| OpenMS 2.5.0

### - 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 , RNPxlReportRow , SiriusMzTabWriter::SiriusAdapterHit , Interpretation
- rank_ : IdentificationHit , PeptideHit , ProteinHit
- rank_sp_weights_ : SequestOutfile
- ransac_params_ : MZTrafoModel
- rate : RateScorePair , SIPIncorporation
- rate_result_ : Ms2IdentificationRate
- ratio_max_ : FuzzyStringComparator
- ratio_max_allowed_ : FuzzyStringComparator
- ratio_value_ : ConsensusFeature::Ratio
- ratios_ : ConsensusFeature
- raw_data_first : TwoDOptimization::Data
- raw_files_ : MSQuantifications::Assay
- raw_rt_score : OpenSwath_Scores
- raw_spec_names : LCMS
- rawIsotopes_ : ConsensusIsotopePattern
- re_ : EnzymaticDigestion
- 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_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_ : IsotopeWaveletTransform< PeakType >::TransSpectrum , MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering
- reference_channel_ : ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
- reference_channel_name_ : IsobaricNormalizer
- reference_formats : SpectrumLookup
- reference_index_ : MapAlignmentAlgorithmIdentification
- reflectron_state_ : MassAnalyzer , MassAnalyzerVisualizer
- reg_models : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- regex_description_ : DigestionEnzyme
- regexp_name_list_ : SpectrumLookup
- regexp_names_ : SpectrumLookup
- region_rt_span_ : EGHTraceFitter , GaussTraceFitter
- registered_at_ : LogStreamNotifier
- registry_ : MetaInfo
- reindexed_peptides : ProteinResolver::ResolverResult
- reindexed_proteins : ProteinResolver::ResolverResult
- rel_loss_intensity_ : TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
- rel_prec_error : RNPxlReportRow
- relative_d : RANSACParam
- relevant : FeatureDistance::DistanceParams_
- reliability : MzTabNucleicAcidSectionRow , MzTabOligonucleotideSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
- remove_fixed_mods_ : MascotXMLHandler
- remove_low_intensity_quantifications_ : IsobaricChannelExtractor
- remove_overlapping_ : PeakPickerMRM
- remove_precursor_near_peaks_ : SequestInfile
- remove_single_traces_ : FeatureFindingMetabo
- 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
- report_tic_ : MRMFeatureFilter
- report_top_hits_ : SimpleSearchEngineAlgorithm
- report_xic_ : MRMFeatureFilter
- reported_mz_ : FeatureFinderAlgorithmPicked
- reporter_mass_shift_ : IsobaricChannelExtractor
- 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
- residual_peak_count : PrecursorPurity::PurityScores
- 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_l : MRMFeatureQC::ComponentGroupPairQCs
- resolution_method_ : MassAnalyzer
- resolution_pair_name : MRMFeatureQC::ComponentGroupPairQCs
- resolution_type_ : MassAnalyzer
- resolution_u : MRMFeatureQC::ComponentGroupPairQCs
- resolve_ambiguous_mods_ : NucleicAcidSearchEngine
- resolver_result_ : ProteinResolver
- response_bytes_ : NetworkGetRequest
- restrictions_ : ListEditorDelegate
- result_ : MultiplexFilteredMSExperiment
- 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
- retentionTimeInterpretation_ : TransitionTSVFile
- 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 >
- ribonucleotides_ : RibonucleotideDB
- 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
- RNA : RNPxlReportRow
- 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_masses_ : CoarseIsotopePatternGenerator
- round_total_ : TOPPASVertex
- rounding_errors_ : RealMassDecomposer
- row_ : BaseVisualizerGUI , QcMLFile
- rownames_ : DataMatrix
- rows_ : Matrix< Value >
- RR : SIPPeptide
- rsd_ : LinearRegression
- rt : CsiFingerIdMzTabWriter::CsiAdapterIdentification
- RT : FeatureFinderAlgorithmIsotopeWavelet::BoxElement
- rt : DataQuery
- RT : SpectrumMeta , IsotopeWaveletTransform< PeakType >::BoxElement
- rt : RNPxlReportRow , SiriusMSFile::CompoundInfo , SiriusMzTabWriter::SiriusAdapterIdentification , SpectrumMetaDataLookup::SpectrumMetaData , 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_coef : ConfidenceScoring::GLM_
- 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_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_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
- RTmax_ : InclusionExclusionList::IEWindow
- RTmin_ : InclusionExclusionList::IEWindow
- rts : ReactionMonitoringTransition , PeptideCompound
- rts_ : IncludeExcludeTarget , SpectrumLookup
- rubber_band_ : SpectrumCanvas
- rules_ : CVMappingFile , SemanticValidator
- run_ : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_
- run_id_ : MzMLSqliteHandler , OpenSwathOSWWriter , QcMLFile
- run_Name_ID_map_ : QcMLFile
- running_ : TOPPASScene
- runQualityAts_ : QcMLFile
- runQualityQPs_ : QcMLFile
- rWidth : PenaltyFactors