- r -

• r_r_obj_ : MzQuantMLHandler
• r_rtemp_ : MzQuantMLHandler
• r_squared_ : LinearRegression
• r_value : PeakShape
• radius : LocalLinearMap::LLMParam
• radius_ : PeakPickerCWT
• rand_gen_ : ConfidenceScoring
• range_x_ : ClusteringGrid
• range_y_ : ClusteringGrid
• rank : CsiFingerIdMzTabWriter::CsiAdapterHit , IDFilter::HasMaxRank< HitType > , OPXLDataStructs::CrossLinkSpectrumMatch , SiriusMzTabWriter::SiriusAdapterHit , Interpretation
• rank_ : IdentificationHit , PeptideHit , ProteinHit
• rank_sp_weights_ : SequestOutfile
• ransac_params_ : MZTrafoModel
• rate : RateScorePair , SIPIncorporation
• ratio_max_ : FuzzyStringComparator
• ratio_max_allowed_ : FuzzyStringComparator
• ratio_value_ : ConsensusFeature::Ratio
• ratios_ : ConsensusFeature
• raw_data_first : TwoDOptimization::Data
• raw_data_points_ : MultiplexFilterResultPeak
• raw_files_ : MSQuantifications::Assay
• raw_rt_score : OpenSwath_Scores
• raw_spec_ : BinnedSpectrum
• raw_spec_names : LCMS
• rawIsotopes_ : ConsensusIsotopePattern
• reachable_ : TOPPASVertex
• reader_ : FASTAFile
• reagent_name_ : Modification
• real_2D_ : TwoDOptimization
• real_RT_votes_cutoff_ : FeatureFinderAlgorithmIsotopeWavelet
• recalculate_peaks_ : MRMTransitionGroupPicker
• recalculate_peaks_max_z_ : MRMTransitionGroupPicker
• recent_actions_ : TOPPViewBase
• recent_files_ : TOPPViewBase
• reconstruction : SIPPeptide
• reconstruction_monoistopic : SIPPeptide
• record_length_ : InspectOutfile
• recursion_depth_ : ProgressLogger
• reduce_by_factor_ : ParentPeakMower
• reestimate_mt_sd_ : MassTraceDetection
• ref_ : PrecisionWrapper< FloatingPointType >
• ref_intens : IsotopeWaveletTransform< PeakType >::BoxElement
• ref_map_id_ : IsobaricNormalizer
• ref_param_ : MzMLHandler
• reference_ : IsotopeWaveletTransform< PeakType >::TransSpectrum , MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering
• reference_channel_ : ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• reference_channel_name_ : IsobaricNormalizer
• reference_formats : SpectrumLookup
• reference_index_ : MapAlignmentAlgorithmIdentification
• reflectron_state_ : MassAnalyzer , MassAnalyzerVisualizer
• reg_models : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• regex_description_ : Enzyme
• regexp_name_list_ : SpectrumLookup
• regexp_names_ : SpectrumLookup
• region_rt_span_ : EGHTraceFitter , GaussTraceFitter
• registered_at_ : LogStreamNotifier
• registry_ : MetaInfo , MultiplexFiltering
• reindexed_peptides : ProteinResolver::ResolverResult
• reindexed_proteins : ProteinResolver::ResolverResult
• rel_loss_intensity_ : TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• rel_prec_error : RNPxlReportRow
• relative_d : RANSACParam
• relevant : FeatureDistance::DistanceParams_
• reliability : MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• remove_fixed_mods_ : MascotXMLHandler
• remove_low_intensity_quantifications_ : IsobaricChannelExtractor
• remove_overlapping_ : PeakPickerMRM
• remove_precursor_near_peaks_ : SequestInfile
• removebutton_ : GradientVisualizer
• removeRowButton_ : ListEditor
• replacement_ : SVOutStream
• reply_ : NetworkGetRequest
• report_chromatograms_ : FeatureFindingMetabo
• report_convex_hulls_ : FeatureFindingMetabo
• report_FWHM_ : PeakPickerHiRes
• report_FWHM_as_ppm_ : PeakPickerHiRes
• report_mode_ : MetaboliteSpectralMatching
• report_summed_ints_ : FeatureFindingMetabo
• reported_mz_ : FeatureFinderAlgorithmPicked
• reporter_mass_shift_ : IsobaricChannelExtractor
• require_args_ : TOPPBase
• required : ParameterInformation
• requirement_level_ : CVMappingRule
• requires_login_ : MascotRemoteQuery
• res_ : IonDetectorVisualizer , MassAnalyzerVisualizer
• res_base_ : RawMSSignalSimulation
• res_method_ : MassAnalyzerVisualizer
• res_model_ : RawMSSignalSimulation
• res_type_ : MassAnalyzerVisualizer
• resample_boundary_ : MRMTransitionGroupPicker
• residue : SvmTheoreticalSpectrumGenerator::IonType
• residue_by_one_letter_code_ : ResidueDB
• residue_mod_names_ : ResidueDB
• residue_names_ : ResidueDB
• residue_sets_ : Residue , ResidueDB
• residue_to_name_ : CompNovoIdentificationBase
• residues : MzIdentMLDOMHandler::ModificationParam
• residues_ : ResidueDB
• residues_by_set_ : ResidueDB
• residues_in_upper_case_ : SequestInfile
• resolution_ : IonDetector , MassAnalyzer
• resolution_method_ : MassAnalyzer
• resolution_type_ : MassAnalyzer
• resolver_result_ : ProteinResolver
• response_bytes_ : NetworkGetRequest
• restrictions : ParamXMLHandler
• restrictions_ : ListEditorDelegate
• restrictions_index : ParamXMLHandler
• result_ : MultiplexFilterResult
• result_windows_even : SignalToNoiseEstimatorMedianRapid::NoiseEstimator
• result_windows_odd : SignalToNoiseEstimatorMedianRapid::NoiseEstimator
• resume_source_ : TOPPASScene
• retention_ : EGHFitter1D , EmgFitter1D , EmgModel
• retention_time : MzTabPeptideSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• retention_time_ : MascotInfile , MSSpectrum
• retention_time_window : MzTabPeptideSectionRow
• retentionTimeInterpretation_ : TransitionTSVReader
• 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_nns_ : GridBasedClustering< Metric >
• right : PeakPickerCWT::PeakArea_
• right_boundary : PeakPickerMaxima::PeakCandidate
• right_child : BinaryTreeNode
• right_endpoint_ : PeakShape
• right_iterator_set_ : PeakShape
• right_splitter_ : HistogramWidget
• right_width : PeakShape
• right_width_ : PeakPickerMRM
• rightWidth : PeakCandidate
• RNA : RNPxlReportRow
• rna_mod_index : RNPxlSearch::AnnotatedHit
• RNA_weight : RNPxlReportRow
• rnd_gen_ : IonizationSimulation , RawMSSignalSimulation , RawTandemMSSignalSimulation , RTSimulation
• rng : RANSACParam
• rng_ : BaseLabeler , UniqueIdGenerator
• root_ : Param::ParamIterator , Param
• round_based_mode_ : TOPPASMergerVertex
• round_counter_ : TOPPASVertex
• round_total_ : TOPPASVertex
• rounding_errors_ : RealMassDecomposer
• row_ : BaseVisualizerGUI , QcMLFile
• rownames_ : DataMatrix
• rows_ : Matrix< Value >
• RR : SIPPeptide
• rsd_ : LinearRegression
• RT : FeatureFinderAlgorithmIsotopeWavelet::BoxElement , SpectrumMeta , IsotopeWaveletTransform< PeakType >::BoxElement
• rt : RNPxlReportRow , SpectrumMetaDataLookup::SpectrumMetaData , LightCompound
• RT : OSSpectrumMeta
• rt : Peptide
• rt_ : KDTreeFeatureMaps , MultiplexFilterResultPeak , MZTrafoModel , PeptideIdentification , PepXMLFile
• rt_bridge_ : InclusionExclusionList::WindowDistance_
• rt_calibrated : TransitionTSVReader::TSVTransition
• rt_coef : ConfidenceScoring
• rt_difference : OpenSwath_Scores
• rt_end : ChromatogramExtractorAlgorithm::ExtractionCoordinates , RawMSSignalSimulation::ContaminantInfo
• rt_extraction_window : ChromExtractParams
• rt_extraction_window_ : MRMFeatureFinderScoring
• 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_range_ : FeatureFileOptions , PeakFileOptions
• 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
• RTmax_ : InclusionExclusionList::IEWindow
• RTmin_ : InclusionExclusionList::IEWindow
• rts : ReactionMonitoringTransition , Compound , Peptide
• rts_ : IncludeExcludeTarget , SpectrumLookup
• rubber_band_ : SpectrumCanvas
• rules_ : CVMappingFile , SemanticValidator
• run_id_ : QcMLFile
• run_Name_ID_map_ : QcMLFile
• running_ : TOPPASScene
• runQualityAts_ : QcMLFile
• runQualityQPs_ : QcMLFile
• runs : ExperimentalDesign
• rWidth : PenaltyFactors