#include <OpenMS/ANALYSIS/ID/PeptideIndexing.h>
#include <OpenMS/APPLICATIONS/SearchEngineBase.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/PepXMLFile.h>
#include <OpenMS/CHEMISTRY/ProteaseDB.h>
#include <OpenMS/CHEMISTRY/ModifiedPeptideGenerator.h>
#include <OpenMS/SYSTEM/JavaInfo.h>
#include <QtCore/QDir>
#include <QtCore/QProcess>
#include <iostream>