#include <OpenMS/APPLICATIONS/SearchEngineBase.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/String.h>
#include <OpenMS/FORMAT/CsvFile.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/MzIdentMLFile.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/SpectrumMetaDataLookup.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/SYSTEM/JavaInfo.h>
#include <QProcessEnvironment>
#include <algorithm>
#include <fstream>
#include <map>
#include <cstddef>