| OpenMS 2.5.0

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
- rand_gen_ : ConfidenceScoring
- random() : String , StringUtils
- 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_params_ : MZTrafoModel
- RANSACParam() : RANSACParam
- raster() : LinearResampler , LinearResamplerAlign
- raster_align() : LinearResamplerAlign
- raster_interpolate() : LinearResamplerAlign
- rasterExperiment() : LinearResampler
- rate : RateScorePair , SIPIncorporation
- 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
- raw_spec_names : LCMS
- RawData() : RawData
- RawDataArrayType : EGHFitter1D::Data , EmgFitter1D::Data , Fitter1D
- RawDataVector : OptimizePeakDeconvolution , OptimizePick
- rawIsotopes_ : ConsensusIsotopePattern
- 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
- readEnzymesFromFile_() : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
- reader_ : FASTAFile
- readExperiment() : MzMLSqliteHandler
- readFromFile_() : ElementDB , RibonucleotideDB
- readFromOBOFile() : CrossLinksDB , ModificationsDB
- readFromUnimodXMLFile() : ModificationsDB
- readMappingFile_() : OMSSAXMLFile
- readMemdump() : CachedMzMLHandler
- readMS1Spectra() : MzMLSqliteSwathHandler
- readMzIdentMLFile() : MzIdentMLDOMHandler
- readNext() : FASTAFile
- readNextLine_() : FuzzyStringComparator
- readOutHeader() : InspectOutfile , SequestOutfile
- readPQPInput_() : TransitionPQPFile
- readProblem() : LPWrapper
- readQuantData() : PeptideAndProteinQuant
- readResiduesFromFile_() : ResidueDB
- readResponse() : MascotRemoteQuery
- readResponseHeader() : MascotRemoteQuery
- readRTMZCharge_() : PepXMLFile
- readSpectra() : MzMLSqliteHandler , SpectrumLookup , SpectrumMetaDataLookup
- readSpectraForWindow() : MzMLSqliteSwathHandler
- readSpectrum() : CachedMzMLHandler
- readSpectrumFast() : CachedMzMLHandler
- readStart() : FASTAFile
- readSwathWindows() : MzMLSqliteSwathHandler , SwathWindowLoader
- 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() : SpectrumCanvas
- recalculateAxes_() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
- recalculateCurrentLayerDotGradient() : Spectrum2DCanvas
- recalculateDotGradient_() : Spectrum2DCanvas , Spectrum3DOpenGLCanvas
- recalculatePeakBorders_() : MRMTransitionGroupPicker
- recalculateRanges_() : SpectrumCanvas
- recalculateSnapFactor_() : Spectrum1DCanvas , Spectrum2DCanvas , SpectrumCanvas
- recalibrateMasses_() : UTILProteomicsLFQ
- recent_actions_ : TOPPViewBase
- recent_files_ : TOPPViewBase
- recomputeConsensus_() : BaseLabeler
- reconstruction : SIPPeptide
- reconstruction_monoistopic : SIPPeptide
- record_length_ : InspectOutfile
- Rectangle : GridBasedCluster , GridBasedClustering< Metric >
- recurseAndGenerateVariableModifiedPeptides_() : ModifiedPeptideGenerator
- recurseAndGenerateVariableModifiedSequences_() : ModifiedNASequenceGenerator
- recursion_depth_ : ProgressLogger
- 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 >
- Reference : Matrix< Value >
- reference : Matrix< Value > , 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
- 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_() : Epifany , NucleicAcidSearchEngine , TOPPBase , TOPPGNPSExport , UTILProteomicsLFQ
- 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_d : RANSACParam
- released() : TOPPASVertex
- relevant : FeatureDistance::DistanceParams_
- reliability : MzTabNucleicAcidSectionRow , MzTabOligonucleotideSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
- remove() : DataFilters , File , LogStream , MultiGradient , Param , String , StringUtils
- remove_() : MetaInfoVisualizer
- remove_background_peak() : LCElutionPeak
- remove_chromatogram_flag() : LayerData
- remove_feature() : LCMS
- remove_feature_by_ID() : LCMS
- remove_feature_from_list() : LCMS
- remove_fixed_mods_ : MascotXMLHandler
- remove_low_intensity_quantifications_ : IsobaricChannelExtractor
- remove_overlapping_ : PeakPickerMRM
- remove_overlapping_features() : MRMTransitionGroupPicker
- remove_precursor_near_peaks_ : SequestInfile
- remove_raw_spec_name() : LCMS
- remove_single_traces_ : FeatureFindingMetabo
- removeAdduct() : Compomer
- removeAll() : Param , TOPPASInputFilesDialog
- removeAllAttachments() : QcMLFile
- removeAllClusters() : ClusteringGrid
- removeAllMS2Information() : SHFeature
- removeAttachment() : QcMLFile
- removeBetaPeptideHits() : OPXLHelper
- removebutton_ : GradientVisualizer
- removeCluster() : ClusteringGrid
- removeCommasAndParseDouble() : ChromeleonFile
- removeCurrentRow() : ListTable
- removeData_() : GradientVisualizer
- removeDecoyHits() : IDFilter
- removeDecoys() : IDFilter
- removeDir() : File
- removeDirRecursively() : File
- removeDuplicatePeptideHits() : IDFilter
- removeEmptyIdentifications() : IDFilter
- removeExtension() : File
- removeExtremeValues_() : Epifany
- removeFile() : FileWatcher
- removeFromSetIf_() : IdentificationData
- removeFromSetIfNotHashed_() : IdentificationData
- removeGraphicalPeakAnnotations_() : TOPPViewIdentificationViewBehavior
- removeHitsMatchingProteins() : IDFilter
- removeHostName_() : MascotRemoteQuery
- removeId() : EnhancedTabBar , TOPPASTabBar
- removeInEdge() : TOPPASVertex
- removeLayer() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas
- removeMatchingItems() : IDFilter
- removeMatchingItemsUnroll() : IDFilter
- removeMatchingPeptideHits() : IDFilter
- removeMetaValue() : MetaInfoInterface
- removeMS2Feature() : SHFeature
- removeNoise() : CentroidData
- removeOutEdge() : TOPPASVertex
- removeOutlierFragments() : ClusteredMS2ConsensusSpectrum
- removeOutliersIterative() : MRMRTNormalizer
- removeOutliersRANSAC() : MRMRTNormalizer
- removeOverlappingPeaks_() : PeakPickerMRM
- removePeakAnnotationsFromPeptideHit() : LayerData
- removePeptidesWithMatchingModifications() : IDFilter
- removePeptidesWithMatchingSequences() : IDFilter
- removePhosphositesFromSequence_() : AScore
- removeQualityParameter() : QcMLFile
- removeRowButton_ : ListEditor
- removeSelected() : TOPPASInputFilesDialog , TOPPASScene
- removeSelectedItems() : Annotations1DContainer
- removeSmallClustersY() : GridBasedClustering< Metric >
- removeSpaces_() : MRMFeatureSelector , MRMFeatureSelector_test
- removeTempDirectory_() : TOPPBase
- removeTemporaryAnnotations_() : TOPPViewIdentificationViewBehavior
- removeTheoreticalSpectrumLayer_() : TOPPViewIdentificationViewBehavior
- removeTreatment() : Sample
- 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() : Spectrum1DWidget
- renderText_() : Spectrum3DOpenGLCanvas
- renormalize() : IsotopeDistribution
- replace() : DataFilters
- replaceCVTerm() : CVTermList , CVTermListInterface
- replaceCVTerms() : CVTermList , CVTermListInterface
- replacement_ : SVOutStream
- 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_tic_ : MRMFeatureFilter
- report_top_hits_ : SimpleSearchEngineAlgorithm
- report_xic_ : MRMFeatureFilter
- reported_mz_ : FeatureFinderAlgorithmPicked
- reporter_mass_shift_ : IsobaricChannelExtractor
- reportFailure_() : FuzzyStringComparator
- reportSuccess_() : FuzzyStringComparator
- requestClipboardContent() : TOPPASScene
- requestVisibleArea1D() : SpectraIdentificationViewWidget
- required : ParameterInformation
- RequiredParameterNotGiven() : RequiredParameterNotGiven
- requirement_level_ : CVMappingRule
- RequirementLevel : CVMappingRule
- requires() : Contaminants , FragmentMassError , MissedCleavages , Ms2IdentificationRate , Ms2SpectrumStats , MzCalibration , QCBase
- Requires : QCBase
- requires() : RTAlignment , 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_ , XMLHandler , IsobaricQuantifierStatistics , Histogram< ValueType, BinSizeType > , MSExperiment , PrecursorIonSelection , StopWatch , SysInfo::MemUsage , TOPPASOutputFileListVertex , TOPPASToolVertex , TOPPASVertex , PatternAuxData< TNeedle >
- resetAlignment() : Spectrum1DCanvas , Spectrum1DWidget
- resetDownstream() : TOPPASScene
- resetErrors() : XMLValidator
- resetInterpretations() : TraMLProduct
- resetMembers_() : FeatureXMLFile , ProtXMLFile
- resetPeakGroupIter() : CentroidData
- resetProcessesQueue() : TOPPASScene
- resetTranslation() : Spectrum3DOpenGLCanvas
- resetZoom() : SpectrumCanvas , 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
- ResidueConstIterator : ResidueDB
- ResidueDB : Residue , ResidueDB
- ResidueIterator : ResidueDB
- ResidueModification() : ResidueModification
- residues : MzIdentMLDOMHandler::ModificationParam
- residues_ : ResidueDB
- 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
- resizeEvent() : HistogramWidget , Spectrum3DCanvas , SpectrumCanvas , TOPPASWidget
- resizeGL() : Spectrum3DOpenGLCanvas
- 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
- resolveAmbiguousMods_() : NucleicAcidSearchEngine
- resolveAutoMode_() : AccurateMassSearchEngine
- resolveBetweenFeatures() : IDConflictResolverAlgorithm
- resolveBetweenFeatures_() : IDConflictResolverAlgorithm
- resolveConflict_() : IDConflictResolverAlgorithm
- resolveConflictKeepMatching_() : IDConflictResolverAlgorithm
- resolveConnectedComponent() : PeptideProteinResolution
- resolveConsensus() : ProteinResolver
- resolveGraph() : PeptideProteinResolution
- resolveGraphPeptideCentric_() : IDBoostGraph
- resolveID() : ProteinResolver
- resolveMisassignedNTermMods_() : PercolatorOutfile
- resolveMixedSequenceGroups_() : TransitionTSVFile
- resolver_result_ : ProteinResolver
- resolveUniqueIdConflicts() : UniqueIdIndexer< RandomAccessContainer >
- response_bytes_ : NetworkGetRequest
- restoreRotationAndZoom() : Spectrum3DOpenGLCanvas
- 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 , FragmentMassError , TIC
- 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
- RetentionTime : IncludeExcludeTarget , ReactionMonitoringTransition , TargetedExperiment , RetentionTime
- retentionTimeInterpretation_ : TransitionTSVFile
- retrieveSwathMaps() : FullSwathFileConsumer
- return_chromatogram() : ChromatogramExtractor
- RETURN_STATUS : NonNegativeLeastSquaresSolver
- returnResultsAndClear() : IDMergerAlgorithm
- 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 >
- ReverseComparator() : ReverseComparator< Cmp >
- ReverseIterator : ConsensusMap , ConstRefVector< ContainerT > , FeatureMap , IsotopeDistribution , Map< Key, T > , Matrix< Value > , MSChromatogram , MSSpectrum , String , StringListUtils , TextFile
- reversePeptide() : MRMDecoy
- reversePeptide_() : MRMDecoy
- 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
- 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 : RANSACParam
- rng_ : BaseLabeler , UniqueIdGenerator
- ROCCurve() : ROCCurve
- rocN() : FalseDiscoveryRate , ROCCurve
- rocN_() : FalseDiscoveryRate
- 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
- rowCount() : CsvFile
- rowIndex() : Matrix< Value >
- rownames_ : DataMatrix
- rows() : Matrix< Value >
- rows_ : Matrix< Value >
- RR : SIPPeptide
- 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 : SpectrumWidget
- rt_band_ : MultiplexFiltering
- rt_bridge_ : InclusionExclusionList::WindowDistance_
- rt_calibrated : TransitionTSVFile::TSVTransition
- rt_coef : ConfidenceScoring::GLM_
- rt_diff_l : MRMFeatureQC::ComponentGroupPairQCs
- rt_diff_u : MRMFeatureQC::ComponentGroupPairQCs
- rt_difference : OpenSwath_Scores
- rt_end : ChromatogramExtractorAlgorithm::ExtractionCoordinates , RawMSSignalSimulation::ContaminantInfo
- 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_light_ : XQuestResultXMLHandler
- rt_max_ : SpectraMerger::SpectraDistance_
- rt_minimum_ : MultiplexClustering
- 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_RECTANGULAR : RawMSSignalSimulation
- rt_sampling_rate_ : RTSimulation
- rt_scaling_ : MultiplexClustering::MultiplexDistance , MultiplexClustering
- rt_set_ : MzMLHandler
- rt_shift_ : Adduct , Compomer
- 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_ : FeatureFinderIdentificationAlgorithm , TargetedSpectraExtractor
- RTAlignment() : RTAlignment
- RTBegin() : MSChromatogram , MSExperiment
- RTEnd() : MSChromatogram , MSExperiment
- RTMap : FeatureFinderIdentificationAlgorithm
- RTmax_ : InclusionExclusionList::IEWindow
- RTmin_ : InclusionExclusionList::IEWindow
- rts : ReactionMonitoringTransition , PeptideCompound
- rts_ : IncludeExcludeTarget , SpectrumLookup
- RTSimulation() : RTSimulation
- RTType : RetentionTime
- RTUnit : RetentionTime
- rubber_band_ : SpectrumCanvas
- rules_ : CVMappingFile , SemanticValidator
- run() : AccurateMassSearchEngine , BaseGroupFinder , BaseSuperimposer , BasicProteinInferenceAlgorithm , CoarseIsotopePatternGenerator , FeatureFinder , FeatureFinderAlgorithm , FeatureFinderAlgorithmIsotopeWavelet , FeatureFinderAlgorithmMRM , FeatureFinderAlgorithmPicked , FeatureFinderAlgorithmSH , FeatureFinderIdentificationAlgorithm , FeatureFinderMultiplexAlgorithm , FeatureFindingMetabo , FIAMSDataProcessor , FIAMSScheduler , FineIsotopePatternGenerator , IsoSpecThresholdWrapper , IsoSpecTotalProbWrapper , IsoSpecWrapper , IsotopePatternGenerator , LabeledPairFinder , MascotRemoteQuery , MassTraceDetection , MetaboliteSpectralMatching , MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , NetworkGetRequest , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , PeptideIndexing , PoseClusteringAffineSuperimposer , PoseClusteringShiftSuperimposer , QTClusterFinder , SimplePairFinder , StablePairFinder , TOPPASInputFileListVertex , TOPPASMergerVertex , TOPPASOutputFileListVertex , TOPPASSplitterVertex , TOPPASToolVertex , TOPPASVertex , UpdateCheck , XFDRAlgorithm
- run_() : MassTraceDetection , MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , QTClusterFinder
- run_id_ : MzMLSqliteHandler , OpenSwathOSWWriter , QcMLFile
- run_internal_() : QTClusterFinder
- run_Name_ID_map_ : QcMLFile
- runAccurateMassSearch() : FIAMSDataProcessor
- runClustering_() : FeatureGroupingAlgorithmKD
- runExternalProcess_() : TOPPBase
- runNextProcess() : TOPPASScene
- running_ : TOPPASScene
- runOnCandidates() : FeatureFinderIdentificationAlgorithm
- runPipeline() : TOPPASBase , TOPPASScene
- runQualityAts_ : QcMLFile
- runQualityQPs_ : QcMLFile
- runScript() : RWrapper
- runTOPPTool_() : TOPPViewBase
- RunToSequenceToChargeToPepHitP : IDFilter
- rWidth : PenaltyFactors