| OpenMS 2.5.0

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

### - u -

- ui_ : DataFilterDialog , FeatureEditDialog , Spectrum1DPrefDialog , Spectrum2DPrefDialog , Spectrum3DPrefDialog , TOPPViewPrefDialog , LayerStatisticsDialog , ParamEditor , Spectrum1DGoToDialog , Spectrum2DGoToDialog , SpectrumAlignmentDialog , 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 , SIPPeptide
- 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
- 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
- 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
- updateBaseline() : FeatureFinderAlgorithmPickedHelperStructs::MassTraces
- updateBoxStates() : IsotopeWaveletTransform< PeakType >
- updateCache_() : LayerData
- updateChannelMap() : ItraqConstants
- updateClusterProxies_() : FeatureGroupingAlgorithmKD
- updateColor() : TOPPASEdge
- updateCombinedILP() : PSLPFormulation
- updateCurrentFeature_() : FeatureXMLFile
- updateCurrentOutputFileNames() : TOPPASToolVertex
- updateCurrentPath() : TOPPASBase , TOPPViewBase
- updateCursor_() : SpectrumCanvas
- updateData_() : SpectraIdentificationViewWidget
- updateEdgeColors() : TOPPASScene
- updateEditorGeometry() : ListEditorDelegate , ParamEditorDelegate
- updateEntries() : SpectraIdentificationViewWidget , SpectraViewWidget
- updateExclusionList_() : OfflinePrecursorIonSelection
- updateFeatureILPVariables() : PSLPFormulation
- updateFeatureVariant_() : ILPDCWrapper
- updateFilterBar() : TOPPViewBase
- 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 , 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
- updateMinElement() : DistanceMatrix< Value >
- updateObjFunction_() : PSLPFormulation
- updateOutpuMap_() : IsobaricIsotopeCorrector
- updatePeptideHitAnnotations_() : LayerData
- updatePercentageFactor_() : Spectrum1DCanvas
- updatePosition() : FuzzyStringComparator::InputLine
- updateProcessLog() : TOPPViewBase
- updateProjections() : Spectrum2DCanvas , Spectrum2DWidget
- updateProteinGroups() : IDFilter
- updateProteinReferences() : IDFilter
- 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
- 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
- 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
- UTILProteomicsLFQ() : UTILProteomicsLFQ