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

- u -

• ui : SwathTabWidget , SwathWizardBase
• ui_ : DataFilterDialog , FeatureEditDialog , InputFile , FilterList , InputFileList , PythonModuleRequirement , PythonSelector , Spectrum1DPrefDialog , Spectrum2DPrefDialog , Spectrum3DPrefDialog , TOPPViewPrefDialog , LayerStatisticsDialog , OutputDirectory , ParamEditor , Spectrum1DGoToDialog , Spectrum2DGoToDialog , SpectrumAlignmentDialog , SwathLibraryStats , TheoreticalSpectrumGenerationDialog , TOPPASInputFileDialog , TOPPASInputFilesDialog , TOPPASIOMappingDialog , TOPPASOutputFilesDialog , TOPPASVertexNameDialog , TOPPViewOpenDialog
• uid_ : MSQuantifications::Assay
• uis_threshold_peak_area_ : MRMFeatureFinderScoring
• uis_threshold_sn_ : MRMFeatureFinderScoring
• uisTransitions() : MRMAssay
• ulod_ : AbsoluteQuantitationMethod
• uloq_ : AbsoluteQuantitationMethod
• UnableToCalibrate() : UnableToCalibrate
• UnableToCreateFile() : UnableToCreateFile
• UnableToFit() : UnableToFit
• unambiguous_score_ : AScore
• Unannotated : NASequence , Residue
• unassigned_contaminants_ratio : Contaminants::ContaminantsSummary
• unassigned_peptide_identifications_ : ConsensusMap , FeatureMap
• unassignedMS2 : FeatureMapping::FeatureToMs2Indices
• UNBOUNDED : LPWrapper
• uncompressString() : ZlibCompression
• UNDEFINED : IsotopeDistribution , LPWrapper , PeakShape
• undo_() : AcquisitionInfoVisualizer , AcquisitionVisualizer , 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_button_ : BaseVisualizerGUI
• undobutton_ : MetaDataBrowser
• UNEXPECTED_RESULT : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , PeptideIndexing , TOPPBase , XFDRAlgorithm
• 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
• uniqueid_to_index_ : UniqueIdIndexer< RandomAccessContainer >
• UniqueIdGenerator() : UniqueIdGenerator
• UniqueIdInterface() : UniqueIdInterface
• UniqueIdMap : UniqueIdIndexer< RandomAccessContainer >
• uniqueIdToIndex() : UniqueIdIndexer< RandomAccessContainer >
• Unit() : CVTerm::Unit
• unit_ : CVTerm , DataValue
• unit_accession : SemanticValidator::CVTerm
• unit_accession_att_ : SemanticValidator
• 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 >
• 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 : MoleculeParentMatch
• UNKNOWN_POSITION : MoleculeParentMatch , PeptideEvidence
• Unmatched : PeptideIndexing
• unmatched_action_ : PeptideIndexing
• unmodified_seq : OPXLDataStructs::AASeqWithMass
• UnnormalizedComparator() : UnnormalizedComparator
• unparsed : ControlledVocabulary::CVTerm
• unquote() : String , StringUtils
• unregister() : LogStreamNotifier
• UnregisteredParameter() : UnregisteredParameter
• unregisterStream() : StreamHandler
• unselectAll() : TOPPASScene
• UnspecificCleavage : EnzymaticDigestion
• untargetedMatching() : TargetedSpectraExtractor
• UNUSED : FeatureFinderDefs
• unWeightData() : TransformationModel
• unWeightDatum() : TransformationModel
• UP : MassAnalyzer
• up_stack_ : MzQuantMLHandler
• update() : AsymmetricStatistics< RealT > , BasicStatistics< RealT > , Param , QTCluster , SwathLibraryStats
• update_() : AcquisitionInfoVisualizer , AcquisitionVisualizer , BaseVisualizer< ObjectType > , ContactPersonVisualizer , DataProcessingVisualizer , DigestionVisualizer , DocumentIdentifierVisualizer , ExperimentalSettingsVisualizer , GradientVisualizer , HPLCVisualizer , InstrumentSettingsVisualizer , InstrumentVisualizer , IonDetectorVisualizer , IonSourceVisualizer , MassAnalyzerVisualizer , MetaInfoDescriptionVisualizer , ModificationVisualizer , PeptideHitVisualizer , PrecursorVisualizer , ProductVisualizer , ProteinHitVisualizer , SampleVisualizer , ScanWindowVisualizer , SoftwareVisualizer , SourceFileVisualizer , Spectrum3DCanvas , SpectrumCanvas , SpectrumSettingsVisualizer , TaggingVisualizer
• update_buffer_ : SpectrumCanvas
• update_CHRGMAP() : LCElutionPeak
• updateAddressLookup_() : IdentificationData
• updateAndMovePepIDs_() : IDMergerAlgorithm
• updateAxes() : SpectrumWidget
• updateBarsAndMenus() : TOPPViewBase
• updateBaseline() : FeatureFinderAlgorithmPickedHelperStructs::MassTraces
• updateBoxStates() : IsotopeWaveletTransform< PeakType >
• updateCache_() : LayerData
• updateChannelMap() : ItraqConstants
• updateClustering_() : QTClusterFinder
• updateClusterProxies_() : FeatureGroupingAlgorithmKD
• updateColor() : TOPPASEdge
• updateCombinedILP() : PSLPFormulation
• updateCurrentFeature_() : FeatureXMLFile
• updateCurrentOutputFileNames() : TOPPASToolVertex
• updateCurrentPath() : TOPPASBase , TOPPViewBase
• updateCursor_() : SpectrumCanvas
• updateCWD_() : InputFileList
• updateData_() : SpectraIdentificationViewWidget
• updatedCWD() : InputFile , InputFileList
• updatedFile() : InputFile
• updateEdgeColors() : TOPPASScene
• updateEditorGeometry() : ListEditorDelegate , ParamEditorDelegate
• updateEntries() : SpectraIdentificationViewWidget , SpectraViewWidget
• updateExclusionList_() : OfflinePrecursorIonSelection
• updateFeatureILPVariables() : PSLPFormulation
• updateFeatureVariant_() : ILPDCWrapper
• updateFilterBar() : TOPPViewBase
• updateFromFile() : SwathLibraryStats
• updateGridDimension_() : HashGrid< Cluster >
• updateHitRanks() : IDFilter
• updateHoveringEdgePos() : TOPPASScene
• updateHScrollbar() : SpectrumCanvas , SpectrumWidget
• updateIntensityScale() : Spectrum3DOpenGLCanvas
• updateIsotopeMatrixFromStringList() : ItraqConstants
• updateIterativeWeightedMeanMZ() : MassTraceDetection
• updateLayer() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas
• updateLayerBar() : TOPPViewBase
• updateMaximum() : FeatureFinderAlgorithmPickedHelperStructs::MassTrace
• updateMeanMZ() : MassTrace
• updateMedianMZ() : MassTrace
• updateMedianRT() : MassTrace
• updateMembers_() : AbsoluteQuantitation , AccurateMassSearchEngine , AScore , BaseModel< D > , BayesianProteinInferenceAlgorithm , BiGaussFitter1D , BiGaussModel , BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSumAgreeingIntensities , CompNovoIdentificationBase , CompNovoIdentificationCID , CompNovoIonScoringBase , ConsensusIDAlgorithm , ConsensusIDAlgorithmPEPIons , ConsensusIDAlgorithmPEPMatrix , DefaultParamHandler , DetectabilitySimulation , DiaPrescore , DIAScoring , EGHFitter1D , EGHModel , EGHTraceFitter , ElutionPeakDetection , EmgFitter1D , EmgGradientDescent , EmgModel , ExtendedIsotopeFitter1D , ExtendedIsotopeModel , FeatureDeconvolution , FeatureDistance , FeatureFinderAlgorithmIsotopeWavelet , FeatureFinderAlgorithmMRM , FeatureFinderAlgorithmPicked , FeatureFinderIdentificationAlgorithm , FeatureFindingMetabo , FIAMSDataProcessor , Fitter1D , GaussFilter , GaussFitter1D , GaussModel , GaussTraceFitter , ICPLLabeler , IDMapper , IDScoreSwitcherAlgorithm , IncludeExcludeTarget , InterpolationModel , IonizationSimulation , IsobaricChannelExtractor , IsobaricQuantifier , IsotopeFitter1D , IsotopeModel , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , ITRAQLabeler , KDTreeFeatureMaps , LevMarqFitter1D , LinearResampler , LinearResamplerAlign , LowessSmoothing , MapAlignmentAlgorithmKD , MapAlignmentAlgorithmPoseClustering , MapAlignmentAlgorithmSpectrumAlignment , MapAlignmentAlgorithmTreeGuided , MascotGenericFile , MascotRemoteQuery , MassDecompositionAlgorithm , MassTraceDetection , MaxLikeliFitter1D , MetaboliteFeatureDeconvolution , MetaboliteSpectralMatching , MRMDecoy , MRMFeatureFilter , MRMFeatureFinderScoring , MRMMapping , MRMTransitionGroupPicker , MSPGenericFile , MSSim , NLargest , Normalizer , NucleicAcidSpectrumGenerator , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , OptimizePeakDeconvolution , PeakIntegrator , PeakPickerCWT , PeakPickerHiRes , PeakPickerIterative , PeakPickerMRM , PeptideAndProteinQuant , PeptideIndexing , PrecursorIonSelection , PrecursorIonSelectionPreprocessing , ProductModel< 2 > , RawMSSignalSimulation , ReactionMonitoringTransition , RTSimulation , SavitzkyGolayFilter , SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container > , SILACLabeler , SimplePairFinder , SimpleSearchEngineAlgorithm , SimpleTSGXLMS , SiriusAdapterAlgorithm , SONARScoring , SpectraMerger::SpectraDistance_ , SpectrumAnnotator , StablePairFinder , SvmTheoreticalSpectrumGenerator , SwathMapMassCorrection , TargetedSpectraExtractor , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod , TraceFitter , TransitionTSVFile , TwoDOptimization , XFDRAlgorithm
• updateMenu() : TOPPASBase , TOPPViewBase
• updateMetaValue() : MRMFeatureFilter
• updateMinElement() : DistanceMatrix< Value >
• updateObjFunction_() : PSLPFormulation
• updateOutpuMap_() : IsobaricIsotopeCorrector
• updatePeptideHitAnnotations_() : LayerData
• updatePercentageFactor_() : Spectrum1DCanvas
• updatePosition() : FuzzyStringComparator::InputLine
• updateProcessLog() : TOPPViewBase
• updateProjections() : Spectrum2DCanvas , Spectrum2DWidget
• updateProteinGroups() : IDFilter
• updateProteinReferences() : IDFilter
• updateRange() : MRMFeatureFilter
• updateRanges() : ConsensusMap , FeatureMap , LayerData , MSChromatogram , MSExperiment , MSSpectrum , RangeManager< D >
• updateRanges_() : RangeManager< D >
• updateRecentMenu_() : TOPPViewBase
• updateRTConstraintsForSequentialILP() : PSLPFormulation
• updateScores() : PosteriorErrorProbabilityModel
• updateScrollbars_() : Spectrum1DCanvas , Spectrum2DCanvas , SpectrumCanvas
• updateSmoothedMaxRT() : MassTrace
• updateSmoothedWeightedMeanRT() : MassTrace
• updateStepSizeConstraint() : PSLPFormulation
• updateSwathParamFromWidgets_() : SwathTabWidget
• updateTabBar() : TOPPASBase , TOPPViewBase
• updateToolBar() : TOPPASBase , TOPPViewBase
• updateTOPPOutputLog() : TOPPASBase
• updateTree_() : PeptideIdentificationVisualizer , ProteinIdentificationVisualizer
• updateUniqueIdToIndex() : UniqueIdIndexer< RandomAccessContainer >
• updateViewBar() : TOPPViewBase
• updateViewMode_() : TOPPViewOpenDialog
• updateVScrollbar() : SpectrumCanvas , SpectrumWidget
• 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 >
• UPSHIFT : PrecursorIonSelection
• uri : MzTabMetaData , MzTabNucleicAcidSectionRow , MzTabOligonucleotideSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• URI : CV
• url : MzTabCVMetaData
• url_ : ContactPerson , ContactPersonVisualizer , NetworkGetRequest , TOPPASResource
• usage() : SysInfo::MemUsage
• 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_ : PeakPickerMRM , TargetedSpectraExtractor
• use_gpus_ : FeatureFinderAlgorithmIsotopeWavelet
• use_IDs_ : QTCluster , QTClusterFinder , StablePairFinder
• use_im_scores : OpenSwath_Scores_Usage
• use_intensity_score_ : 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_ : OpenSwathWorkflowBase
• use_ms1_mi : OpenSwath_Scores_Usage
• use_ms1_traces_ : OpenSwathOSWWriter , OpenSwathTSVWriter , OpenSwathWorkflowBase
• use_mz_scoring_by_element_range_ : FeatureFindingMetabo
• use_mz_scoring_C13_ : FeatureFindingMetabo
• use_nr_peaks_score_ : OpenSwath_Scores_Usage
• use_ppm_ : CalibrationData , MZTrafoModel
• use_ppm_tolerance_ : GaussFilterAlgorithm
• use_precursor_data_ : PepXMLFile
• use_precursors_ : MRMTransitionGroupPicker
• use_prefix_ : FuzzyStringComparator
• 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_params_ : MSQuantifications::AnalysisSummary
• user_specified_out_dir_ : TOPPASScene
• user_ticks : StopWatch::TimeDiff_
• userTime() : StopWatch::TimeDiff_