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_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
- recent_actions_
: TOPPViewBase
- recent_files_
: TOPPViewBase
- recomputeConsensus_()
: BaseLabeler
- 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_()
: 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
- 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
- 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
- Requires
: QCBase
- requires()
: QCBase
, 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 >
- 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 >
- 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_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