#include <OpenMS/APPLICATIONS/SearchEngineBase.h>
#include <OpenMS/ANALYSIS/ID/PeptideIndexing.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/PepXMLFile.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/HANDLERS/IndexedMzMLDecoder.h>
#include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/CHEMISTRY/ProteaseDB.h>
#include <OpenMS/CHEMISTRY/ResidueDB.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/SYSTEM/File.h>
#include <fstream>
#include <QStringList>