RNPxlSearch.cpp File Reference

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/METADATA/SpectrumSettings.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/CHEMISTRY/ProteaseDigestion.h>
#include <OpenMS/DATASTRUCTURES/ListUtilsIO.h>
#include <OpenMS/ANALYSIS/ID/PeptideIndexing.h>
#include <OpenMS/ANALYSIS/ID/FalseDiscoveryRate.h>
#include <OpenMS/ANALYSIS/RNPXL/RNPxlDeisotoper.h>
#include <OpenMS/ANALYSIS/RNPXL/RNPxlModificationsGenerator.h>
#include <OpenMS/ANALYSIS/RNPXL/ModifiedPeptideGenerator.h>
#include <OpenMS/ANALYSIS/RNPXL/RNPxlReport.h>
#include <OpenMS/ANALYSIS/RNPXL/MorpheusScore.h>
#include <OpenMS/ANALYSIS/RNPXL/RNPxlMarkerIonExtractor.h>
#include <OpenMS/ANALYSIS/RNPXL/RNPxlFragmentAnnotationHelper.h>
#include <OpenMS/CHEMISTRY/ElementDB.h>
#include <OpenMS/CHEMISTRY/ResidueDB.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/CHEMISTRY/ProteaseDB.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/FILTERING/TRANSFORMERS/ThresholdMower.h>
#include <OpenMS/FILTERING/TRANSFORMERS/NLargest.h>
#include <OpenMS/FILTERING/TRANSFORMERS/WindowMower.h>
#include <OpenMS/FILTERING/TRANSFORMERS/Normalizer.h>
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/ANALYSIS/RNPXL/HyperScore.h>
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <boost/regex.hpp>
#include <map>
#include <algorithm>

Classes
class	RNPxlSearch
struct	RNPxlSearch::FragmentAdductDefinition_
struct	RNPxlSearch::MS2AdductsOfSinglePrecursorAdduct
struct	RNPxlSearch::RNPxlParameterParsing
struct	RNPxlSearch::AnnotatedHit
	Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space. More...
class	RNPxlSearch::RNPxlFragmentIonGenerator

Macros
#define	NUMBER_OF_THREADS   (1)

Functions
int	main (int argc, const char **argv)

Macro Definition Documentation

NUMBER_OF_THREADS

#define NUMBER_OF_THREADS   (1)

Function Documentation

main()

int main	(	int	argc,
		const char **	argv
	)

References TOPPBase::main().