- r -

r_r_obj_ : MzQuantMLHandler
r_rtemp_ : MzQuantMLHandler
r_squared_ : LinearRegression
r_value : PeakShape
radius_ : PeakPickerCWT
range_x_ : ClusteringGrid
range_y_ : ClusteringGrid
rank : CsiFingerIdMzTabWriter::CsiAdapterHit , IDFilter::HasMaxRank< HitType > , MzTabMSmallMoleculeEvidenceSectionRow , OPXLDataStructs::CrossLinkSpectrumMatch , RNPxlReportRow , SiriusMzTabWriter::SiriusAdapterHit , Interpretation
rank_ : IdentificationHit , PeptideHit , ProteinHit
rank_sp_weights_ : SequestOutfile
ransac_params_ : MZTrafoModel
ransac_seed_ : MZTrafoModel
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
re_ : EnzymaticDigestion
reachable_ : TOPPASVertex
reagent_name_ : Modification
real_2D_ : TwoDOptimization
real_RT_votes_cutoff_ : FeatureFinderAlgorithmIsotopeWavelet
recalculate_peaks_ : MRMTransitionGroupPicker
recalculate_peaks_max_z_ : MRMTransitionGroupPicker
recent_actions_ : RecentFilesMenu
recent_files_ : RecentFilesMenu , TOPPViewBase
recent_files_menu_ : TOPPASBase
recent_menu_ : RecentFilesMenu
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 , TMTEighteenPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
reference_channel_name_ : IsobaricNormalizer
reference_formats : SpectrumLookup
reference_index_ : MapAlignmentAlgorithmIdentification
reflectron_state_ : MassAnalyzer , MassAnalyzerVisualizer
regex_description_ : DigestionEnzyme
regexp_name_list_ : SpectrumLookup
regexp_names_ : SpectrumLookup
regexstr_prefix : DecoyHelper
regexstr_suffix : DecoyHelper
region_rt_span_ : EGHTraceFitter , GaussTraceFitter
registered_at_ : LogStreamNotifier
registered_mod_ : PepXMLFile::AminoAcidModification
registry_ : MetaInfo
reindexed_peptides : ProteinResolver::ResolverResult
reindexed_proteins : ProteinResolver::ResolverResult
rel_loss_intensity_ : TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
rel_prec_error : RNPxlReportRow
relative_allowable_product_mass_ : TargetedSpectraExtractor
relative_d : RANSACParam
relative_intensities : TIC::Result
relevant : FeatureDistance::DistanceParams_
reliability : MzTabMSmallMoleculeSectionRow , MzTabNucleicAcidSectionRow , MzTabOligonucleotideSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
reload_plugins_button_ : ToolsDialog
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
rep_charge : FLASHDeconvHelperStructs::MassFeature
rep_mz : FLASHDeconvHelperStructs::MassFeature
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_top_hits_ : SimpleSearchEngineAlgorithm
reported_mz_ : FeatureFinderAlgorithmPicked
reporter_mass_shift_ : IsobaricChannelExtractor
required : ParameterInformation
required_modules_ : PythonModuleRequirement
requirement_level_ : CVMappingRule
requires_login_ : MascotRemoteQuery
res_ : IonDetectorVisualizer , MassAnalyzerVisualizer
res_method_ : MassAnalyzerVisualizer
res_type_ : MassAnalyzerVisualizer
resample_boundary_ : MRMTransitionGroupPicker
residual_peak_count : PrecursorPurity::PurityScores
residue_by_one_letter_code_ : ResidueDB
residue_mod_names_ : ResidueDB
residue_names_ : ResidueDB
residue_sets_ : Residue , ResidueDB
residues : MzIdentMLDOMHandler::ModificationParam
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 , DBSuitability , FragmentMassError , PSMExplainedIonCurrent
resume_source_ : TOPPASScene
retention_ : EmgFitter1D , EmgModel
retention_time : MzTabMSmallMoleculeFeatureSectionRow , MzTabOligonucleotideSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
retention_time_ : MascotInfile , Mobilogram , 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
retention_times : TIC::Result
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_count_from_apex_ : FLASHDeconvHelperStructs::PrecalculatedAveragine
right_endpoint_ : PeakShape
right_iterator_set_ : PeakShape
right_neighbor : ParentMatch
right_splitter_ : HistogramWidget
RIGHT_TERMINUS : ParentMatch
right_width : PeakShape
right_width_ : PeakPickerMRM
rightWidth : PeakCandidate
RNA : RNPxlReportRow
RNA_weight : RNPxlReportRow
rng_ : RandomShuffler , 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_ : OverlapDetector , Matrix< Value >
rsd_ : LinearRegression
rt : CsiFingerIdMzTabWriter::CsiAdapterIdentification
RT : FeatureFinderAlgorithmIsotopeWavelet::BoxElement
rt : Observation
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 : PlotWidget
rt_band_ : MultiplexFiltering
rt_calibrated : TransitionTSVFile::TSVTransition
rt_coef : ConfidenceScoring::GLM_
rt_delta_ : OSWPeakGroup
rt_diff_l : MRMFeatureQC::ComponentGroupPairQCs
rt_diff_u : MRMFeatureQC::ComponentGroupPairQCs
rt_difference : OpenSwath_Scores
rt_end : ChromatogramExtractorAlgorithm::ExtractionCoordinates , MzTabMSmallMoleculeFeatureSectionRow
rt_experimental_ : OSWPeakGroup
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_left_width_ : OSWPeakGroup
rt_light_ : XQuestResultXMLHandler
rt_max : FeatureFinderAlgorithmMetaboIdent::MassTraceBounds
rt_max_ : SpectraMerger::SpectraDistance_
rt_min : FeatureFinderAlgorithmMetaboIdent::MassTraceBounds
rt_norm_ : ConfidenceScoring
rt_normalization_factor_ : MRMFeatureFinderScoring , OpenSwathScoring
rt_quantile_ : FeatureFinderIdentificationAlgorithm
rt_range_ : FeatureFileOptions , PeakFileOptions
rt_ranges_ : FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound
rt_right_width_ : OSWPeakGroup
rt_scaling_ : MultiplexClustering::MultiplexDistance , MultiplexClustering
rt_set_ : MzMLHandler
rt_shift_ : Adduct , Compomer
rt_shift_mean : FeatureSummary::Result
rt_start : ChromatogramExtractorAlgorithm::ExtractionCoordinates , MzTabMSmallMoleculeFeatureSectionRow
rt_tol_secs_ : FeatureGroupingAlgorithmKD , MapAlignmentAlgorithmKD
rt_tolerance : SpectrumLookup
rt_tolerance_ : IDMapper
rt_trafo_ : ConfidenceScoring
rt_typical_ : MultiplexClustering
RT_votes_cutoff_ : FeatureFinderAlgorithmIsotopeWavelet
rt_window_ : FeatureFinderAlgorithmMetaboIdent , FeatureFinderIdentificationAlgorithm , TargetedSpectraExtractor
rts : ReactionMonitoringTransition , PeptideCompound
rts_ : FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound , IncludeExcludeTarget , SpectrumLookup
rubber_band_ : PlotCanvas
rules_ : CVMappingFile , SemanticValidator
run_ : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , TriqlerFile::TriqlerLine_
run_id_ : MzMLSqliteHandler , OpenSwathOSWWriter , OSWData , QcMLFile
run_Name_ID_map_ : QcMLFile
run_to_search_engines_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
run_to_search_engines_settings_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
running_ : TOPPASScene
runpath_to_identifier : ProteinIdentification::Mapping
runQualityAts_ : QcMLFile
runQualityQPs_ : QcMLFile
rWidth : PenaltyFactors