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
• RAIICleanup() : RAIICleanup
• random() : String , StringUtils
• RandomShuffler() : RandomShuffler
• range_x_ : ClusteringGrid
• range_y_ : ClusteringGrid
• RangeManager() : RangeManager< D >
• RangeManagerType : ConsensusMap , FeatureMap , MSExperiment
• rank : CsiFingerIdMzTabWriter::CsiAdapterHit , IDFilter::HasMaxRank< HitType > , OPXLDataStructs::CrossLinkSpectrumMatch , RNPxlReportRow , SiriusMzTabWriter::SiriusAdapterHit , Interpretation
• rank_ : IdentificationHit , PeptideHit , ProteinHit
• rank_sp_weights_ : SequestOutfile
• rankWeightedPermutationPeptideScores_() : AScore
• RANSAC() : RANSAC< TModelType >
• ransac() : RANSAC< TModelType >
• ransac_params_ : MZTrafoModel
• ransac_seed_ : MZTrafoModel
• RANSACParam() : RANSACParam
• raster() : LinearResampler , LinearResamplerAlign
• raster_align() : LinearResamplerAlign
• raster_interpolate() : LinearResamplerAlign
• rasterExperiment() : LinearResampler
• rate_result_ : Ms2IdentificationRate
• Ratio() : ConsensusFeature::Ratio
• ratio_max_ : FuzzyStringComparator
• ratio_max_allowed_ : FuzzyStringComparator
• ratio_value_ : ConsensusFeature::Ratio
• ratios_ : ConsensusFeature
• RAW : FileTypes
• raw_data_first : TwoDOptimization::Data
• raw_files_ : MSQuantifications::Assay
• raw_rt_score : OpenSwath_Scores
• RawDataArrayType : EGHFitter1D::Data , EmgFitter1D::Data , Fitter1D
• RawDataVector : OptimizePeakDeconvolution , OptimizePick
• RawMSSignalSimulation() : RawMSSignalSimulation
• RawTandemMSSignalSimulation() : RawTandemMSSignalSimulation
• rbegin() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , IsotopeDistribution , MassTrace
• rdbuf() : LogStream
• re_ : EnzymaticDigestion
• reachable_ : TOPPASVertex
• ReactionMonitoringTransition() : ReactionMonitoringTransition
• read() : Bzip2Ifstream , CsiFingerIdMzTabWriter , GzipIfstream , OSWFile , SiriusMzTabWriter
• readable() : File
• readAt() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• readBytes() : Bzip2InputStream , GzipInputStream
• readChromatogram() : CachedMzMLHandler
• readChromatogramFast() : CachedMzMLHandler
• readChromatograms() : MzMLSqliteHandler
• readConsoleSize_() : ConsoleUtils
• readDataFast_() : CachedMzMLHandler
• readEntry_() : FASTAFile
• readEnzymesFromFile_() : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• readExperiment() : MzMLSqliteHandler
• readFromFile_() : RibonucleotideDB
• readFromOBOFile() : CrossLinksDB , ModificationsDB
• readFromUnimodXMLFile() : ModificationsDB
• readMappingFile_() : OMSSAXMLFile
• readMemdump() : CachedMzMLHandler
• readMeta_() : OSWFile
• readMinimal() : OSWFile
• readMS1Spectra() : MzMLSqliteSwathHandler
• readMzIdentMLFile() : MzIdentMLDOMHandler
• readNext() : FASTAFile
• readNextLine_() : FuzzyStringComparator
• readOutHeader() : InspectOutfile , SequestOutfile
• readPQPInput_() : TransitionPQPFile
• readProblem() : LPWrapper
• readProtein() : OSWFile
• readQuantData() : PeptideAndProteinQuant
• readResponse() : MascotRemoteQuery
• readResponseHeader() : MascotRemoteQuery
• readRTMZCharge_() : PepXMLFile
• readSpectra() : MzMLSqliteHandler , SpectrumLookup , SpectrumMetaDataLookup
• readSpectraForWindow() : MzMLSqliteSwathHandler
• readSpectrum() : CachedMzMLHandler
• readSpectrumFast() : CachedMzMLHandler
• readStart() : FASTAFile
• readSwathWindows() : MzMLSqliteSwathHandler , SwathWindowLoader
• readToPIN() : OSWFile
• readTransitions_() : OSWFile
• readUnstructuredTSVInput_() : TransitionTSVFile
• reagent_name_ : Modification
• real_2D_ : TwoDOptimization
• real_RT_votes_cutoff_ : FeatureFinderAlgorithmIsotopeWavelet
• RealMassDecomposer() : RealMassDecomposer
• RealType : AsymmetricStatistics< RealT > , BasicStatistics< RealT >
• reannotateTransitions() : MRMAssay
• recalculate_peaks_ : MRMTransitionGroupPicker
• recalculate_peaks_max_z_ : MRMTransitionGroupPicker
• recalculateAxes() : PlotCanvas
• recalculateAxes_() : Plot1DWidget , Plot2DWidget , Plot3DWidget , PlotWidget
• recalculateCurrentLayerDotGradient() : Plot2DCanvas
• recalculateDotGradient_() : Plot2DCanvas , Plot3DOpenGLCanvas
• recalculatePeakBorders_() : MRMTransitionGroupPicker
• recalculateRanges_() : PlotCanvas
• recalculateSnapFactor_() : Plot1DCanvas , Plot2DCanvas , PlotCanvas
• recent_actions_ : RecentFilesMenu
• recent_files_ : RecentFilesMenu , TOPPViewBase
• recent_files_menu_ : TOPPASBase
• recent_menu_ : RecentFilesMenu
• recentFileClicked() : RecentFilesMenu
• RecentFilesMenu() : RecentFilesMenu
• recomputeConsensus_() : BaseLabeler
• recomputeNeighbors_() : QTCluster
• record_length_ : InspectOutfile
• Rectangle : GridBasedCluster , GridBasedClustering< Metric >
• recurseAndGenerateVariableModifiedPeptides_() : ModifiedPeptideGenerator
• recurseAndGenerateVariableModifiedSequences_() : ModifiedNASequenceGenerator
• recursion_depth_ : ProgressLogger
• Red : ColorBrewer::Distinct
• reduce() : DistanceMatrix< Value >
• reduce_by_factor_ : ParentPeakMower
• reducePermuts_() : CompNovoIdentification , CompNovoIdentificationCID
• reestimate_mt_sd_ : MassTraceDetection
• ref() : MatchedIterator< CONT_T, TRAIT, CONST_T >
• ref_ : PrecisionWrapper< FloatingPointType >
• ref_begin_ : MatchedIterator< CONT_T, TRAIT, CONST_T >
• ref_end_ : MatchedIterator< CONT_T, TRAIT, CONST_T >
• ref_intens : IsotopeWaveletTransform< PeakType >::BoxElement
• ref_map_id_ : IsobaricNormalizer
• ref_param_ : MzMLHandler
• reference : _Iterator< _Val, _Ref, _Ptr > , KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , AASequence::ConstIterator , AASequence::Iterator , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType >
• Reference : FeatureMap
• reference : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , IntensityIteratorWrapper< IteratorT > , MatchedIterator< CONT_T, TRAIT, CONST_T > , Matrix< Value >
• Reference : Matrix< Value >
• reference : NASequence::ConstIterator , NASequence::Iterator
• reference_ : IsotopeWaveletTransform< PeakType >::TransSpectrum , MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering
• reference_channel_ : ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• reference_channel_name_ : IsobaricNormalizer
• reference_formats : SpectrumLookup
• reference_index_ : MapAlignmentAlgorithmIdentification
• refIdx() : MatchedIterator< CONT_T, TRAIT, CONST_T >
• REFLECTRON : Instrument
• reflectron_state_ : MassAnalyzer , MassAnalyzerVisualizer
• ReflectronState : MassAnalyzer
• REFLSTATENULL : MassAnalyzer
• refreshParameters() : TOPPASBase , TOPPASScene , TOPPASToolVertex
• refreshPipelineParameters() : TOPPASBase
• RefreshStatus : TOPPASScene
• reg_models : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• regex_description_ : DigestionEnzyme
• regexp_name_list_ : SpectrumLookup
• regexp_names_ : SpectrumLookup
• region_rt_span_ : EGHTraceFitter , GaussTraceFitter
• registerAt() : LogStreamNotifier
• registerChannelsInOutputMap_() : IsobaricChannelExtractor
• registerChildren() : BaseGroupFinder , BaseLabeler , BaseModel< D > , BaseSuperimposer , BinnedSpectrumCompareFunctor , ClusterFunctor , FeatureFinderAlgorithm , FeatureGroupingAlgorithm , FilterFunctor , Fitter1D , MapAlignmentEvaluationAlgorithm , PeakSpectrumCompareFunctor , ProgressLogger::ProgressLoggerImpl
• registerDataProcessingSoftware() : IdentificationData
• registerDataProcessingStep() : IdentificationData
• registerDataQuery() : IdentificationData
• registerDBSearchParam() : IdentificationData
• registerDoubleList_() : TOPPBase
• registerDoubleOption_() : TOPPBase
• registered_at_ : LogStreamNotifier
• registered_mod_ : PepXMLFile::AminoAcidModification
• registeredProducts() : Factory< FactoryProduct >
• registerExperiment() : MSQuantifications
• registerFactory() : SingletonRegistry
• registerFlag_() : TOPPBase
• registerFullParam_() : TOPPBase
• registerIdentifiedCompound() : IdentificationData
• registerIdentifiedOligo() : IdentificationData
• registerIdentifiedPeptide() : IdentificationData
• registerIDMetaData_() : NucleicAcidSearchEngine
• registerInputFile() : IdentificationData
• registerInputFile_() : TOPPBase
• registerInputFileList_() : TOPPBase
• registerIntList_() : TOPPBase
• registerIntOption_() : TOPPBase
• registerMoleculeQueryMatch() : IdentificationData
• registerName() : MetaInfoRegistry
• registerOptionsAndFlags_() : NucleicAcidSearchEngine , TOPPBase , TOPPGNPSExport
• registerOutputFile_() : TOPPBase
• registerOutputFileList_() : TOPPBase
• registerParamSubsectionsAsTOPPSubsections_() : TOPPBase
• registerParentMolecule() : IdentificationData
• registerParentMoleculeGrouping() : IdentificationData
• registerProduct() : Factory< FactoryProduct >
• registerProtein_() : ProtXMLFile
• registerQueryMatchGroup() : IdentificationData
• registerRun() : QcMLFile
• registerScoreType() : IdentificationData
• registerSet() : QcMLFile
• registerStream() : StreamHandler
• registerStringList_() : TOPPBase
• registerStringOption_() : TOPPBase
• registerSubsection_() : TOPPBase
• registerTOPPSubsection_() : TOPPBase
• registry() : MetaInfo
• registry_ : MetaInfo
• RegularSwathFileConsumer() : RegularSwathFileConsumer
• reindexed_peptides : ProteinResolver::ResolverResult
• reindexed_proteins : ProteinResolver::ResolverResult
• reindexingNodes_() : ProteinResolver
• rel_loss_intensity_ : TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• rel_prec_error : RNPxlReportRow
• relative_allowable_product_mass_ : TargetedSpectraExtractor
• relative_d : RANSACParam
• relative_intensities : TIC::Result
• released() : TOPPASVertex
• relevant : FeatureDistance::DistanceParams_
• reliability : MzTabNucleicAcidSectionRow , MzTabOligonucleotideSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• remove() : DataFilters , File , LogStream , MultiGradient , Param , String , StringUtils
• remove_() : MetaInfoVisualizer
• remove_chromatogram_flag() : LayerData
• remove_fixed_mods_ : MascotXMLHandler
• remove_low_intensity_quantifications_ : IsobaricChannelExtractor
• remove_overlapping_ : PeakPickerMRM
• remove_overlapping_features() : MRMTransitionGroupPicker
• remove_precursor_near_peaks_ : SequestInfile
• remove_single_traces_ : FeatureFindingMetabo
• removeAdduct() : Compomer
• removeAll() : InputFileList , Param
• removeAllAttachments() : QcMLFile
• removeAllClusters() : ClusteringGrid
• removeAttachment() : QcMLFile
• removeBetaPeptideHits() : OPXLHelper
• removeBlackListItems() : FilterableList
• removebutton_ : GradientVisualizer
• removeCluster() : ClusteringGrid
• removeCommasAndParseDouble() : ChromeleonFile
• removeCurrentLayer() : LayerStack
• removeCurrentRow() : ListTable
• removeData_() : GradientVisualizer
• removeDecoyHits() : IDFilter
• removeDecoys() : IDFilter
• removeDir() : File
• removeDirRecursively() : File
• removeDuplicatePeptideHits() : IDFilter
• removeEmptyIdentifications() : IDFilter
• removeFile() : FileWatcher
• removeFromElementMapping_() : QTClusterFinder
• removeFromSetIf_() : IdentificationData
• removeFromSetIfNotHashed_() : IdentificationData
• removeGraphicalPeakAnnotations_() : TVIdentificationViewController
• removeHitsMatchingProteins() : IDFilter
• removeHostName_() : MascotRemoteQuery
• removeId() : EnhancedTabBar
• removeInEdge() : TOPPASVertex
• removeLayer() : LayerStack , Plot1DCanvas , Plot2DCanvas , Plot3DCanvas , PlotCanvas
• removeLayers() : PlotCanvas
• removeMatchingItems() : IDFilter
• removeMatchingItemsUnroll() : IDFilter
• removeMatchingPeptideHits() : IDFilter
• removeMatchingPeptideIdentifications() : IDFilter
• removeMetaValue() : MetaInfoInterface
• removeMS2SpectraPeaks_() : TargetedSpectraExtractor
• removeOutEdge() : TOPPASVertex
• removeOutliersIterative() : MRMRTNormalizer
• removeOutliersRANSAC() : MRMRTNormalizer
• removeOverlappingPeaks_() : PeakPickerMRM
• removePeakAnnotationsFromPeptideHit() : LayerData
• removePeptidesWithMatchingModifications() : IDFilter
• removePeptidesWithMatchingRegEx() : IDFilter
• removePeptidesWithMatchingSequences() : IDFilter
• removePhosphositesFromSequence_() : AScore
• removeQualityParameter() : QcMLFile
• removeRowButton_ : ListEditor
• removeSelected() : InputFileList , TOPPASScene
• removeSelectedItems() : Annotations1DContainer
• removeSmallClustersY() : GridBasedClustering< Metric >
• removeSpaces_() : MRMFeatureSelector , MRMFeatureSelector_test
• removeTemporaryAnnotations_() : TVIdentificationViewController
• removeTheoreticalSpectrumLayer_() : TVIdentificationViewController
• removeTreatment() : Sample
• removeUngroupedProteins() : IDFilter
• removeUnreferencedProteins() : IDFilter
• removeValue() : MetaInfo
• removeWhitespaces() : String , StringUtils
• removeZeroedElements_() : EmpiricalFormula
• REMPI : IonSource
• rename() : File
• renameOutput_() : TOPPASToolVertex
• rend() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , IsotopeDistribution , MassTrace
• renderForImage() : Plot1DWidget
• renderText_() : Plot3DOpenGLCanvas
• renormalize() : IsotopeDistribution
• replace() : DataFilters
• replaceCVTerm() : CVTermList , CVTermListInterface
• replaceCVTerms() : CVTermList , CVTermListInterface
• replacement_ : SVOutStream
• replaceWhiteSpaces_() : MzTab
• reply_ : NetworkGetRequest
• replyFinished() : NetworkGetRequest
• report_chromatograms_ : FeatureFindingMetabo
• report_convex_hulls_ : FeatureFindingMetabo
• report_FWHM_ : PeakPickerHiRes
• report_FWHM_as_ppm_ : PeakPickerHiRes
• report_mode_ : MetaboliteSpectralMatching
• report_summed_ints_ : FeatureFindingMetabo
• report_top_hits_ : SimpleSearchEngineAlgorithm
• reported_mz_ : FeatureFinderAlgorithmPicked
• reporter_mass_shift_ : IsobaricChannelExtractor
• reportFailure_() : FuzzyStringComparator
• reportSuccess_() : FuzzyStringComparator
• requestClipboardContent() : TOPPASScene
• requestVisibleArea1D() : SpectraIDViewTab
• required : ParameterInformation
• required_modules_ : PythonModuleRequirement
• RequiredParameterNotGiven() : RequiredParameterNotGiven
• requirement_level_ : CVMappingRule
• RequirementLevel : CVMappingRule
• requires() : Contaminants , FeatureSummary , FragmentMassError , FWHM , IdentificationSummary , MissedCleavages , Ms2IdentificationRate , Ms2SpectrumStats , MzCalibration , PeptideMass , PSMExplainedIonCurrent
• Requires : QCBase
• requires() : QCBase , RTAlignment , SpectrumCount , TIC
• requires_login_ : MascotRemoteQuery
• 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
• resample_boundary_ : MRMTransitionGroupPicker
• resampleChromatogram_() : MRMTransitionGroupPicker
• rescaleFragmentFeature_() : PercolatorFeatureSetHelper
• rescore() : PrecursorIonSelection
• rescore_() : PrecursorIonSelection
• reserve() : ConstRefVector< ContainerT > , MSExperiment
• reserveSpaceChromatograms() : MSExperiment
• reserveSpaceSpectra() : MSExperiment
• RESERVOIR : IonSource
• reset() : squared_difference_counted< _Tp, _Dist > , FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector > , FuzzyStringComparator::StreamElement_ , shared_xerces_ptr< T > , XMLHandler , IsobaricQuantifierStatistics , Histogram< ValueType, BinSizeType > , MSExperiment , PrecursorIonSelection , StopWatch , SysInfo::MemUsage , TOPPASOutputFileListVertex , TOPPASToolVertex , TOPPASVertex , PatternAuxData< TNeedle >
• resetAlignment() : Plot1DCanvas , Plot1DWidget
• resetDownstream() : TOPPASScene
• resetErrors() : XMLValidator
• resetInterpretations() : TraMLProduct
• resetMembers_() : FeatureXMLFile , ProtXMLFile
• resetProcessesQueue() : TOPPASScene
• resetProteinScores_() : BayesianProteinInferenceAlgorithm
• resetTranslation() : Plot3DOpenGLCanvas
• resetZoom() : PlotCanvas , TOPPViewBase
• residual_peak_count : PrecursorPurity::PurityScores
• residualOutlierCandidate_() : AbsoluteQuantitation , MRMRTNormalizer
• Residue() : Residue
• residue : SvmTheoreticalSpectrumGenerator::IonType
• residue_by_one_letter_code_ : ResidueDB
• residue_mod_names_ : ResidueDB
• residue_names_ : ResidueDB
• residue_sets_ : Residue , ResidueDB
• residue_to_name_ : CompNovoIdentificationBase
• ResidueDB : Residue , ResidueDB
• ResidueModification() : ResidueModification
• residues : MzIdentMLDOMHandler::ModificationParam
• residues_by_set_ : ResidueDB
• residues_in_upper_case_ : SequestInfile
• residues_table_row_type : IntegerMassDecomposer< ValueType, DecompositionValueType >
• residues_table_type : IntegerMassDecomposer< ValueType, DecompositionValueType >
• residuesMatch_() : ModificationsDB
• ResidueType : Residue
• residueTypeToIonLetter() : Residue
• residueTypeToIonLetter_() : TheoreticalSpectrumGenerator
• ResidueTypeToString_() : SvmTheoreticalSpectrumGenerator
• resize() : ConstRefVector< ContainerT > , DistanceMatrix< Value > , IsotopeDistribution , Matrix< Value > , MSExperiment
• resized() : TableView
• resizeEvent() : HistogramWidget , Plot3DCanvas , PlotCanvas , TableView , TOPPASWidget
• resizeGL() : Plot3DOpenGLCanvas
• RESMETHNULL : MassAnalyzer
• resolution_ : IonDetector , MassAnalyzer
• resolution_l : MRMFeatureQC::ComponentGroupPairQCs
• resolution_method_ : MassAnalyzer
• resolution_pair_name : MRMFeatureQC::ComponentGroupPairQCs
• resolution_type_ : MassAnalyzer
• resolution_u : MRMFeatureQC::ComponentGroupPairQCs
• ResolutionMethod : MassAnalyzer
• RESOLUTIONMODEL : RawMSSignalSimulation
• ResolutionType : MassAnalyzer
• resolve() : IDConflictResolverAlgorithm , PeptideProteinResolution
• resolve_ambiguous_mods_ : NucleicAcidSearchEngine
• resolveAmbiguityGroup() : MetaboTargetedAssay
• resolveAmbiguousMods_() : NucleicAcidSearchEngine
• resolveAutoMode_() : AccurateMassSearchEngine
• resolveBetweenFeatures() : IDConflictResolverAlgorithm
• resolveBetweenFeatures_() : IDConflictResolverAlgorithm
• resolveConflict_() : IDConflictResolverAlgorithm
• resolveConflictKeepMatching_() : IDConflictResolverAlgorithm
• resolveConnectedComponent() : PeptideProteinResolution
• resolveConsensus() : ProteinResolver
• resolveGraph() : PeptideProteinResolution
• resolveGraphPeptideCentric() : IDBoostGraph
• resolveGraphPeptideCentric_() : IDBoostGraph
• resolveID() : ProteinResolver
• resolveMisassignedNTermMods_() : PercolatorOutfile
• resolveMixedSequenceGroups_() : TransitionTSVFile
• resolveOverlappingFeatures_() : FeatureFinderAlgorithmMetaboIdent
• resolveOverlappingTargetDecoyMassesByIndividualMassShift() : MetaboTargetedTargetDecoy
• resolver_result_ : ProteinResolver
• resolveUniqueIdConflicts() : UniqueIdIndexer< RandomAccessContainer >
• response_bytes_ : NetworkGetRequest
• restoreRotationAndZoom() : Plot3DOpenGLCanvas
• restrictions_ : ListEditorDelegate
• restrictTransitions() : MRMAssay
• RESTYPENULL : MassAnalyzer
• result_ : MultiplexFilteredMSExperiment
• result_type : _Bracket_accessor< _Val > , mean_and_stddev
• result_windows_even : SignalToNoiseEstimatorMedianRapid::NoiseEstimator
• result_windows_odd : SignalToNoiseEstimatorMedianRapid::NoiseEstimator
• results_ : Contaminants , DBSuitability , FragmentMassError , PSMExplainedIonCurrent
• resume() : StopWatch
• resume_source_ : TOPPASScene
• retention_ : EGHFitter1D , EmgFitter1D , EmgModel
• retention_time : MzTabOligonucleotideSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• retention_time_ : MascotInfile , MSSpectrum , RetentionTime
• retention_time_l : MRMFeatureQC::ComponentGroupQCs , MRMFeatureQC::ComponentQCs
• retention_time_set_ : RetentionTime
• retention_time_type : RetentionTime
• retention_time_u : MRMFeatureQC::ComponentGroupQCs , MRMFeatureQC::ComponentQCs
• retention_time_unit : RetentionTime
• retention_time_window : MzTabOligonucleotideSectionRow , MzTabPeptideSectionRow
• retention_times : TIC::Result
• RetentionTime : IncludeExcludeTarget , ReactionMonitoringTransition , TargetedExperiment , RetentionTime
• retentionTimeInterpretation_ : TransitionTSVFile
• retrieveSwathMaps() : FullSwathFileConsumer
• return_chromatogram() : ChromatogramExtractor
• RETURN_STATUS : NonNegativeLeastSquaresSolver
• returnResultsAndClear() : IDMergerAlgorithm
• RETURNSTATE : ExternalProcess
• reverse() : String , StringUtils
• reverse_ : HasActivationMethod< SpectrumType > , HasMetaValue< MetaContainer > , HasPrecursorCharge< SpectrumType > , HasScanMode< SpectrumType > , HasScanPolarity< SpectrumType > , InIntensityRange< PeakType > , InMSLevelRange< SpectrumType > , InMzRange< PeakType > , InPrecursorMZRange< SpectrumType > , InRTRange< SpectrumType > , IsEmptySpectrum< SpectrumType > , IsInCollisionEnergyRange< SpectrumType > , IsInIsolationWindow< SpectrumType > , IsInIsolationWindowSizeRange< SpectrumType > , IsZoomSpectrum< SpectrumType >
• reverse_iterator : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , IsotopeDistribution , MassTrace , Matrix< Value >
• reverse_nns_ : GridBasedClustering< Metric >
• reverseComparator() : ReverseComparator< Cmp >
• ReverseComparator() : ReverseComparator< Cmp >
• ReverseIterator : ConsensusMap , ConstRefVector< ContainerT > , FeatureMap , IsotopeDistribution , Map< Key, T > , Matrix< Value > , MSChromatogram , MSSpectrum , String , StringListUtils , TextFile
• reversePeptide() : MRMDecoy
• reversePeptide_() : MRMDecoy
• reversePeptides() : DecoyGenerator
• reverseProtein() : DecoyGenerator
• Ribonucleotide() : Ribonucleotide
• RibonucleotideDB : Ribonucleotide , RibonucleotideDB
• ribonucleotides_ : RibonucleotideDB
• RichPeak2D() : RichPeak2D
• RIGHT : AxisPainter , Compomer
• right : PeakPickerCWT::PeakArea_
• right_boundary : PeakPickerMaxima::PeakCandidate , Range
• right_child : BinaryTreeNode
• right_endpoint_ : PeakShape
• right_iterator_set_ : PeakShape
• right_neighbor : MoleculeParentMatch
• right_splitter_ : HistogramWidget
• RIGHT_TERMINUS : MoleculeParentMatch
• right_width : PeakShape
• right_width_ : PeakPickerMRM
• rightBorderOfBin() : Histogram< ValueType, BinSizeType >
• rightWidth : PeakCandidate
• rip() : IDRipper
• rm_fit() : RansacModel< ModelT >
• rm_fit_impl() : RansacModelLinear , RansacModelQuadratic
• rm_inliers() : RansacModel< ModelT >
• rm_inliers_impl() : RansacModelLinear , RansacModelQuadratic
• rm_rsq() : RansacModel< ModelT >
• rm_rsq_impl() : RansacModelLinear , RansacModelQuadratic
• rm_rss() : RansacModel< ModelT >
• rm_rss_impl() : RansacModelLinear , RansacModelQuadratic
• RNA : RNPxlReportRow
• RNA_weight : RNPxlReportRow
• RNaseDB() : RNaseDB
• rnd_gen_ : IonizationSimulation , RawMSSignalSimulation , RawTandemMSSignalSimulation , RTSimulation
• rng_ : BaseLabeler , RandomShuffler , UniqueIdGenerator
• ROCCurve() : ROCCurve
• rocN() : FalseDiscoveryRate , ROCCurve
• root_ : Param::ParamIterator , Param
• round_based_mode_ : TOPPASMergerVertex
• round_counter_ : TOPPASVertex
• round_masses_ : CoarseIsotopePatternGenerator
• round_total_ : TOPPASVertex
• roundBasedMode() : TOPPASMergerVertex
• rounding_errors_ : RealMassDecomposer
• RoundPackage : TOPPASVertex
• RoundPackageConstIt : TOPPASVertex
• RoundPackageIt : TOPPASVertex
• RoundPackages : TOPPASVertex
• row() : Matrix< Value >
• row_ : BaseVisualizerGUI , QcMLFile
• rowClicked_() : DIATreeTab
• rowCount() : CsvFile
• rowDoubleClicked_() : DIATreeTab
• rowIndex() : Matrix< Value >
• rownames_ : DataMatrix
• rows() : Matrix< Value >
• rows_ : OverlapDetector , Matrix< Value >
• rowSelectionChange_() : DIATreeTab
• rsd_ : LinearRegression
• rt : CsiFingerIdMzTabWriter::CsiAdapterIdentification
• RT : FeatureFinderAlgorithmIsotopeWavelet::BoxElement , FeatureFinderAlgorithmMRM
• rt : DataQuery
• RT : SpectrumMeta , IsotopeWaveletTransform< PeakType >::BoxElement
• rt() : KDTreeFeatureMaps
• RT : Peak2D , QTClusterFinder
• rt : RNPxlReportRow , SiriusMSFile::CompoundInfo , SiriusMzTabWriter::SiriusAdapterIdentification , SpectrumMetaDataLookup::SpectrumMetaData
• RT : StablePairFinder
• rt : LightCompound
• RT : OSSpectrumMeta
• rt : Peptide
• rt_ : KDTreeFeatureMaps , MultiplexFilteredPeak , MultiplexSatelliteProfile , MZTrafoModel , PeptideIdentification , PepXMLFile
• RT_AXIS_TITLE : PlotWidget
• rt_band_ : MultiplexFiltering
• rt_bridge_ : InclusionExclusionList::WindowDistance_
• rt_calibrated : TransitionTSVFile::TSVTransition
• rt_coef : ConfidenceScoring::GLM_
• rt_delta_ : OSWPeakGroup
• rt_diff_l : MRMFeatureQC::ComponentGroupPairQCs
• rt_diff_u : MRMFeatureQC::ComponentGroupPairQCs
• rt_difference : OpenSwath_Scores
• rt_end : ChromatogramExtractorAlgorithm::ExtractionCoordinates , RawMSSignalSimulation::ContaminantInfo
• rt_experimental_ : OSWPeakGroup
• rt_extraction_window : ChromExtractParams
• rt_extraction_window_ : MRMFeatureFinderScoring
• RT_GAUSSIAN : RawMSSignalSimulation
• rt_heavy_ : XQuestResultXMLHandler
• rt_idx_ : MultiplexFilteredPeak , MultiplexSatelliteCentroided
• RT_index : IsotopeWaveletTransform< PeakType >::BoxElement
• rt_initialized_ : MSDataAggregatingConsumer
• RT_interleave_ : FeatureFinderAlgorithmIsotopeWavelet
• rt_label_ : TOPPViewBase
• rt_left_width_ : OSWPeakGroup
• rt_light_ : XQuestResultXMLHandler
• rt_max : FeatureFinderAlgorithmMetaboIdent::MassTraceBounds
• rt_max_ : SpectraMerger::SpectraDistance_
• rt_min : FeatureFinderAlgorithmMetaboIdent::MassTraceBounds
• rt_model_file_ : RTSimulation
• rt_norm_ : ConfidenceScoring
• rt_normalization_factor_ : MRMFeatureFinderScoring , OpenSwathScoring
• rt_probability : PSLPFormulation::IndexTriple
• rt_prot_map_ : PrecursorIonSelectionPreprocessing
• rt_quantile_ : FeatureFinderIdentificationAlgorithm
• rt_range_ : FeatureFileOptions , PeakFileOptions
• rt_ranges : FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound
• RT_RECTANGULAR : RawMSSignalSimulation
• rt_right_width_ : OSWPeakGroup
• rt_sampling_rate_ : RTSimulation
• rt_scaling_ : MultiplexClustering::MultiplexDistance , MultiplexClustering
• rt_set_ : MzMLHandler
• rt_shift_ : Adduct , Compomer
• rt_shift_mean : FeatureSummary::Result
• rt_start : ChromatogramExtractorAlgorithm::ExtractionCoordinates , RawMSSignalSimulation::ContaminantInfo
• rt_tol_secs_ : FeatureGroupingAlgorithmKD , MapAlignmentAlgorithmKD
• rt_tolerance : SpectrumLookup
• rt_tolerance_ : IDMapper
• rt_trafo_ : ConfidenceScoring
• rt_typical_ : MultiplexClustering
• RT_votes_cutoff_ : FeatureFinderAlgorithmIsotopeWavelet
• rt_window_ : FeatureFinderAlgorithmMetaboIdent , FeatureFinderIdentificationAlgorithm , TargetedSpectraExtractor
• RTAlignment() : RTAlignment
• RTBegin() : MSChromatogram , MSExperiment
• RTEnd() : MSChromatogram , MSExperiment
• RTMap : FeatureFinderIdentificationAlgorithm
• RTmax_ : InclusionExclusionList::IEWindow
• RTmin_ : InclusionExclusionList::IEWindow
• rts : FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound , ReactionMonitoringTransition , PeptideCompound
• rts_ : IncludeExcludeTarget , SpectrumLookup
• RTSimulation() : RTSimulation
• RTType : RetentionTime
• RTUnit : RetentionTime
• rubber_band_ : PlotCanvas
• rules_ : CVMappingFile , SemanticValidator
• run() : AccurateMassSearchEngine , BaseGroupFinder , BaseSuperimposer , BasicProteinInferenceAlgorithm , CoarseIsotopePatternGenerator , ExternalProcess , ExternalProcessMBox , FeatureFinder , FeatureFinderAlgorithm , FeatureFinderAlgorithmIsotopeWavelet , FeatureFinderAlgorithmMetaboIdent , FeatureFinderAlgorithmMRM , FeatureFinderAlgorithmPicked , FeatureFinderIdentificationAlgorithm , FeatureFinderMultiplexAlgorithm , FeatureFindingMetabo , FIAMSDataProcessor , FIAMSScheduler , FineIsotopePatternGenerator , IsoSpecThresholdWrapper , IsoSpecTotalProbWrapper , IsoSpecWrapper , IsotopePatternGenerator , LabeledPairFinder , MascotRemoteQuery , MassTraceDetection , MetaboliteSpectralMatching , MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , NetworkGetRequest , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , PeptideIndexing , PeptideProteinResolution , PoseClusteringAffineSuperimposer , PoseClusteringShiftSuperimposer , QTClusterFinder , SimplePairFinder , StablePairFinder , TOPPASInputFileListVertex , TOPPASMergerVertex , TOPPASOutputFileListVertex , TOPPASSplitterVertex , TOPPASToolVertex , TOPPASVertex , UpdateCheck , XFDRAlgorithm
• run_() : MassTraceDetection , MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , QTClusterFinder , TriqlerFile::TriqlerLine_
• run_id_ : MzMLSqliteHandler , OpenSwathOSWWriter , OSWData , QcMLFile
• run_internal_() : QTClusterFinder
• run_Name_ID_map_ : QcMLFile
• run_to_search_engines_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• run_to_search_engines_settings_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• runAccurateMassSearch() : FIAMSDataProcessor
• runClustering_() : FeatureGroupingAlgorithmKD
• runExternalProcess_() : TOPPBase
• runNextProcess() : TOPPASScene
• running_ : TOPPASScene
• runOnCandidates() : FeatureFinderIdentificationAlgorithm
• runpath_to_identifier : ProteinIdentification::Mapping
• runPipeline() : TOPPASBase , TOPPASScene
• runQualityAts_ : QcMLFile
• runQualityQPs_ : QcMLFile
• runScript() : RWrapper
• runTOPPTool_() : TOPPViewBase
• RunToSequenceToChargeToPepHitP : IDFilter
• rWidth : PenaltyFactors