- r -

RAIICleanup() : RAIICleanup
random() : String
RandomShuffler() : RandomShuffler
RangeBase() : RangeBase , RangeIntensity , RangeMobility , RangeMZ , RangeRT
RankScaler() : RankScaler
rankWeightedPermutationPeptideScores_() : AScore
RANSAC() : RANSAC< TModelType >
ransac() : RANSAC< TModelType >
RANSACParam() : RANSACParam
raster() : LinearResampler , LinearResamplerAlign
raster_align() : LinearResamplerAlign
raster_interpolate() : LinearResamplerAlign
rasterExperiment() : LinearResampler
Ratio() : ConsensusFeature::Ratio
rbegin() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , IsotopeDistribution , MassTrace , Mobilogram
rdbuf() : LogStream
ReactionMonitoringTransition() : ReactionMonitoringTransition
read() : Bzip2Ifstream , GzipIfstream , OSWFile
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
readFromJSON_() : RibonucleotideDB
readFromOBOFile() : CrossLinksDB , ModificationsDB
readFromUnimodXMLFile() : ModificationsDB
readMappingFile_() : OMSSAXMLFile
readMemdump() : CachedMzMLHandler
readMeta_() : OSWFile
readMinimal() : OSWFile
readMS1Spectra() : MzMLSqliteSwathHandler
readMzIdentMLFile() : MzIdentMLDOMHandler
readNext() : FASTAFile
readNextLine_() : FuzzyStringComparator
readNextWithProgress() : FASTAFile
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
readStartWithProgress() : FASTAFile
readSwathWindows() : MzMLSqliteSwathHandler , SwathWindowLoader
readToPIN() : OSWFile
readTransitions_() : OSWFile
readUnstructuredTSVInput_() : TransitionTSVFile
RealMassDecomposer() : RealMassDecomposer
reannotateTransitions() : MRMAssay
recalculateAxes() : PlotCanvas
recalculateAxes_() : Plot1DWidget , Plot2DWidget , Plot3DWidget , PlotWidget
recalculateCurrentLayerDotGradient() : Plot2DCanvas
recalculateDotGradient_() : Plot2DCanvas , Plot3DOpenGLCanvas
recalculatePeakBorders_() : MRMTransitionGroupPicker
recalculatePercentageFactor_() : Plot1DCanvas
recalculateRanges_() : Plot1DCanvas , PlotCanvas
recalculateSnapFactor_() : Plot2DCanvas , PlotCanvas
recentFileClicked() : RecentFilesMenu
RecentFilesMenu() : RecentFilesMenu
recomputeNeighbors_() : QTCluster
recruitAllPeaksInSpectrum() : PeakGroup
recurseAndGenerateVariableModifiedSequences_() : ModifiedNASequenceGenerator
reduce() : DistanceMatrix< Value >
ref() : MatchedIterator< CONT_T, TRAIT, CONST_T >
refIdx() : MatchedIterator< CONT_T, TRAIT, CONST_T >
refreshParameters() : TOPPASBase , TOPPASScene , TOPPASToolVertex
refreshPipelineParameters() : TOPPASBase
registerAdduct() : IdentificationData
registerAt() : LogStreamNotifier
registerBasename_() : IDRipper
registerChannelsInOutputMap_() : IsobaricChannelExtractor
registerDBSearchParam() : IdentificationData
registerDoubleList_() : TOPPBase
registerDoubleOption_() : TOPPBase
registerFlag_() : TOPPBase
registerFullParam_() : TOPPBase
registerIdentifiedCompound() : IdentificationData
registerIdentifiedOligo() : IdentificationData
registerIdentifiedPeptide() : IdentificationData
registerInputFile() : IdentificationData
registerInputFile_() : TOPPBase
registerInputFileList_() : TOPPBase
registerIntList_() : TOPPBase
registerIntOption_() : TOPPBase
registerName() : MetaInfoRegistry
registerObservation() : IdentificationData
registerObservationMatch() : IdentificationData
registerObservationMatchGroup() : IdentificationData
registerOptionsAndFlags_() : NucleicAcidSearchEngine , TOPPBase , TOPPFLASHDeconv , TOPPGNPSExport
registerOutputDir_() : TOPPBase
registerOutputFile_() : TOPPBase
registerOutputFileList_() : TOPPBase
registerOutputPrefix_() : TOPPBase
registerParamSubsectionsAsTOPPSubsections_() : TOPPBase
registerParentGroupSet() : IdentificationData
registerParentSequence() : IdentificationData
registerPeptideIndexingParameter_() : SearchEngineBase
registerPrecursor_() : FLASHDeconvAlgorithm
registerProcessingSoftware() : IdentificationData
registerProcessingStep() : IdentificationData
registerProtein_() : ProtXMLFile
registerRun() : QcMLFile
registerScoreType() : IdentificationData
registerSet() : QcMLFile
registerStream() : StreamHandler
registerStringList_() : TOPPBase
registerStringOption_() : TOPPBase
registerSubsection_() : TOPPBase
registerTOPPSubsection_() : TOPPBase
registry() : MetaInfo
RegularSwathFileConsumer() : RegularSwathFileConsumer
reindex_() : SearchEngineBase
released() : TOPPASVertex
reloadPlugins_() : ToolsDialog
remove() : DataFilters , File , LogStream , MultiGradient , Param , String
remove_() : MetaInfoVisualizer
remove_chromatogram_flag() : LayerDataPeak
remove_overlapping_features() : MRMTransitionGroupPicker
removeAdduct() : Compomer
removeAll() : InputFileList , Param
removeAllAttachments() : QcMLFile
removeAllClusters() : ClusteringGrid
removeAllStreams() : LogStream
removeAttachment() : QcMLFile
removeBetaPeptideHits() : OPXLHelper
removeBlackListItems() : FilterableList
removeChargeErrorPeakGroups_() : FLASHDeconvAlgorithm
removeCluster() : ClusteringGrid
removeCommasAndParseDouble() : ChromeleonFile
removeCurrentLayer() : LayerStack
removeCurrentRow() : ListTable
removeData_() : GradientVisualizer
removeDecoyHits() : IDFilter
removeDecoys() : IDFilter
removeDecoyStringIfPresent_() : IDScoreGetterSetter
removeDir() : File
removeDirRecursively() : File
removeDuplicatePeptideHits() : IDFilter
removeEmptyIdentifications() : IDFilter
removeFile() : FileWatcher
removeFromElementMapping_() : QTClusterFinder
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() : IdentificationData , MetaInfoInterface
removeMS2SpectraPeaks_() : TargetedSpectraExtractor
removeObservationMatchesIf() : IdentificationData
removeOutEdge() : TOPPASVertex
removeOutliersIterative() : MRMRTNormalizer
removeOutliersRANSAC() : MRMRTNormalizer
removeOverlappingPeakGroups_() : FLASHDeconvAlgorithm
removeOverlappingPeaks_() : PeakPickerChromatogram
removeParentSequencesIf() : IdentificationData
removePeakAnnotationsFromPeptideHit() : LayerData1DPeak
removePeptidesWithMatchingModifications() : IDFilter
removePeptidesWithMatchingRegEx() : IDFilter
removePeptidesWithMatchingSequences() : IDFilter
removePhosphositesFromSequence_() : AScore
removeQualityParameter() : QcMLFile
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
removeZeroedElements_() : EmpiricalFormula
rename() : File
renameOutput_() : TOPPASToolVertex
rend() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , IsotopeDistribution , MassTrace , Mobilogram
renderForImage() : Plot1DWidget
renderText_() : Plot3DOpenGLCanvas
renormalize() : IsotopeDistribution
replace() : DataFilters , ParamCTDFile
replaceCVTerm() : CVTermList , CVTermListInterface
replaceCVTerms() : CVTermList , CVTermListInterface
replyFinished() : NetworkGetRequest
reportFailure_() : FuzzyStringComparator
reportSuccess_() : FuzzyStringComparator
requestClipboardContent() : TOPPASScene
requestVisibleArea1D() : SpectraIDViewTab
RequiredParameterNotGiven() : RequiredParameterNotGiven
requirements() : Contaminants , FeatureSummary , FragmentMassError , FWHM , IdentificationSummary , MissedCleavages , Ms2IdentificationRate , Ms2SpectrumStats , MzCalibration , PeptideMass , PSMExplainedIonCurrent , QCBase , RTAlignment , SpectrumCount , TIC
rerunTOPPTool() : TOPPViewBase
resample() : ConsensusMapNormalizerAlgorithmQuantile
resampleChromatogram_() : MRMTransitionGroupPicker
rescaleFragmentFeature_() : PercolatorFeatureSetHelper
reserve() : ConstRefVector< ContainerT > , DeconvolvedSpectrum , ExposedVector< VectorElement > , Mobilogram , MSExperiment , PeakGroup
reserveSpaceChromatograms() : MSExperiment
reserveSpaceSpectra() : MSExperiment
reset() : squared_difference_counted< _Tp, _Dist > , FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector > , FuzzyStringComparator::StreamElement_ , shared_xerces_ptr< T > , XMLHandler , IsobaricQuantifierStatistics , Histogram< ValueType, BinSizeType > , MSExperiment , StopWatch , SysInfo::MemUsage , TOPPASOutputVertex , TOPPASToolVertex , TOPPASVertex
resetAlignment() : Plot1DCanvas , Plot1DWidget
resetDownstream() : TOPPASScene
resetErrors() : XMLValidator
resetInterpretations() : TraMLProduct
resetMembers_() : FeatureXMLHandler , ProtXMLFile
resetProcessesQueue() : TOPPASScene
resetProteinScores_() : BayesianProteinInferenceAlgorithm
resetTranslation() : Plot3DOpenGLCanvas
resetZoom() : Plot1DCanvas , PlotCanvas , TOPPViewBase
reshapeIMFrameToMany() : IMDataConverter
reshapeIMFrameToSingle() : IMDataConverter
residualOutlierCandidate_() : AbsoluteQuantitation , MRMRTNormalizer
Residue() : Residue
ResidueDB() : ResidueDB
ResidueModification() : ResidueModification
residuesMatch_() : ModificationsDB
residueTypeToIonLetter() : Residue
resize() : ConstRefVector< ContainerT > , DistanceMatrix< Value > , ExposedVector< VectorElement > , IsotopeDistribution , Matrix< Value > , Mobilogram , MSExperiment
resized() : TableView
resizeEvent() : HistogramWidget , Plot3DCanvas , PlotCanvas , SpectraIDViewTab::SelfResizingTableView_ , TableView , TOPPASWidget
resizeGL() : Plot3DOpenGLCanvas
resolve() : IDConflictResolverAlgorithm , PeptideProteinResolution
resolveAmbiguityGroup() : MetaboTargetedAssay
resolveAmbiguousMods_() : NucleicAcidSearchEngine
resolveAutoMode_() : AccurateMassSearchEngine
resolveBetweenFeatures() : IDConflictResolverAlgorithm
resolveBetweenFeatures_() : IDConflictResolverAlgorithm
resolveConflict_() : IDConflictResolverAlgorithm
resolveConflictKeepMatching_() : IDConflictResolverAlgorithm
resolveConnectedComponent() : PeptideProteinResolution
resolveGraph() : PeptideProteinResolution
resolveGraphPeptideCentric() : IDBoostGraph
resolveGraphPeptideCentric_() : IDBoostGraph
resolveMisassignedNTermMods_() : PercolatorOutfile
resolveMixedSequenceGroups_() : TransitionTSVFile
resolveOverlappingTargetDecoyMassesByDecoyMassShift() : MetaboTargetedTargetDecoy
resolveUniqueIdConflicts() : UniqueIdIndexer< T >
restoreRotationAndZoom() : Plot3DOpenGLCanvas
restrictTransitions() : MRMAssay
resume() : StopWatch
RetentionTime() : RetentionTime
retrieveSwathMaps() : FullSwathFileConsumer
return_chromatogram() : ChromatogramExtractor
returnResultsAndClear() : IDMergerAlgorithm
reverse() : String
reversePeptide() : MRMDecoy
reversePeptide_() : MRMDecoy
reversePeptides() : DecoyGenerator
reverseProtein() : DecoyGenerator
Ribonucleotide() : Ribonucleotide
RibonucleotideDB() : RibonucleotideDB
RichPeak2D() : RichPeak2D
rightBorderOfBin() : Histogram< ValueType, BinSizeType >
rip() : IDRipper
RipFileContent() : IDRipper::RipFileContent
RipFileIdentifier() : IDRipper::RipFileIdentifier
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
roundBasedMode() : TOPPASMergerVertex
rowClicked_() : DIATreeTab
rowCount() : CsvFile
rowDoubleClicked_() : DIATreeTab
rowMajor() : Matrix< Value >
rowSelectionChange_() : DIATreeTab
rt() : KDTreeFeatureMaps
RTAlignment() : RTAlignment
RTBegin() : MSChromatogram , MSExperiment
RTEnd() : MSChromatogram , MSExperiment
run() : AccurateMassSearchEngine , BaseGroupFinder , BaseSuperimposer , BasicProteinInferenceAlgorithm , CoarseIsotopePatternGenerator , ExternalProcess , ExternalProcessMBox , FeatureFinderAlgorithm , FeatureFinderAlgorithmMetaboIdent , 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 , SiriusExportAlgorithm , StablePairFinder , TOPPASInputFileListVertex , TOPPASMergerVertex , TOPPASOutputFileListVertex , TOPPASOutputFolderVertex , TOPPASSplitterVertex , TOPPASToolVertex , TOPPASVertex , UpdateCheck , XFDRAlgorithm
run_() : MassTraceDetection , PeptideIndexing , QTClusterFinder
run_internal_() : QTClusterFinder
runAccurateMassSearch() : FIAMSDataProcessor
runClustering_() : FeatureGroupingAlgorithmKD
runExternalProcess_() : TOPPBase
runIdentificationSearch_() : DBSuitability
runNextProcess() : TOPPASScene
runOnCandidates() : FeatureFinderIdentificationAlgorithm
runPipeline() : TOPPASBase , TOPPASScene
runScript() : RWrapper
runTOPPTool_() : TOPPViewBase