Here is a list of all class members with links to the classes they belong to:

- u -

• ui : FLASHDeconvWizardBase , FLASHDeconvTabWidget , SwathTabWidget , SwathWizardBase
• ui_ : DataFilterDialog , FeatureEditDialog , InputFile , FilterableList , FilterList , InputFileList , Plot1DPrefDialog , Plot2DPrefDialog , Plot3DPrefDialog , PythonModuleRequirement , PythonSelector , TOPPViewPrefDialog , LayerStatisticsDialog , ListFilterDialog , OutputDirectory , ParamEditor , Plot1DGoToDialog , Plot2DGoToDialog , SpectrumAlignmentDialog , SwathLibraryStats , TheoreticalSpectrumGenerationDialog , TOPPASInputFileDialog , TOPPASInputFilesDialog , TOPPASIOMappingDialog , TOPPASOutputFilesDialog , TOPPASVertexNameDialog , TOPPViewOpenDialog
• uis_threshold_peak_area_ : MRMFeatureFinderScoring
• uis_threshold_sn_ : MRMFeatureFinderScoring
• uisTransitions() : MRMAssay
• ulod_ : AbsoluteQuantitationMethod
• uloq_ : AbsoluteQuantitationMethod
• umap_index2children_naive_ : ACTrie
• umap_index2needles_ : ACTrie
• UnableToCalibrate() : UnableToCalibrate
• UnableToCreateFile() : UnableToCreateFile
• UnableToFit() : UnableToFit
• unambiguous_score_ : AScore
• Unannotated : NASequence , Residue
• unassigned_contaminants_ratio : Contaminants::ContaminantsSummary
• unassigned_peptide_identifications_ : ConsensusMap , FeatureMap
• unassignedIDs_ : FeatureFinderIdentificationAlgorithm
• unassignedMS2 : FeatureMapping::FeatureToMs2Indices
• UNBOUNDED : LPWrapper
• uncalibrated_calibrated_mz_mda : MQExporterHelper::MQCommonOutputs
• uncalibrated_calibrated_mz_ppm : MQExporterHelper::MQCommonOutputs
• uncalibrated_mass_error_da : MQExporterHelper::MQCommonOutputs
• uncalibrated_mass_error_ppm : MQExporterHelper::MQCommonOutputs
• uncompressString() : ZlibCompression
• UNDEFINED : IsotopeDistribution , LPWrapper
• undo() : Colorizer
• undo_() : AcquisitionInfoVisualizer , AcquisitionVisualizer , Colorizer , ContactPersonVisualizer , DataProcessingVisualizer , DigestionVisualizer , DocumentIdentifierVisualizer , ExperimentalSettingsVisualizer , GradientVisualizer , HPLCVisualizer , InstrumentSettingsVisualizer , InstrumentVisualizer , IonDetectorVisualizer , IonSourceVisualizer , MassAnalyzerVisualizer , MetaInfoDescriptionVisualizer , MetaInfoVisualizer , ModificationVisualizer , PeptideHitVisualizer , PeptideIdentificationVisualizer , PrecursorVisualizer , ProductVisualizer , ProteinHitVisualizer , ProteinIdentificationVisualizer , SampleVisualizer , ScanWindowVisualizer , SoftwareVisualizer , SourceFileVisualizer , SpectrumSettingsVisualizer , TaggingVisualizer
• undo_all_ : Colorizer
• undo_button_ : BaseVisualizerGUI
• undoAll() : Colorizer
• undobutton_ : MetaDataBrowser
• undos_only : Colorizer
• UNEXPECTED_RESULT : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , PeptideIndexing , TOPPBase , XFDRAlgorithm
• unfindable() : NeighborSeq::NeighborStats
• unfindable_peptides : NeighborSeq::NeighborStats
• unidentified : IDMapper::SpectraIdentificationState
• unify() : SpectrumSettings
• unimod_ : MzIdentMLDOMHandler , MzIdentMLHandler
• unimod_id : Peptide::Modification , LightModification
• unimod_record_id_ : ResidueModification
• UnimodXMLFile() : UnimodXMLFile
• UnimodXMLHandler() : UnimodXMLHandler
• uniprot_id : TransitionTSVFile::TSVTransition
• unique : MzTabOligonucleotideSectionRow , MzTabPeptideSectionRow , MzTabPSMSectionRow
• unique_id : ConsensusMap::ColumnHeader
• unique_id_ : UniqueIdInterface
• unique_id_scores_ : XFDRAlgorithm
• unique_ids_ : XFDRAlgorithm
• unique_peptides : IdentificationSummary::Result
• unique_proteins : IdentificationSummary::Result
• unique_xerces_ptr() : unique_xerces_ptr< T >
• uniqueid_to_index_ : UniqueIdIndexer< T >
• UniqueIdGenerator() : UniqueIdGenerator
• UniqueIdInterface() : UniqueIdInterface
• UniqueIdMap : UniqueIdIndexer< T >
• uniqueIdToIndex() : UniqueIdIndexer< T >
• Unit() : CVTerm::Unit
• unit_ : CVTerm , DataValue , DimBase
• unit_accession : SemanticValidator::CVTerm
• unit_accession_att_ : SemanticValidator
• unit_mapper_ : PlotCanvas
• unit_multiplier : MzMLHandlerHelper::BinaryData
• unit_name : SemanticValidator::CVTerm
• unit_name_att_ : SemanticValidator
• UNIT_ONTOLOGY : DataValue
• unit_ppm_ : BinnedSpectrum
• unit_type_ : DataValue
• unitAcc : QcMLFile::Attachment , QcMLFile::QualityParameter
• united() : DRange< D >
• UnitRange : PlotCanvas
• unitRef : QcMLFile::Attachment , QcMLFile::QualityParameter
• units : ControlledVocabulary::CVTerm
• UnitType : DataValue
• UNKNOWN : FileTypes , Instrument , InstrumentSettings , ReactionMonitoringTransition , ResidueModification , SpectrumSettings
• UNKNOWN_AA : PeptideEvidence
• UNKNOWN_CHECKSUM : SourceFile
• UNKNOWN_ERROR : TOPPBase
• UNKNOWN_LOG_LEVEL : LogStreamBuf
• UNKNOWN_NEIGHBOR : ParentMatch
• UNKNOWN_OAF : IDRipper
• UNKNOWN_POSITION : ParentMatch , PeptideEvidence
• unlock() : GUILock
• Unmatched : PeptideIndexing
• unmatched_action_ : PeptideIndexing
• unmodified_seq : OPXLDataStructs::AASeqWithMass
• UnnormalizedComparator() : UnnormalizedComparator
• unparsed : ControlledVocabulary::CVTerm
• unquote() : String
• unregister() : LogStreamNotifier
• UnregisteredParameter() : UnregisteredParameter
• unregisterStream() : StreamHandler
• unselectAll() : TOPPASScene
• UnspecificCleavage : EnzymaticDigestion
• untargetedMatching() : TargetedSpectraExtractor
• UNUSED : FeatureFinderDefs
• unWeightData() : TransformationModel
• unWeightDatum() : TransformationModel
• UP : MassAnalyzer
• update() : LayerListView , BasicStatistics< RealT > , Param , QTCluster , SwathLibraryStats , TOPPViewMenu
• update_() : AcquisitionInfoVisualizer , AcquisitionVisualizer , BaseVisualizer< ObjectType > , ContactPersonVisualizer , DataProcessingVisualizer , DigestionVisualizer , DocumentIdentifierVisualizer , ExperimentalSettingsVisualizer , GradientVisualizer , HPLCVisualizer , InstrumentSettingsVisualizer , InstrumentVisualizer , IonDetectorVisualizer , IonSourceVisualizer , MassAnalyzerVisualizer , MetaInfoDescriptionVisualizer , ModificationVisualizer , PeptideHitVisualizer , Plot3DCanvas , PlotCanvas , PrecursorVisualizer , ProductVisualizer , ProteinHitVisualizer , SampleVisualizer , ScanWindowVisualizer , SoftwareVisualizer , SourceFileVisualizer , SpectrumSettingsVisualizer , TaggingVisualizer
• update_buffer_ : PlotCanvas
• updateAllIDReferences() : Feature
• updateAndMovePepIDs_() : IDMergerAlgorithm
• updateAvgDaError_() : PeakGroup
• updateAvgPPMError_() : PeakGroup
• updateAxes() : PlotWidget
• updateBarsAndMenus() : TOPPViewBase
• updateBaseline() : FeatureFinderAlgorithmPickedHelperStructs::MassTraces
• updateCandidateMassBins_() : FLASHDeconvAlgorithm
• updateChannelMap() : ItraqConstants
• updateChargeFitScoreAndChargeIntensities_() : PeakGroup
• updateChargeRange_() : PeakGroup
• updateCheckBoxItem() : TableView
• updateClustering_() : QTClusterFinder
• updateClusterProxies_() : FeatureGroupingAlgorithmKD
• updateColor() : TOPPASEdge
• updateCurrentFeature_() : FeatureXMLHandler
• updateCurrentOutputFileNames() : TOPPASToolVertex
• updateCurrentPath() : TOPPASBase , TOPPViewBase
• updateCursor_() : PlotCanvas
• updateCWD_() : InputFileList
• updatedCWD() : InputFile , InputFileList
• updatedFile() : InputFile
• updatedSingleCell_() : SpectraIDViewTab
• updatedSingleProteinCell_() : SpectraIDViewTab
• updateEdgeColors() : TOPPASScene
• updateEditorGeometry() : ListEditorDelegate , ParamEditorDelegate
• updateEntries() : DataTabBase , DIATreeTab , SpectraIDViewTab , SpectraTreeTab
• updateEntries_() : SpectraIDViewTab
• updateFeatureVariant_() : ILPDCWrapper
• updateFilterBar() : TOPPViewBase
• updateFLASHDeconvParamFromWidgets_() : FLASHDeconvTabWidget
• updateFromFile() : SwathLibraryStats
• updateGridDimension_() : HashGrid< Cluster >
• updateHitRanks() : IDFilter
• updateHoveringEdgePos() : TOPPASScene
• updateHScrollbar() : PlotCanvas , PlotWidget
• updateIDReferences() : BaseFeature
• updateIntensityScale() : Plot3DOpenGLCanvas
• updateInternalList_() : FilterableList
• updateIonTypes_() : TheoreticalSpectrumGenerationDialog
• updateIsotopeMatrixFromStringList() : ItraqConstants
• updateIterativeWeightedMeanMZ() : MassTraceDetection
• updateLayer() : Plot1DCanvas , Plot2DCanvas , Plot3DCanvas , PlotCanvas
• updateLayerBar() : TOPPViewBase
• updateLogMzPeaks_() : FLASHDeconvAlgorithm
• updateMassBins_() : FLASHDeconvAlgorithm
• updateMaximum() : FeatureFinderAlgorithmPickedHelperStructs::MassTrace
• updateMeanMZ() : MassTrace
• updateMedianMZ() : MassTrace
• updateMedianRT() : MassTrace
• updateMembers_() : AbsoluteQuantitation , AccurateMassSearchEngine , AScore , BaseModel , BayesianProteinInferenceAlgorithm , BiGaussFitter1D , BiGaussModel , BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSumAgreeingIntensities , ConsensusIDAlgorithm , ConsensusIDAlgorithmPEPIons , ConsensusIDAlgorithmPEPMatrix , DefaultParamHandler , DiaPrescore , DIAScoring , EGHTraceFitter , ElutionPeakDetection , EmgFitter1D , EmgGradientDescent , EmgModel , ExtendedIsotopeFitter1D , ExtendedIsotopeModel , FeatureDeconvolution , FeatureDistance , FeatureFinderAlgorithmMetaboIdent , FeatureFinderAlgorithmPicked , FeatureFinderIdentificationAlgorithm , FeatureFindingMetabo , FIAMSDataProcessor , Fitter1D , FLASHDeconvAlgorithm , GaussFilter , GaussFitter1D , GaussModel , GaussTraceFitter , IDMapper , IDScoreSwitcherAlgorithm , IncludeExcludeTarget , InterpolationModel , IsobaricChannelExtractor , IsobaricQuantifier , IsotopeFitter1D , IsotopeLabelingMDVs , IsotopeModel , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , KDTreeFeatureMaps , LevMarqFitter1D , LinearResampler , LinearResamplerAlign , LowessSmoothing , MapAlignmentAlgorithmKD , MapAlignmentAlgorithmPoseClustering , MapAlignmentAlgorithmTreeGuided , MascotGenericFile , MascotRemoteQuery , MassDecompositionAlgorithm , MassFeatureTrace , MassTraceDetection , MaxLikeliFitter1D , MetaboliteFeatureDeconvolution , MetaboliteSpectralMatching , MRMDecoy , MRMFeatureFilter , MRMFeatureFinderScoring , MRMMapping , MRMTransitionGroupPicker , MSPGenericFile , NLargest , Normalizer , NucleicAcidSpectrumGenerator , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , PeakIntegrator , PeakPickerChromatogram , PeakPickerHiRes , PeakPickerIterative , PeptideAndProteinQuant , PeptideIndexing , ReactionMonitoringTransition , SavitzkyGolayFilter , SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container > , SimpleSearchEngineAlgorithm , SimpleTSGXLMS , SONARScoring , SpectraMerger::SpectraDistance_ , SpectrumAnnotator , StablePairFinder , SwathMapMassCorrection , TargetedSpectraExtractor , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS , TMTEighteenPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod , TraceFitter , TransitionTSVFile , XFDRAlgorithm
• updateMenu() : TOPPASBase , TOPPViewBase
• updateMetaValue() : MRMFeatureFilter
• updateMinElement() : DistanceMatrix< Value >
• updateMonoMassAndIsotopeIntensities() : PeakGroup
• updateMzBins_() : FLASHDeconvAlgorithm
• updateOutpuMap_() : IsobaricIsotopeCorrector
• updateOutputParamFromPerInputFile() : FLASHDeconvTabWidget
• updateOutputParamFromWidgets_() : FLASHDeconvTabWidget
• updatePeakGroupQvalues() : Qvalue
• updatePeptideHitAnnotations_() : LayerData1DPeak
• updatePerChargeCos_() : PeakGroup
• updatePerChargeInformation_() : PeakGroup
• updatePosition() : FuzzyStringComparator::InputLine
• updateProcessLog() : TOPPViewBase
• updateProteinEntries_() : SpectraIDViewTab
• updateProteinGroups() : IDFilter
• updateProteinReferences() : IDFilter
• updateProteinScores_() : BasicProteinInferenceAlgorithm
• updateQscore() : PeakGroup
• updateRange() : MRMFeatureFilter
• updateRanges() : ConsensusMap , FeatureMap , LayerData1DChrom , LayerData1DIonMobility , LayerData1DPeak , LayerDataBase , LayerDataChrom , LayerDataConsensus , LayerDataFeature , LayerDataIdent , LayerDataIonMobility , LayerDataPeak , Mobilogram , MSChromatogram , MSExperiment , MSSpectrum , RangeManagerContainer< RangeBases >
• updateScores() : PosteriorErrorProbabilityModel
• updateScrollbars_() : Plot1DCanvas , Plot2DCanvas , PlotCanvas
• updateSmoothedMaxRT() : MassTrace
• updateSmoothedWeightedMeanRT() : MassTrace
• updateSNR_() : PeakGroup
• updateSwathParamFromWidgets_() : SwathTabWidget
• updateTabBar() : TOPPASBase
• updateToolBar() : TOPPASBase , TOPPViewBase
• updateTOPPOutputLog() : TOPPASBase
• updateTree_() : PeptideIdentificationVisualizer , ProteinIdentificationVisualizer
• updateUniqueIdToIndex() : UniqueIdIndexer< T >
• updateViewBar() : TOPPViewBase
• updateViewMode_() : TOPPViewOpenDialog
• updateVisibleList_() : FilterableList
• updateVScrollbar() : PlotCanvas , PlotWidget
• updateWeightedMeanMZ() : MassTrace
• updateWeightedMeanRT() : MassTrace
• updateWeightedMZsd() : MassTrace
• updateWhiteMSExperiment_() : MultiplexFiltering
• updateWidgetsfromSwathParam_() : SwathTabWidget
• updateWindowTitle() : INIFileEditorWindow
• uploadProgress() : MascotRemoteQuery
• upper : SwathMap
• upper_ : LinearRegression
• UPPER_BOUND_ONLY : LPWrapper
• upperq : SummaryStatistics< T >
• uri : MzTabMDatabaseMetaData , MzTabMetaData , MzTabMMetaData , MzTabMSmallMoleculeEvidenceSectionRow , MzTabMSmallMoleculeSectionRow , MzTabNucleicAcidSectionRow , MzTabOligonucleotideSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• URI : CV
• url() : ControlledVocabulary , MzTabCVMetaData
• url_ : ContactPerson , ContactPersonVisualizer , ControlledVocabulary , NetworkGetRequest , TOPPASResource
• usage() : SysInfo::MemUsage
• use_adducts_ : MapAlignmentAlgorithmIdentification
• use_chauvenet_ : AbsoluteQuantitation
• use_coelution_score_ : OpenSwath_Scores_Usage
• use_consensus_ : MRMTransitionGroupPicker
• use_dia_scores_ : OpenSwath_Scores_Usage
• use_elution_model_score_ : OpenSwath_Scores_Usage
• use_external_boundaries_ : FullSwathFileConsumer
• use_feature_rt_ : MapAlignmentAlgorithmIdentification
• use_gauss_ : PeakPickerChromatogram , TargetedSpectraExtractor
• use_IDs_ : QTCluster , QTClusterFinder , StablePairFinder
• use_im_scores : OpenSwath_Scores_Usage
• use_intensity_score_ : OpenSwath_Scores_Usage
• use_ionseries_scores : OpenSwath_Scores_Usage
• use_library_score_ : OpenSwath_Scores_Usage
• use_lossy_compression_ : MzMLSqliteHandler
• use_lossy_numpress : SqMassFile::SqMassConfig
• use_mi_score_ : OpenSwath_Scores_Usage
• use_ms1_correlation : OpenSwath_Scores_Usage
• use_ms1_fullscan : OpenSwath_Scores_Usage
• use_ms1_ion_mobility_ : MRMFeatureFinderScoring , OpenSwathScoring , OpenSwathWorkflowBase
• use_ms1_mi : OpenSwath_Scores_Usage
• use_ms1_traces_ : OpenSwathTSVWriter , OpenSwathWorkflowBase
• use_ms2_isotope_scores : OpenSwath_Scores_Usage
• use_mz_scoring_by_element_range_ : FeatureFindingMetabo
• use_mz_scoring_C13_ : FeatureFindingMetabo
• use_nr_peaks_score_ : OpenSwath_Scores_Usage
• use_peak_shape_metrics : OpenSwath_Scores_Usage
• use_ppm_ : CalibrationData , MZTrafoModel
• use_ppm_tolerance_ : GaussFilterAlgorithm
• use_precursor_data_ : PepXMLFile
• use_precursors_ : MRMTransitionGroupPicker
• use_prefix_ : FuzzyStringComparator
• use_psm_cutoff_ : FeatureFinderIdentificationAlgorithm
• use_rt_score_ : OpenSwath_Scores_Usage
• use_sequence_tags_ : OpenPepXLLFAlgorithm
• use_shape_score_ : OpenSwath_Scores_Usage
• use_smoothed_intensities_ : FeatureFindingMetabo
• use_sn_score_ : OpenSwath_Scores_Usage
• use_sonar_scores : OpenSwath_Scores_Usage
• use_ssl_ : MascotRemoteQuery
• use_term_ : CVMappingTerm
• use_term_name_ : CVMappingTerm
• use_total_mi_score_ : OpenSwath_Scores_Usage
• use_total_prob_ : FineIsotopePatternGenerator
• use_total_xic_score_ : OpenSwath_Scores_Usage
• use_uis_scores : OpenSwath_Scores_Usage
• USED : FeatureFinderDefs
• usePPM() : CalibrationData
• user_specified_out_dir_ : TOPPASScene
• user_ticks : StopWatch::TimeDiff_
• userTime() : StopWatch::TimeDiff_