- r -

• random() : String , StringUtils
• RangeManager() : RangeManager< D >
• rankWeightedPermutationPeptideScores_() : AScore
• ransac() : RANSAC< TModelType >
• RANSACParam() : RANSACParam
• raster() : LinearResampler , LinearResamplerAlign
• raster_align() : LinearResamplerAlign
• raster_interpolate() : LinearResamplerAlign
• rasterExperiment() : LinearResampler
• Ratio() : ConsensusFeature::Ratio
• RawData() : RawData
• RawMSSignalSimulation() : RawMSSignalSimulation
• RawTandemMSSignalSimulation() : RawTandemMSSignalSimulation
• rbegin() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , IsotopeDistribution , MassTrace
• rdbuf() : LogStream
• 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 >
• 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
• RealMassDecomposer() : RealMassDecomposer
• reannotateTransitions() : MRMAssay
• recalculateAxes() : SpectrumCanvas
• recalculateAxes_() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
• recalculateCurrentLayerDotGradient() : Spectrum2DCanvas
• recalculateDotGradient_() : Spectrum2DCanvas , Spectrum3DOpenGLCanvas
• recalculatePeakBorders_() : MRMTransitionGroupPicker
• recalculateRanges_() : SpectrumCanvas
• recalculateSnapFactor_() : Spectrum1DCanvas , Spectrum2DCanvas , SpectrumCanvas
• recomputeConsensus_() : BaseLabeler
• recurseAndGenerateVariableModifiedPeptides_() : ModifiedPeptideGenerator
• recurseAndGenerateVariableModifiedSequences_() : ModifiedNASequenceGenerator
• reduce() : DistanceMatrix< Value >
• reducePermuts_() : CompNovoIdentification , CompNovoIdentificationCID
• ref() : MatchedIterator< CONT_T, TRAIT, CONST_T >
• refIdx() : MatchedIterator< CONT_T, TRAIT, CONST_T >
• refreshParameters() : TOPPASBase , TOPPASScene , TOPPASToolVertex
• refreshPipelineParameters() : TOPPASBase
• 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
• 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 , TOPPOpenPepXL , TOPPOpenPepXLLF , TOPPXFDR
• 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
• RegularSwathFileConsumer() : RegularSwathFileConsumer
• reindexingNodes_() : ProteinResolver
• released() : TOPPASVertex
• 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_overlapping_features() : MRMTransitionGroupPicker
• remove_raw_spec_name() : LCMS
• removeAdduct() : Compomer
• removeAll() : Param , TOPPASInputFilesDialog
• removeAllAttachments() : QcMLFile
• removeAllClusters() : ClusteringGrid
• removeAllMS2Information() : SHFeature
• removeAttachment() : QcMLFile
• removeBetaPeptideHits() : OPXLHelper
• removeCluster() : ClusteringGrid
• removeCommasAndParseDouble() : ChromeleonFile
• removeCurrentRow() : ListTable
• removeData_() : GradientVisualizer
• removeDecoyHits() : IDFilter
• removeDecoys() : IDFilter
• removeDir() : File
• removeDirRecursively() : File
• removeDuplicatePeptideHits() : IDFilter
• removeEmptyIdentifications() : IDFilter
• removeExtension() : File
• 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
• 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
• 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
• replyFinished() : NetworkGetRequest
• reportFailure_() : FuzzyStringComparator
• reportSuccess_() : FuzzyStringComparator
• requestClipboardContent() : TOPPASScene
• requestVisibleArea1D() : SpectraIdentificationViewWidget
• RequiredParameterNotGiven() : RequiredParameterNotGiven
• requires() : Contaminants , FragmentMassError , MissedCleavages , Ms2IdentificationRate , Ms2SpectrumStats , MzCalibration , QCBase , RTAlignment , TIC
• rerunTOPPTool() : TOPPViewBase
• resample() : ConsensusMapNormalizerAlgorithmQuantile
• resampleChromatogram_() : MRMTransitionGroupPicker
• rescaleFragmentFeature_() : PercolatorFeatureSetHelper
• rescore() : PrecursorIonSelection
• rescore_() : PrecursorIonSelection
• reserve() : ConstRefVector< ContainerT > , MSExperiment
• reserveSpaceChromatograms() : MSExperiment
• reserveSpaceSpectra() : MSExperiment
• 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
• residualOutlierCandidate_() : AbsoluteQuantitation , MRMRTNormalizer
• Residue() : Residue
• ResidueDB() : ResidueDB
• ResidueModification() : ResidueModification
• residuesMatch_() : ModificationsDB
• residueTypeToIonLetter() : Residue
• residueTypeToIonLetter_() : TheoreticalSpectrumGenerator
• ResidueTypeToString_() : SvmTheoreticalSpectrumGenerator
• resize() : ConstRefVector< ContainerT > , DistanceMatrix< Value > , IsotopeDistribution , Matrix< Value > , MSExperiment
• resizeEvent() : HistogramWidget , Spectrum3DCanvas , SpectrumCanvas , TOPPASWidget
• resizeGL() : Spectrum3DOpenGLCanvas
• resolve() : IDConflictResolverAlgorithm , PeptideProteinResolution
• 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
• resolveUniqueIdConflicts() : UniqueIdIndexer< RandomAccessContainer >
• restoreRotationAndZoom() : Spectrum3DOpenGLCanvas
• restrictTransitions() : MRMAssay
• RetentionTime() : RetentionTime
• retrieveSwathMaps() : FullSwathFileConsumer
• return_chromatogram() : ChromatogramExtractor
• returnResultsAndClear() : IDMergerAlgorithm
• reverse() : String , StringUtils
• ReverseComparator() : ReverseComparator< Cmp >
• reverseComparator() : ReverseComparator< Cmp >
• ReverseComparator() : ReverseComparator< Cmp >
• reversePeptide() : MRMDecoy
• reversePeptide_() : MRMDecoy
• Ribonucleotide() : Ribonucleotide
• RibonucleotideDB() : RibonucleotideDB
• RichPeak2D() : RichPeak2D
• 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
• RNaseDB() : RNaseDB
• ROCCurve() : ROCCurve
• rocN() : FalseDiscoveryRate , ROCCurve
• rocN_() : FalseDiscoveryRate
• roundBasedMode() : TOPPASMergerVertex
• row() : Matrix< Value >
• rowCount() : CsvFile
• rowIndex() : Matrix< Value >
• rows() : Matrix< Value >
• rt() : KDTreeFeatureMaps
• RTAlignment() : RTAlignment
• RTBegin() : MSChromatogram , MSExperiment
• RTEnd() : MSChromatogram , MSExperiment
• RTSimulation() : RTSimulation
• 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 , QTClusterFinder
• run_internal_() : QTClusterFinder
• runAccurateMassSearch() : FIAMSDataProcessor
• runClustering_() : FeatureGroupingAlgorithmKD
• runExternalProcess_() : TOPPBase
• runNextProcess() : TOPPASScene
• runOnCandidates() : FeatureFinderIdentificationAlgorithm
• runPipeline() : TOPPASBase , TOPPASScene
• runScript() : RWrapper
• runTOPPTool_() : TOPPViewBase