Here is a list of all class members with links to the classes they belong to:

- r -

• r_r_obj_ : MzQuantMLHandler
• r_rtemp_ : MzQuantMLHandler
• r_squared_ : LinearRegression
• r_value : PeakShape
• RADIALEJECTIONLINEARIONTRAP : MassAnalyzer
• radius : LocalLinearMap::LLMParam
• radius_ : PeakPickerCWT
• random() : String
• range : SILACFiltering::BlacklistEntry
• RangeManager() : RangeManager< D >
• RangeManagerType : ConsensusMap , FeatureMap< FeatureT > , MSExperiment< PeakT, ChromatogramPeakT >
• rank_ : PeptideHit , ProteinHit , IdentificationHit
• rank_sp_weights_ : SequestOutfile
• ranked_() : ConsensusID
• raster() : LinearResampler , LinearResamplerAlign
• raster_align() : LinearResamplerAlign
• raster_interpolate() : LinearResamplerAlign
• rasterExperiment() : LinearResampler
• Ratio() : ConsensusFeature::Ratio
• ratio_max_ : FuzzyStringComparator
• ratio_max_allowed_ : FuzzyStringComparator
• ratio_value_ : ConsensusFeature::Ratio
• ratios_ : ConsensusFeature
• raw_data_first : TwoDOptimization::Data
• raw_files_ : MSQuantifications::Assay
• raw_spec_names : LCMS
• RAWDATA : SpectrumSettings
• RawData() : RawData
• RawDataArrayType : EGHFitter1D::Data , EmgFitter1D::Data , Fitter1D , LmaGaussFitter1D::Data , LmaIsotopeFitter1D::Data , ModelFitter< PeakType, FeatureType >
• RawDataVector : OptimizePeakDeconvolution , OptimizePick
• rawIsotopes_ : ConsensusIsotopePattern
• RawMSSignalSimulation() : RawMSSignalSimulation
• RawTandemMSSignalSimulation() : RawTandemMSSignalSimulation
• rbegin() : ConstRefVector< ContainerT > , SparseVector< Value > , MassTrace
• rdbuf() : LogStream
• reachable_ : TOPPASVertex
• ReactionMonitoringTransition() : ReactionMonitoringTransition
• read() : GzipIfstream , Bzip2Ifstream
• readable() : File
• readBytes() : Bzip2InputStream , GzipInputStream
• readChromatogram_() : CachedmzML
• readChromatogramFast() : CachedmzML
• readConsoleSize_() : TOPPBase
• readElementsFromFile_() : EmpiricalFormula
• readFromFile() : PILISModel
• readFromFile_() : ElementDB
• readFromOBOFile() : ModificationsDB
• readFromUnimodXMLFile() : ModificationsDB
• readMappingFile_() : OMSSAXMLFile
• readMemdump() : CachedmzML
• readNextLine_() : FuzzyStringComparator
• readOutHeader() : InspectOutfile , SequestOutfile
• readProblem() : LPWrapper
• readResiduesFromFile_() : ResidueDB
• readResponseHeader() : MascotRemoteQuery
• readRTMZCharge_() : PepXMLFile
• readSingleSpectrum() : CachedmzML
• readSpectrum_() : CachedmzML
• readSpectrumFast() : CachedmzML
• readTSVInput_() : TransitionTSVReader
• readUnstructuredTSVInput_() : TransitionTSVReader
• readyReadSlot() : MascotRemoteQuery
• reagent_name_ : Modification
• real_2D_ : TwoDOptimization
• real_RT_votes_cutoff_ : FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >
• RealMassDecomposer() : RealMassDecomposer
• RealType : AsymmetricStatistics< Real > , BasicStatistics< RealT >
• recalculateAxes() : SpectrumCanvas
• recalculateAxes_() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
• recalculateCurrentLayerDotGradient() : Spectrum2DCanvas
• recalculateDotGradient_() : Spectrum2DCanvas , Spectrum3DOpenGLCanvas
• recalculateRanges_() : SpectrumCanvas
• recalculateSnapFactor_() : Spectrum1DCanvas , Spectrum2DCanvas , SpectrumCanvas
• recent_actions_ : TOPPViewBase
• recent_files_ : TOPPViewBase
• recomputeConsensus_() : BaseLabeler
• reconstructChannelInfo_() : ItraqQuantifier
• record_length_ : InspectOutfile
• recursion_depth_ : ProgressLogger
• reduce() : DistanceMatrix< Value >
• reduce_by_factor_ : ParentPeakMower
• reducePermuts_() : CompNovoIdentification , CompNovoIdentificationCID
• reestimate_mt_sd_ : MassTraceDetection
• ref : HierarchicalClustering< PointRef >::TreeNode
• ref_ : PrecisionWrapper< FloatingPointType >
• ref_intens : IsotopeWaveletTransform< PeakType >::BoxElement
• ref_param_ : MzMLHandler< MapType >
• Reference : FeatureMap< FeatureT >
• reference : AASequence::ConstIterator , AASequence::Iterator , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType > , Matrix< Value > , SparseVector< Value > , IntensityIteratorWrapper< IteratorT > , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
• Reference : Matrix< Value >
• reference_ : MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering , IsotopeWaveletTransform< PeakType >::TransSpectrum
• reference_index_ : MapAlignmentAlgorithmIdentification
• refine_ : XTandemInfile
• refine_max_valid_evalue_ : XTandemInfile
• REFLECTRON : Instrument
• reflectron_state_ : MassAnalyzer , MassAnalyzerVisualizer
• ReflectronState : MassAnalyzer
• REFLSTATENULL : MassAnalyzer
• refreshModificationList() : ModifierRep
• refreshParameters() : TOPPASBase , TOPPASScene , TOPPASToolVertex
• refreshPipelineParameters() : TOPPASBase
• RefreshStatus : TOPPASScene
• reg_models : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• region_ : SimpleExtender< PeakType, FeatureType >
• region_rt_span_ : EGHTraceFitter< PeakType > , GaussTraceFitter< PeakType >
• registerAt() : LogStreamNotifier
• registerChildren() : BaseGroupFinder , BaseSuperimposer , FeatureGroupingAlgorithm , MapAlignmentAlgorithm , MapAlignmentEvaluationAlgorithm , PepIterator , ClusterFunctor , BinnedSpectrumCompareFunctor , PeakSpectrumCompareFunctor , FilterFunctor , BaseLabeler , BaseModel< D > , FeatureFinderAlgorithm< PeakType, FeatureType > , Fitter1D , BaseModel< D >
• registerDoubleList_() : TOPPBase
• registerDoubleOption_() : TOPPBase
• registered_at_ : LogStreamNotifier
• registeredProducts() : Factory< FactoryProduct >
• registerExperiment() : MSQuantifications
• registerFactory() : SingletonRegistry
• registerFlag_() : TOPPBase
• registerFullParam_() : TOPPBase
• registerInputFile_() : TOPPBase
• registerInputFileList_() : TOPPBase
• registerIntList_() : TOPPBase
• registerIntOption_() : TOPPBase
• registerName() : MetaInfoRegistry
• registerOptionsAndFlags_() : TOPPBase , TOPPRNPxl , TOPPRNPxlXICFilter
• registerOutputFile_() : TOPPBase
• registerOutputFileList_() : TOPPBase
• registerParamEntry_() : TOPPBase
• registerProduct() : Factory< FactoryProduct >
• registerProtein_() : ProtXMLFile
• registerStream() : StreamHandler
• registerStringList_() : TOPPBase
• registerStringOption_() : TOPPBase
• registerSubsection_() : TOPPBase
• registerTOPPSubsection_() : TOPPBase
• registry() : MetaInfo
• registry_ : MetaInfo
• reindexed_peptides : ProteinResolver::ResolverResult
• reindexed_proteins : ProteinResolver::ResolverResult
• reindexingNodes_() : ProteinResolver
• rel_error_ : LevMarqFitter1D
• rel_prec_error : RNPxlReportRow
• relative_peak_position : SILACFiltering::BlacklistEntry
• released() : TOPPASVertex
• relevant : FeatureDistance::DistanceParams_
• reliability : MzTabProteinSectionRow , MzTabPeptideSectionRow , MzTabSmallMoleculeSectionRow
• reliability_score_ : MzTabModification
• remove() : LogStream , Param , String , DataFilters , File , MultiGradient
• remove_() : MetaInfoVisualizer
• remove_background_peak() : LCElutionPeak
• remove_chromatogram_flag() : LayerData
• remove_feature() : LCMS
• remove_feature_by_ID() : LCMS
• remove_feature_from_list() : LCMS
• remove_overlapping_features() : MRMTransitionGroupPicker
• remove_precursor_near_peaks_ : SequestInfile
• remove_raw_spec_name() : LCMS
• removeAdduct() : Compomer
• removeAll() : Param , TOPPASInputFilesDialog
• removeAllAttachments() : QcMLFile
• removeAllMS2Information() : SHFeature
• removeAttachment() : QcMLFile
• removebutton_ : GradientVisualizer
• removeCurrentRow() : ListTable
• removeData_() : GradientVisualizer
• removeDirRecursively() : File
• removeExtension() : File
• removeFile() : FileWatcher
• removeId() : EnhancedTabBar , TOPPASTabBar
• removeInEdge() : TOPPASVertex
• removeLayer() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas
• removeMetaValue() : MetaInfoInterface
• removeMS2Feature() : SHFeature
• removeNoise() : CentroidData
• removeOutEdge() : TOPPASVertex
• removeOutlierFragments() : ClusteredMS2ConsensusSpectrum
• removeQualityParameter() : QcMLFile
• removeRowButton_ : ListEditor
• removeSelected() : TOPPASInputFilesDialog , TOPPASScene
• removeSelectedItems() : Annotations1DContainer
• removeSmall_() : SILACClustering
• removeTemporaryAnnotations_() : TOPPViewIdentificationViewBehavior
• removeTheoreticalSpectrumLayer_() : TOPPViewIdentificationViewBehavior
• removeTreatment() : Sample
• removeUnreferencedProteinHits() : IDFilter
• removeValue() : MetaInfo
• removeWhitespaces() : String
• removeZeroedElements_() : EmpiricalFormula
• REMPI : IonSource
• renameOutput_() : TOPPASToolVertex
• rend() : ConstRefVector< ContainerT > , SparseVector< Value > , MassTrace
• render() : DBConnection
• renderForImage() : Spectrum1DWidget
• renormalize() : IsotopeDistribution
• replace() : DataFilters
• replaceCVTerm() : CVTermList
• replaceCVTerms() : TraMLProduct , CVTermList
• replacement_ : SVOutStream
• report_summed_ints_ : FeatureFindingMetabo
• reported_mz_ : FeatureFinderAlgorithmPicked< PeakType, FeatureType >
• reportFailure_() : FuzzyStringComparator
• reportSuccess_() : FuzzyStringComparator
• requestClipboardContent() : TOPPASScene
• requestVisibleArea1D() : SpectraIdentificationViewWidget
• require_args_ : TOPPBase
• required : ParameterInformation
• RequiredParameterNotGiven() : RequiredParameterNotGiven
• requirement_level_ : CVMappingRule
• RequirementLevel : CVMappingRule
• rerunTOPPTool() : TOPPViewBase
• res_ : IonDetectorVisualizer , MassAnalyzerVisualizer
• res_base_ : RawMSSignalSimulation
• RES_CONSTANT : RawMSSignalSimulation
• RES_LINEAR : RawMSSignalSimulation
• res_method_ : MassAnalyzerVisualizer
• res_model_ : RawMSSignalSimulation
• RES_SQRT : RawMSSignalSimulation
• res_type_ : MassAnalyzerVisualizer
• resample() : ConsensusMapNormalizerAlgorithmQuantile
• resampleChromatogram_() : MRMTransitionGroupPicker
• rescore() : PrecursorIonSelection
• rescore_() : PrecursorIonSelection
• reserve() : ConstRefVector< ContainerT >
• RESERVOIR : IonSource
• reset() : TOPPASVertex , PrecursorIonSelection , FuzzyStringComparator::StreamElement_ , XMLHandler , MSExperiment< PeakT, ChromatogramPeakT > , Histogram< ValueType, BinSizeType > , StopWatch , TOPPASOutputFileListVertex , TOPPASToolVertex
• resetAlignment() : Spectrum1DCanvas , Spectrum1DWidget
• resetDownstream() : TOPPASScene
• resetErrors() : XMLValidator
• resetMembers_() : FeatureXMLFile , ProtXMLFile
• resetPeakGroupIter() : CentroidData
• resetProcessesQueue() : TOPPASScene
• resetTranslation() : Spectrum3DOpenGLCanvas
• resetZoom() : IDEvaluationBase , TOPPViewBase , SpectrumCanvas
• residual2D_() : TwoDOptimization
• residual_() : EmgFitter1D , EGHFitter1D , EGHTraceFitter< PeakType > , GaussTraceFitter< PeakType > , LmaGaussFitter1D , LmaIsotopeFitter1D
• Residue() : Residue
• residue : SvmTheoreticalSpectrumGenerator::IonType
• residue_mod_names_ : ResidueDB
• residue_names_ : ResidueDB
• residue_sets_ : Residue , ResidueDB
• residue_to_name_ : CompNovoIdentificationBase
• ResidueConstIterator : ResidueDB
• ResidueDB() : ResidueDB
• ResidueIterator : ResidueDB
• ResidueModification() : ResidueModification
• residues_ : ResidueDB
• residues_by_set_ : ResidueDB
• residues_in_upper_case_ : SequestInfile
• residues_table_row_type : IntegerMassDecomposer< ValueType, DecompositionValueType >
• residues_table_type : IntegerMassDecomposer< ValueType, DecompositionValueType >
• ResidueType : Residue
• ResidueTypeToString_() : SvmTheoreticalSpectrumGenerator
• resize() : ConstRefVector< ContainerT > , DistanceMatrix< Value > , Matrix< Value > , SparseVector< Value >
• resizeEvent() : Spectrum3DCanvas , SpectrumCanvas , TOPPASWidget , HistogramWidget
• resizeGL() : Spectrum3DOpenGLCanvas
• RESMETHNULL : MassAnalyzer
• resolution_ : IonDetector , MassAnalyzer
• resolution_method_ : MassAnalyzer
• resolution_type_ : MassAnalyzer
• ResolutionMethod : MassAnalyzer
• RESOLUTIONMODEL : RawMSSignalSimulation
• ResolutionType : MassAnalyzer
• resolveConsensus() : ProteinResolver
• resolveID() : ProteinResolver
• resolver_result_ : ProteinResolver
• resolveUniqueIdConflicts() : UniqueIdIndexer< RandomAccessContainer >
• restoreRotationAndZoom() : Spectrum3DOpenGLCanvas
• restrictions : ParamXMLHandler
• restrictions_ : ListEditorDelegate
• restrictions_index : ParamXMLHandler
• restrictTransitions() : MRMDecoy
• RESTYPENULL : MassAnalyzer
• Result() : PeakWidthEstimator::Result
• result_ : DBOpenDialog
• result_type : mean_and_stddev
• results_path_ : MascotRemoteQuery
• resume_source_ : TOPPASScene
• retention_ : EGHFitter1D , EmgFitter1D , EmgModel
• retention_time : MzTabPeptideSectionRow , MzTabSmallMoleculeSectionRow
• retention_time_ : MascotInfile , MSSpectrum< PeakT >
• RetentionTime() : RetentionTime , TargetedExperiment , IncludeExcludeTarget , ReactionMonitoringTransition
• RETURN_STATUS : NonNegativeLeastSquaresSolver
• reverse() : String
• reverse_ : InPrecursorMZRange< SpectrumType > , HasScanMode< SpectrumType > , IsEmptySpectrum< SpectrumType > , HasPrecursorCharge< SpectrumType > , HasMetaValue< MetaContainer > , InMSLevelRange< SpectrumType > , HasActivationMethod< SpectrumType > , InIntensityRange< PeakType > , InRTRange< SpectrumType > , IsZoomSpectrum< SpectrumType > , InMzRange< PeakType >
• reverse_iterator : Matrix< Value > , ConstRefVector< ContainerT > , MassTrace , SparseVector< Value >
• reverse_map_const_iterator : SparseVector< Value >
• reverse_map_iterator : SparseVector< Value >
• reverseComparator() : ReverseComparator< Cmp >
• ReverseComparator() : ReverseComparator< Cmp >
• ReverseIterator : MSSpectrum< PeakT > , Map< Key, T > , StringList , MSChromatogram< PeakT > , SparseVector< Value > , FeatureMap< FeatureT > , ConstRefVector< ContainerT > , Matrix< Value > , String , ConsensusMap
• reversePeptide() : MRMDecoy
• rhop() : SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstReverseIterator
• RichPeak1D() : RichPeak1D
• RichPeak2D() : RichPeak2D
• RichPeakChromatogram : MRMTransitionGroupPicker , MRMFeatureFinderScoring
• RIGHT : AxisPainter , Compomer
• right : HierarchicalClustering< PointRef >::TreeDistance , HierarchicalClustering< PointRef >::TreeNode , PeakPickerCWT::PeakArea_
• right_child : BinaryTreeNode
• right_endpoint_ : PeakShape
• right_iterator_set_ : PeakShape
• right_splitter_ : HistogramWidget
• right_width : PeakShape
• rip() : IDRipper
• rm_outliers() : MRMRTNormalizer
• RNA : RNPxlReportRow
• RNA_weight : RNPxlReportRow
• rnd_gen_ : RTSimulation , RawMSSignalSimulation , IonizationSimulation , RawTandemMSSignalSimulation
• rng_ : BaseLabeler
• ROCCurve() : ROCCurve
• root_ : Param::ParamIterator , Param
• round_based_mode_ : TOPPASMergerVertex
• round_counter_ : TOPPASVertex
• round_total_ : TOPPASVertex
• roundBasedMode() : TOPPASMergerVertex
• rounding_errors_ : RealMassDecomposer
• RoundPackage : TOPPASVertex
• RoundPackageConstIt : TOPPASVertex
• RoundPackageIt : TOPPASVertex
• RoundPackages : TOPPASVertex
• row() : Matrix< Value >
• row_ : QcMLFile , BaseVisualizerGUI
• rowIndex() : Matrix< Value >
• rownames_ : DataMatrix
• rows() : Matrix< Value >
• rows_ : Matrix< Value >
• rsd_ : LinearRegression
• RT : SpectrumMeta , StablePairFinder , QTClusterFinder , Peak2D , FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::BoxElement , FeatureFinderAlgorithmMRM< PeakType, FeatureType > , ModelFitter< PeakType, FeatureType >
• rt : SILACPoint , RNPxlReportRow , Peptide , LightPeptide
• RT : IsotopeWaveletTransform< PeakType >::BoxElement
• rt_ : PepXMLFile
• rt_bridge_ : InclusionExclusionList::WindowDistance_
• rt_calibrated : TransitionTSVReader::TSVTransition
• rt_end : RawMSSignalSimulation::ContaminantInfo
• rt_extraction_window_ : MRMFeatureFinderScoring
• RT_GAUSSIAN : RawMSSignalSimulation
• RT_index : IsotopeWaveletTransform< PeakType >::BoxElement
• rt_input_data_ : ModelFitter< PeakType, FeatureType >
• RT_interleave_ : FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >
• rt_label_ : TOPPViewBase
• rt_mapping_ : MascotXMLHandler
• rt_max_ : SpectraMerger::SpectraDistance_
• rt_max_spacing : SILACClustering
• rt_min : SILACClustering
• rt_model_file_ : RTSimulation
• rt_normalization_factor_ : MRMFeatureFinderScoring
• rt_probability : PSLPFormulation::IndexTriple
• rt_prot_map_ : PrecursorIonSelectionPreprocessing
• rt_range_ : PeakFileOptions , FeatureFileOptions
• RT_RECTANGULAR : RawMSSignalSimulation
• rt_sampling_rate_ : RTSimulation
• rt_shift_ : Adduct , Compomer
• rt_start : RawMSSignalSimulation::ContaminantInfo
• rt_stat_ : ModelFitter< PeakType, FeatureType >
• rt_tol_ : PepXMLFile
• rt_tolerance_ : IDMapper
• RT_votes_cutoff_ : FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >
• RTBegin() : MSExperiment< PeakT, ChromatogramPeakT > , MSChromatogram< PeakT >
• RTEnd() : MSChromatogram< PeakT > , MSExperiment< PeakT, ChromatogramPeakT > , MSChromatogram< PeakT >
• RtIterator() : RtIterator< FeaFiModuleType >
• RTMapping : MascotXMLFile , MascotXMLHandler
• RTmax_ : InclusionExclusionList::IEWindow
• RTmin_ : InclusionExclusionList::IEWindow
• rts : ReactionMonitoringTransition , Compound , Peptide
• rts_ : IncludeExcludeTarget
• RTSimulation() : RTSimulation
• rubber_band_ : SpectrumCanvas
• rules_ : CVMappingFile , SemanticValidator
• run() : SimplePairFinder , FeatureFindingMetabo , FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType > , ItraqChannelExtractor , MassTraceDetection , ItraqQuantifier , FeatureFinderAlgorithmSimplest< PeakType, FeatureType > , TOPPASVertex , BaseGroupFinder , FeatureFinderAlgorithmSH< PeakType, FeatureType > , FeatureFinderAlgorithmSimple< PeakType, FeatureType > , TOPPASInputFileListVertex , FeatureFinderAlgorithm< PeakType, FeatureType > , TOPPASMergerVertex , PoseClusteringShiftSuperimposer , LabeledPairFinder , StablePairFinder , FeatureFinderAlgorithmPicked< PeakType, FeatureType > , MassTraceDetection , TOPPASOutputFileListVertex , FeatureFinderAlgorithmMRM< PeakType, FeatureType > , TOPPASToolVertex , MascotRemoteQuery , QTClusterFinder , BaseSuperimposer , FeatureFinder , QTClusterFinder , PoseClusteringAffineSuperimposer
• run_() : QTClusterFinder
• runNextProcess() : TOPPASScene
• running_ : TOPPASScene
• running_avg_ : SimpleExtender< PeakType, FeatureType >
• runPipeline() : TOPPASBase , TOPPASScene
• runQualityAts_ : QcMLFile
• runQualityQPs_ : QcMLFile
• runTOPPTool_() : TOPPViewBase
• rWidth : PenaltyFactors