTEM/JavaInfo.h>
#include <boost/interprocess/sync/file_lock.hpp>
#include <algorithm>
#include <fstream>
#include <map>
#include <cstddef>