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OpenMS
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#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/String.h>#include <OpenMS/FORMAT/CsvFile.h>#include <OpenMS/FORMAT/FileHandler.h>#include <OpenMS/FORMAT/MzMLFile.h>#include <OpenMS/METADATA/ProteinIdentification.h>#include <OpenMS/METADATA/SpectrumMetaDataLookup.h>#include <OpenMS/SYSTEM/File.h>#include <OpenMS/SYSTEM/JavaInfo.h>#include <QProcessEnvironment>#include <QLockFile>#include <algorithm>#include <fstream>#include <map>#include <cstddef>