| OpenMS 2.5.0

### - 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
- recalibrateMasses_() : UTILProteomicsLFQ
- 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_() : 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
- 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
- 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
- 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