OpenNuXL.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/FileHandler.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/FILTERING/CALIBRATION/PrecursorCorrection.h>
#include <OpenMS/ANALYSIS/XLMS/OPXLSpectrumProcessingAlgorithms.h>
#include <OpenMS/CHEMISTRY/DecoyGenerator.h>
#include <OpenMS/FORMAT/LibSVMEncoder.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderIdentificationAlgorithm.h>
#include <OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLModificationsGenerator.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLReport.h>
#include <OpenMS/ANALYSIS/NUXL/MorpheusScore.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLAnnotatedHit.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLAnnotateAndLocate.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLConstants.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLFDR.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLMarkerIonExtractor.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLFeatureAugmentation.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLFragmentAnnotationHelper.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLFragmentIonGenerator.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLParameterParsing.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLPresets.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/CHEMISTRY/ModifiedPeptideGenerator.h>
#include <OpenMS/FILTERING/CALIBRATION/InternalCalibration.h>
#include <OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h>
#include <OpenMS/ANALYSIS/QUANTITATION/KDTreeFeatureMaps.h>
#include <OpenMS/ANALYSIS/ID/PrecursorPurity.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/FILTERING/TRANSFORMERS/SqrtMower.h>
#include <OpenMS/COMPARISON/SPECTRA/BinnedSpectralContrastAngle.h>
#include <OpenMS/METADATA/SpectrumLookup.h>
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/ANALYSIS/NUXL/HyperScore.h>
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>
#include <OpenMS/MATH/STATISTICS/StatisticFunctions.h>
#include <boost/regex.hpp>
#include <boost/math/distributions/binomial.hpp>
#include <boost/math/distributions/normal.hpp>
#include <boost/math/distributions/beta.hpp>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderMultiplexAlgorithm.h>
#include <OpenMS/CONCEPT/VersionInfo.h>
#include <OpenMS/ANALYSIS/SVM/SimpleSVM.h>
#include <map>
#include <algorithm>
#include <iterator>
#include <OpenMS/ANALYSIS/ID/AScore.h>
#include <OpenMS/FILTERING/ID/IDFilter.h>
#include <OpenMS/COMPARISON/SPECTRA/BinnedSpectrum.h>
#include <QtCore/QDir>
#include <OpenMS/ANALYSIS/NUXL/unused.h>

Classes
struct	NuXLRTPrediction
struct	ImmoniumIonsInPeptide

Macros
#define	NUMBER_OF_THREADS   (1)
#define	CALCULATE_LONGEST_TAG
#define	CONSIDER_AA_LOSSES   1

Macro Definition Documentation

CALCULATE_LONGEST_TAG

#define CALCULATE_LONGEST_TAG

CONSIDER_AA_LOSSES

#define CONSIDER_AA_LOSSES   1

NUMBER_OF_THREADS

#define NUMBER_OF_THREADS   (1)