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

- o -

• O : ExtendedIsotopeModel , IsotopeModel
• OBO : FileTypes
• Observation : IdentificationData , Observation
• observation_keys_ : OMSFileStore
• observation_lookup_ : IdentificationData
• observation_match_groups_ : IdentificationData
• observation_match_keys_ : OMSFileStore
• observation_match_lookup_ : IdentificationData
• observation_match_refs : IdentificationData::RefTranslator , ObservationMatchGroup
• observation_match_refs_ : OMSFileLoad
• observation_matches_ : IdentificationData
• observation_ref : ObservationMatch
• observation_refs : IdentificationData::RefTranslator
• observation_refs_ : OMSFileLoad
• ObservationMatch : IdentificationData , ObservationMatch
• ObservationMatches : IdentificationData
• ObservationMatchGroup : IdentificationData
• ObservationMatchGroups : IdentificationData
• ObservationMatchRef : IdentificationData
• ObservationRef : IdentificationData
• Observations : IdentificationData
• observations_ : IdentificationData
• observed_intensity_ : AccurateMassSearchResult
• observed_mz_ : AccurateMassSearchResult
• observed_precursor_mass_ : SpectralMatch
• observed_precursor_rt_ : SpectralMatch
• observed_rt_ : AccurateMassSearchResult
• observed_spectrum_idx_ : SpectralMatch
• observed_spectrum_native_id_ : SpectralMatch
• obsolete : ControlledVocabulary::CVTerm
• ODExperimentSharedPtrType : LayerDataDefs , PlotCanvas , TOPPViewBase
• OFF : MassAnalyzer
• official_ : TOPPBase
• OfflinePrecursorIonSelection() : OfflinePrecursorIonSelection
• offset_ : BinnedSpectrum , LinearInterpolation< Key, Value >
• offset_0_ : BilinearInterpolation< Key, Value >
• offset_1_ : BilinearInterpolation< Key, Value >
• offset_max_ : TransformationModelBSpline
• offset_min_ : TransformationModelBSpline
• offsets_ : FASTAContainer< TFI_File >
• OffsetVector : IndexedMzMLDecoder
• ofs : OpenSwathTSVWriter
• ofs_ : MSDataCachedConsumer , MSDataWritingConsumer , SVOutStream
• ok() : BSpline2d , FuzzyStringComparator::InputLine
• ok_() : ToolsDialog , TOPPASToolConfigDialog
• ok_button_ : ToolsDialog
• OkButton_ : ListEditor
• old_ : WizardGUILock< TWidgetClass >
• old_score_ : IDScoreSwitcherAlgorithm
• oligo_ref : NucleicAcidSearchEngine::AnnotatedHit
• oligonucleotide_data_ : MzTab
• oligonucleotide_search_engine_score : MzTabMetaData
• OLINKED_GLYCOSYLATION : ResidueModification
• OMS : FileTypes
• OMSFile() : OMSFile
• OMSFileLoad() : OMSFileLoad
• OMSFileStore() : OMSFileStore
• omssa_id_ : DigestionEnzymeProtein
• OMSSACSVFile() : OMSSACSVFile
• OMSSAXML : FileTypes
• OMSSAXMLFile() : OMSSAXMLFile
• ON : MassAnalyzer
• on_actionExit_triggered() : FLASHDeconvWizardBase , SwathWizardBase
• on_actionReport_new_issue_triggered() : FLASHDeconvWizardBase , SwathWizardBase
• on_actionVisit_FLASHDeconv_homepage_triggered() : FLASHDeconvWizardBase
• on_actionVisit_OpenSwath_homepage_triggered() : SwathWizardBase
• on_btn_pyresults_clicked() : SwathTabWidget
• on_btn_runPyProphet_clicked() : SwathTabWidget
• on_disc_peaks_ : LayerDataChrom , LayerDataPeak
• on_edit_advanced_parameters_clicked() : FLASHDeconvTabWidget , SwathTabWidget
• on_open_output_directory_clicked() : FLASHDeconvTabWidget
• on_pushButton_clicked() : SwathTabWidget
• on_run_fd_clicked() : FLASHDeconvTabWidget
• on_run_swath_clicked() : SwathTabWidget
• OnDiscMSExperiment() : OnDiscMSExperiment
• one_letter_code_ : Residue
• op : DataFilters::DataFilter
• op_changed_() : DataFilterDialog
• open() : Bzip2Ifstream , GzipIfstream
• open_boxes_ : IsotopeWaveletTransform< PeakType >
• open_tag_ : PTMXMLHandler
• open_tags_ : SemanticValidator , XMLHandler
• openAsNewWindow() : TOPPViewOpenDialog
• openContainingFolder() : TOPPASInputFileListVertex , TOPPASOutputFileListVertex , TOPPASToolVertex
• openDatabase_() : SqliteConnector
• opened : Param::ParamIterator::TraceInfo
• openExampleDialog() : TOPPASBase
• openFile() : INIFileEditorWindow , IndexedMzMLHandler , OnDiscMSExperiment , TOPPViewBase
• openFilesByDialog() : TOPPASBase , TOPPViewBase
• openFilesInTOPPView() : TOPPASBase
• openglcanvas_ : Plot3DCanvas
• openglwidget() : Plot3DCanvas
• openInputFileStream_() : FuzzyStringComparator
• openInTOPPView() : TOPPASScene , TOPPASToolVertex
• openms_param_name : SiriusAdapterAlgorithm::ParameterModifier
• openms_to_sirius : SiriusAdapterAlgorithm::ParameterSection
• OpenMSLineEdit() : OpenMSLineEdit
• OpenMSOSInfo() : OpenMSOSInfo
• openOnlinePipelineRepository() : TOPPASBase
• OpenPepXLAlgorithm() : OpenPepXLAlgorithm
• OpenPepXLLFAlgorithm() : OpenPepXLLFAlgorithm
• openPreferences() : PlotWidget
• OPENSPLIT : IonSource
• OpenSwath_Ind_Scores() : OpenSwath_Ind_Scores
• OpenSwath_Scores() : OpenSwath_Scores
• OpenSwathCalibrationWorkflow() : OpenSwathCalibrationWorkflow
• OpenSwathOSWWriter() : OpenSwathOSWWriter
• OpenSwathScoring() : OpenSwathScoring
• OpenSwathTSVWriter() : OpenSwathTSVWriter
• OpenSwathWorkflow() : OpenSwathWorkflow
• OpenSwathWorkflowBase() : OpenSwathWorkflowBase
• OpenSwathWorkflowSonar() : OpenSwathWorkflowSonar
• openToppasFile() : TOPPASBase
• openUniProtSiteWithAccession_() : SpectraIDViewTab
• operator double() : DataValue , ParamValue
• operator DoubleList() : DataValue
• operator float() : DataValue , ParamValue
• operator int() : DataValue , ParamValue
• operator IntList() : DataValue
• operator long double() : DataValue , ParamValue
• operator long int() : DataValue , ParamValue
• operator long long() : DataValue , ParamValue
• operator ParamValue() : DataValue
• operator RangeIntensity() : RangeBase
• operator RangeMobility() : RangeBase
• operator RangeMZ() : RangeBase
• operator RangeRT() : RangeBase
• operator short int() : DataValue , ParamValue
• operator std::string() : DataValue , ParamValue
• operator std::vector< double >() : ParamValue
• operator std::vector< int >() : ParamValue
• operator std::vector< std::string >() : ParamValue
• operator StringList() : DataValue
• operator uintptr_t() : IteratorWrapper< Iterator >
• operator unsigned int() : DataValue , ParamValue
• operator unsigned long int() : DataValue , ParamValue
• operator unsigned long long() : DataValue , ParamValue
• operator unsigned short int() : DataValue , ParamValue
• operator!= : _Iterator< _Val, _Ref, _Ptr > , AASequence::ConstIterator , AASequence::Iterator , AASequence , AbsoluteQuantitationMethod , Acquisition , AcquisitionInfo , Area< N_DIM > , BaseFeature , BinnedSpectrum , ChargePair , ChromatogramPeak , ChromatogramSettings , ClusterProxyKD , ConsensusMap , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT > , ContactPerson , CVMappingRule , CVMappings , CVMappingTerm , CVReference , CVTerm , CVTerm::Unit , CVTermList , CVTermListInterface , DataFilters::DataFilter , DataProcessing , DataValue , DateTime , DigestionEnzyme , DigestionEnzymeProtein , DimMapper< N_DIM > , DPosition< D, TCoordinateType > , Element , EmpiricalFormula , ExperimentalSettings , FeatureHandle , FeatureMap , Gradient , HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator , HPLC , Identification , ObservationMatchGroup , IdentificationHit , IMSElement , IMSIsotopeDistribution , IncludeExcludeTarget , Instrument , InstrumentSettings , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , DIntervalBase< D > , IntensityIteratorWrapper< IteratorT > , IonDetector , IonSource , IsotopeDistribution , MassAnalyzer , MatchedIterator< CONT_T, TRAIT, CONST_T > , Histogram< ValueType, BinSizeType > , MetaInfo , MetaInfoInterface , MobilityPeak1D , MobilityPeak2D , Mobilogram , ModelDescription< D > , ModificationDefinition , ModificationDefinitionsSet , MRMFeatureQC::ComponentGroupQCs , MRMFeatureQC::ComponentQCs , MSChromatogram , MSExperiment , MSQuantifications , MSSpectrum , NASequence::ConstIterator , NASequence::Iterator , NASequence , OnDiscMSExperiment , Param::ParamIterator , ParamValue , Peak1D , Peak2D , PeakIndex , PeakShape , PeptideEvidence , PeptideHit , PeptideIdentification , Precursor , Product , ProteinHit , ProteinIdentification , ProteinIdentification::SearchParameters , RangeManager< RangeBases > , ReactionMonitoringTransition , Residue , ResidueModification , RichPeak2D , ScanWindow , Software , SourceFile , SpectrumIdentification , SpectrumSettings , StopWatch , TargetedExperiment , Interpretation , VersionInfo::VersionDetails
• operator&() : FlagSet< ENUM >
• operator&=() : FlagSet< ENUM >
• operator()() : _Bracket_accessor< _Val > , _Node_compare< _Val, _Acc, _Cmp > , always_true< _Tp > , squared_difference< _Tp, _Dist > , squared_difference_counted< _Tp, _Dist > , NucleicAcidSearchEngine::HasInvalidLength , AA , AccurateMassSearchEngine::CompareEntryAndMass_ , AverageLinkage , BaseFeature::QualityLess , BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSpectrumCompareFunctor , BinnedSumAgreeingIntensities , ChromatogramPeak::IntensityLess , ChromatogramPeak::PositionLess , ChromatogramPeak::RTLess , ClusterFunctor , CmpHypothesesByScore , CmpMassTraceByMZ , Colorizer , CompareMzTabMMatchRef , CompleteLinkage , ConfidenceScoring::GLM_ , ConfidenceScoring::RTNorm_ , ConsensusFeature::MapsLess , ConsensusFeature::SizeLess , DiaPrescore , DistanceMatrix< Value > , EGHTraceFitter::EGHTraceFunctor , EmgFitter1D::EgmFitterFunctor , EuclideanSimilarity , FeatureDistance , FeatureFinderAlgorithmMetaboIdent::FeatureCompare , FeatureFinderAlgorithmMetaboIdent::FeatureFilterQuality , FeatureFinderIdentificationAlgorithm::FeatureCompare , FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides , FeatureFinderIdentificationAlgorithm::FeatureFilterQuality , FeatureFinderIdentificationAlgorithm::PeptideCompare , FeatureHandle::IndexLess , GaussTraceFitter::GaussTraceFunctor , HasActivationMethod< SpectrumType > , HasMetaValue< MetaContainer > , HasPrecursorCharge< SpectrumType > , HasScanMode< SpectrumType > , HasScanPolarity< SpectrumType > , IdentificationDataConverter::PepIDCompare , IdentificationDataConverter::StepOptCompare , AdductCompare , IDFilter::DigestionFilter , IDFilter::HasDecoyAnnotation< HitType > , IDFilter::HasGoodScore< HitType > , IDFilter::HasMatchingAccession< HitType > , IDFilter::HasMatchingAccessionUnordered< HitType > , IDFilter::HasMaxMetaValue< HitType > , IDFilter::HasMaxRank< HitType > , IDFilter::HasMetaValue< HitType > , IDFilter::HasNoHits< IdentificationType > , IDFilter::PeptideDigestionFilter , IDRipper::RipFileIdentifierIdxComparator , IMSAlphabet::MassSortingCriteria_ , Index , InIntensityRange< PeakType > , InMSLevelRange< SpectrumType > , InMzRange< PeakType > , InPrecursorMZRange< SpectrumType > , InRTRange< SpectrumType > , IDBoostGraph::GetPosteriorVisitor , IDBoostGraph::GetScoreTgTVisitor , IDBoostGraph::LabelVisitor , IDBoostGraph::PrintAddressVisitor< CharT > , IDBoostGraph::SetPosteriorVisitor , IsEmptySpectrum< SpectrumType > , IsInCollisionEnergyRange< SpectrumType > , IsInIsolationWindow< SpectrumType > , IsInIsolationWindowSizeRange< SpectrumType > , IsZoomSpectrum< SpectrumType > , LevMarqFitter1D::GenericFunctor , ListUtils::DoubleTolerancePredicate_ , MapAlignmentAlgorithmSpectrumAlignment::Compare , ROCCurve::simsortdec , Matrix< Value > , MobilityPeak1D::IntensityLess , MobilityPeak1D::MobilityLess , MobilityPeak1D::PositionLess , MobilityPeak2D::IMLess , MobilityPeak2D::IntensityLess , MobilityPeak2D::MZLess , MobilityPeak2D::PositionLess , Mobilogram::RTLess , MSChromatogram::MZLess , MSSpectrum::IMLess , MSSpectrum::RTLess , MultiplexClustering::MultiplexDistance , MzTabNucleicAcidSectionRow::RowCompare , MzTabOligonucleotideSectionRow::RowCompare , MzTabOSMSectionRow::RowCompare , MzTabPeptideSectionRow::RowCompare , MzTabProteinSectionRow::RowCompare , MzTabPSMSectionRow::RowCompare , MZTrafoModel::RTLess , OfflinePrecursorIonSelection::PairComparatorSecondElement< PairType > , OptimizePick::OptPeakFunctor , OPXLDataStructs::AASeqWithMassComparator , OPXLDataStructs::CLSMScoreComparator , OPXLDataStructs::XLPrecursorComparator , OPXLHelper::PeptideIDScoreComparator , Peak1D::IntensityLess , Peak1D::MZLess , Peak1D::PositionLess , Peak2D::IntensityLess , Peak2D::MZLess , Peak2D::PositionLess , Peak2D::RTLess , PeakAlignment , PeakShape , PeakShape::PositionLess , PeakSpectrumCompareFunctor , PeptideHit::RankLess , PeptideHit::ScoreLess , PeptideHit::ScoreMore , PeptideHit::SequenceLessComparator , PercolatorFeatureSetHelper::lq_PeptideEvidence , PercolatorFeatureSetHelper::lq_ProteinHit , PrecursorMassComparator , ProteinHit::ProteinHitAccessionHash , ProteinHit::ProteinHitPtrAccessionHash , ProteinHit::ScoreLess , ProteinHit::ScoreMore , ReactionMonitoringTransition::NameLess , ReactionMonitoringTransition::ProductMZLess , SimpleTSGXLMS::SimplePeakComparator , SingleLinkage , SpectralMatchScoreComparator , SpectraMerger::SpectraDistance_ , SpectraSTSimilarityScore , SpectrumAlignmentScore , SpectrumCheapDPCorr , SpectrumPrecursorComparator , SteinScottImproveScore , TraceFitter::GenericFunctor , TwoDOptimization::TwoDOptFunctor , ZhangSimilarityScore , mean_and_stddev , OSSpectrumMeta::RTLess , pair_hash , hash< OpenMS::Index > , hash< OpenMS::String >
• operator*() : _Iterator< _Val, _Ref, _Ptr > , AASequence::ConstIterator , AASequence::Iterator , Adduct , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , DPosition< D, TCoordinateType > , EmpiricalFormula , HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , IntensityIteratorWrapper< IteratorT > , MatchedIterator< CONT_T, TRAIT, CONST_T > , NASequence::ConstIterator , NASequence::Iterator , Param::ParamIterator
• operator*=() : DPosition< D, TCoordinateType > , IMSIsotopeDistribution
• operator+() : AASequence::ConstIterator , AASequence::Iterator , AASequence , Adduct , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , DPosition< D, TCoordinateType > , EmpiricalFormula , FeatureMap , FlagSet< ENUM > , DIntervalBase< D > , MassDecomposition , NASequence::ConstIterator , NASequence::Iterator , String , TargetedExperiment
• operator++() : _Iterator< _Val, _Ref, _Ptr > , AA , AASequence::ConstIterator , AASequence::Iterator , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , IntensityIteratorWrapper< IteratorT > , MatchedIterator< CONT_T, TRAIT, CONST_T > , NASequence::ConstIterator , NASequence::Iterator , Param::ParamIterator
• operator+=() : AASequence , Adduct , AnnotationStatistics , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , DPosition< D, TCoordinateType > , EmpiricalFormula , FeatureMap , FlagSet< ENUM > , DIntervalBase< D > , MassDecomposition , StopWatch::TimeDiff_ , String , TargetedExperiment
• operator-() : AA , AASequence::ConstIterator , AASequence::Iterator , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , DPosition< D, TCoordinateType > , EmpiricalFormula , FlagSet< ENUM > , DIntervalBase< D > , IntensityIteratorWrapper< IteratorT > , NASequence::ConstIterator , NASequence::Iterator , StopWatch::TimeDiff_
• operator--() : _Iterator< _Val, _Ref, _Ptr > , AASequence::ConstIterator , AASequence::Iterator , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , NASequence::ConstIterator , NASequence::Iterator
• operator-=() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , DPosition< D, TCoordinateType > , EmpiricalFormula , FlagSet< ENUM > , DIntervalBase< D >
• operator->() : _Iterator< _Val, _Ref, _Ptr > , AASequence::ConstIterator , AASequence::Iterator , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , LogStream , MatchedIterator< CONT_T, TRAIT, CONST_T > , NASequence::ConstIterator , NASequence::Iterator , Param::ParamIterator
• operator/=() : DPosition< D, TCoordinateType >
• operator<() : AASequence , ClusterProxyKD , Compomer , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT > , DataValue , DateTime , DigestionEnzyme , DigestionEnzymeProtein , DPosition< D, TCoordinateType > , Element , EmpiricalFormula , FeatureFinderAlgorithmPickedHelperStructs::Seed , FLASHDeconvHelperStructs::LogMzPeak , GridBasedCluster , DBSearchParam , IteratorWrapper< Iterator > , ParentMatch , ProcessingStep , ScoreType , RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ , ToolDescriptionInternal , IsotopeDistribution , MassDecomposition , Matrix< Value > , MinimumDistance , ModificationDefinition , MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , MzTabDouble , NASequence , ParamValue , PeakGroup , PeptideEvidence , PeptideHit::PeakAnnotation , ProteinIdentification::ProteinGroup , QcMLFile::Attachment , QcMLFile::QualityParameter , QTCluster , RangeStatsType , ResidueModification , Software , StopWatch , StringView , TOPPASToolVertex::IOInfo , TransformationModel::DataPoint , TriqlerFile::TriqlerLine_ , VersionInfo::VersionDetails
• operator<< : AASequence , AccurateMassSearchResult , Adduct , Colorizer , Compomer , ConnectedComponent , ControlledVocabulary , DataValue , DBoundingBox< D > , DigestionEnzyme , DigestionEnzymeProtein , DistanceMatrix< Value > , Element , EmpiricalFormula , IndentedStream , LogConfigHandler , BasicStatistics< RealT > , Matrix< Value > , MobilityPeak2D , NASequence , ParamValue , Peak2D , Residue , Ribonucleotide , StreamHandler , SVOutStream , TextFile
• operator<=() : AA , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType > , StopWatch
• operator=() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , AASequence::ConstIterator , AASequence::Iterator , AASequence , AccurateMassSearchResult , Acquisition , AcquisitionInfo , Annotations1DContainer , AnnotationStatistics , Area< N_DIM > , AverageLinkage , BaseFeature , BaseGroupFinder , BaseModel< D > , BaseSuperimposer , BernNorm , BiGaussFitter1D , BiGaussModel , BinaryTreeNode , BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSpectrum , BinnedSpectrumCompareFunctor , BinnedSumAgreeingIntensities , Bzip2Ifstream , Bzip2InputStream , ChargePair , ChromatogramPeak , ChromatogramSettings , ClusterAnalyzer , ClusterFunctor , ClusterProxyKD , CoarseIsotopePatternGenerator , ComplementFilter , ComplementMarker , CompleteLinkage , Compomer , CompressedInputSource , ConsensusFeature , ConsensusFeature::Ratio , ConsensusIDAlgorithm , ConsensusIDAlgorithmAverage , ConsensusIDAlgorithmBest , ConsensusIDAlgorithmIdentity , ConsensusIDAlgorithmPEPIons , ConsensusIDAlgorithmPEPMatrix , ConsensusIDAlgorithmRanks , ConsensusIDAlgorithmSimilarity , ConsensusIDAlgorithmWorst , ConsensusMap::ColumnHeader , ConsensusMap , ConsensusMapNormalizerAlgorithmMedian , ConsensusMapNormalizerAlgorithmQuantile , ConsensusMapNormalizerAlgorithmThreshold , ConsoleUtils , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , ConstRefVector< ContainerT > , ContactPerson , ControlledVocabulary::CVTerm , ConvexHull2D , CrossLinksDB , CVMappingFile , CVMappingRule , CVMappings , CVMappingTerm , CVReference , CVTerm , CVTerm::Unit , CVTermList , CVTermListInterface , DataProcessing , DataValue , Date , DateTime , DBoundingBox< D > , DeconvolvedSpectrum , DefaultParamHandler , DIAScoring , Digestion , DigestionEnzyme , DigestionEnzymeDB< DigestionEnzymeType, InstanceType > , DigestionEnzymeProtein , DimBase , DimMapper< N_DIM > , DistanceMatrix< Value > , DocumentIdentifier , DPosition< D, TCoordinateType > , DRange< D > , EGHTraceFitter , Element , ElementDB , EmgFitter1D , EmgModel , EmpiricalFormula , EnzymaticDigestion , EuclideanSimilarity , ExperimentalSettings , ExposedVector< VectorElement > , ExtendedIsotopeFitter1D , ExtendedIsotopeModel , FalseDiscoveryRate , FASTAFile::FASTAEntry , Feature , FeatureDeconvolution , FeatureDistance , FeatureFinderAlgorithm , FeatureFinderAlgorithmPicked , FeatureGroupingAlgorithm , FeatureGroupingAlgorithmKD , FeatureGroupingAlgorithmLabeled , FeatureGroupingAlgorithmQT , FeatureGroupingAlgorithmUnlabeled , FeatureHandle , FeatureHypothesis , FeatureMap , FIAMSDataProcessor , FIAMSScheduler , File::TempDir , File::TemporaryFiles_ , FilterFunctor , Fitter1D , FlagSet< ENUM > , FLASHDeconvAlgorithm , FLASHDeconvHelperStructs::PrecalculatedAveragine , FuzzyStringComparator , GaussFitter1D , GaussModel , GaussTraceFitter , GoodDiffFilter , Gradient , GUILock , GzipIfstream , GzipInputStream , HiddenMarkovModel , HMMState , HPLC , IBSpectraFile , IDDecoyProbability , IDDecoyProbability::Transformation_ , Identification , IdentificationData , IdentificationHit , IDMapper , IDRipper , IMSElement , IMSIsotopeDistribution , Weights , IncludeExcludeTarget , InspectInfile , InspectOutfile , Instrument , InstrumentSettings , IntensityBalanceFilter , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::Param , CachedMzMLHandler , DIntervalBase< D > , FileMapping , MappingParam , MzDataValidator , MzIdentMLDOMHandler , MzIdentMLHandler , MzIdentMLValidator , MzMLHandlerHelper::BinaryData , MzMLValidator , MzQuantMLHandler , MzQuantMLValidator , SemanticValidator , shared_xerces_ptr< T > , ToolDescription , ToolDescriptionHandler , ToolDescriptionInternal , TraMLHandler , TraMLValidator , unique_xerces_ptr< T > , InterpolationModel , IonDetector , IonSource , IsobaricChannelExtractor , IsobaricNormalizer , IsobaricQuantifier , IsobaricQuantifierStatistics , IsotopeDiffFilter , IsotopeDistribution , IsotopeFitter1D , IsotopeMarker , IsotopeModel , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , KDTreeFeatureNode , LabeledPairFinder , LayerDataBase , LayerDataChrom , LayerDataConsensus , LayerDataFeature , LayerDataIdent , LayerDataIonMobility , LayerDataPeak , LevMarqFitter1D , LogConfigHandler , MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering , MapAlignmentAlgorithmSpectrumAlignment , MapAlignmentAlgorithmTreeGuided , MapAlignmentEvaluationAlgorithm , MapAlignmentEvaluationAlgorithmPrecision , MapAlignmentEvaluationAlgorithmRecall , MarkerMower , MascotRemoteQuery , MassAnalyzer , MassDecomposition , MassDecompositionAlgorithm , MassExplainer , MassFeatureTrace , MassTrace , MatchedIterator< CONT_T, TRAIT, CONST_T > , BasicStatistics< RealT > , BilinearInterpolation< Key, Value > , GammaDistributionFitter , GaussFitter , GumbelDistributionFitter , GumbelMaxLikelihoodFitter , Histogram< ValueType, BinSizeType > , LinearInterpolation< Key, Value > , LinearRegression , PosteriorErrorProbabilityModel , ROCCurve , Matrix< Value > , MaxLikeliFitter1D , MetaboliteFeatureDeconvolution , MetaInfo , MetaInfoDescription , MetaInfoInterface , MetaInfoInterfaceUtils , MetaInfoRegistry , MobilityPeak1D , MobilityPeak2D , Mobilogram , ModelDescription< D > , Modification , ModificationDefinition , ModificationDefinitionsSet , ModificationsDB , MRMFeature , MRMFragmentSelection , MRMMapping , MRMTransitionGroup< ChromatogramType, TransitionType > , MRMTransitionGroupPicker , MSChromatogram , MSExperiment , MSPFile , MSQuantifications::AnalysisSummary , MSQuantifications::Assay , MSQuantifications , MSSpectrum , MultiGradient , NASequence::ConstIterator , NASequence::Iterator , NASequence , NetworkGetRequest , NeutralLossDiffFilter , NeutralLossMarker , NLargest , Normalizer , NucleicAcidSpectrumGenerator , OMSSAXMLFile , OnDiscMSExperiment , PenaltyFactors , PenaltyFactorsIntensity , OptimizePeakDeconvolution , OSWFile , OSWPeakGroup , OSWPeptidePrecursor , OSWProtein , OSWTransition , Param , Param::ParamEntry , Param::ParamNode , ParameterInformation , ParamValue , ParentPeakMower , Peak1D , Peak2D , PeakAlignment , PeakFileOptions , PeakGroup , PeakMarker , PeakPickerMRM , PeakShape , PeakSpectrumCompareFunctor , PepNovoInfile , PepNovoOutfile , PeptideEvidence , PeptideHit , PeptideIdentification , PepXMLFile::AminoAcidModification , Precursor , Product , ProductModel< 2 > , ProgressLogger , ProteinHit , ProteinIdentification , ProteinIdentification::SearchParameters , ProteinInference , ProteinResolver , ProtonDistributionModel , QcMLFile::Attachment , QcMLFile::QualityParameter , QTCluster , QuantitativeExperimentalDesign , RangeBase , ReactionMonitoringTransition , Residue , ResidueDB , ResidueModification , Ribonucleotide , RibonucleotideDB , RichPeak2D , Sample , SampleTreatment , Scaler , ScanWindow , SequestInfile , SequestOutfile , SignalToNoiseEstimator< Container > , SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container > , SimpleTSGXLMS , SingleLinkage , Software , SONARScoring , SourceFile , SpectralMatch , SpectraMerger , SpectraSTSimilarityScore , SpectrumAlignment , SpectrumAlignmentScore , SpectrumAnnotator , SpectrumCheapDPCorr , SpectrumIdentification , SpectrumLookup , SpectrumMetaDataLookup , SpectrumMetaDataLookup::SpectrumMetaData , SpectrumPrecursorComparator , SpectrumSettings , SqrtMower , SteinScottImproveScore , StreamHandler , String , StringListUtils , StringView , Tagging , TargetedExperiment , Compound , Peptide , PeptideCompound , RetentionTime , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS , ThresholdMower , TICFilter , TMTEighteenPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod , TOPPASEdge , TOPPASInputFileListVertex , TOPPASMergerVertex , TOPPASOutputFileListVertex , TOPPASResource , TOPPASResources , TOPPASSplitterVertex , TOPPASToolVertex::IOInfo , TOPPASToolVertex , TOPPASVertex , TraceFitter , TransformationDescription , TransformationDescription::TransformationStatistics , TransformationModel , TVToolDiscovery , TwoDOptimization , UnimodXMLFile , UniqueIdInterface , VersionInfo::VersionDetails , WindowMower , XTandemInfile , XTandemXMLFile , ZhangSimilarityScore
• operator== : _Iterator< _Val, _Ref, _Ptr > , AA , AASequence::ConstIterator , AASequence::Iterator , AASequence , AbsoluteQuantitationMethod , Acquisition , AcquisitionInfo , Adduct , AdductInfo , AnnotationStatistics , Area< N_DIM > , BaseFeature , BinnedSpectrum , ChargePair , ChromatogramPeak , ChromatogramSettings , ClusterProxyKD , Compomer , ConsensusMap , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT > , ContactPerson , ConvexHull2D , CVMappingRule , CVMappings , CVMappingTerm , CVReference , CVTerm , CVTerm::Unit , CVTermList , CVTermListInterface , DataFilters::DataFilter , DataProcessing , DataValue , DateTime , DBoundingBox< D > , DecoyHelper::DecoyStatistics , DecoyHelper::Result , DefaultParamHandler , Digestion , DigestionEnzyme , DigestionEnzymeProtein , DimBase , DimMapper< N_DIM > , DistanceMatrix< Value > , DocumentIdentifier , DPosition< D, TCoordinateType > , DRange< D > , Element , EmpiricalFormula , ExperimentalSettings , FASTAFile::FASTAEntry , Feature , FeatureHandle , FeatureMap , FeatureSummary::Result , FlagSet< ENUM > , FLASHDeconvHelperStructs::LogMzPeak , Gradient , GridBasedCluster , HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator , Hit , HPLC , Identification , AppliedProcessingStep , DBSearchParam , ObservationMatchGroup , ParentMatch , ProcessingStep , ScoreType , IdentificationHit , IdentificationSummary::Result , IMSElement , IMSIsotopeDistribution , IMSIsotopeDistribution::Peak , IncludeExcludeTarget , Index , InspectInfile , InspectOutfile , Instrument , InstrumentSettings , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , DIntervalBase< D > , IntensityIteratorWrapper< IteratorT > , RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ , ToolDescriptionInternal , IonDetector , IonSource , IsotopeDistribution , MassAnalyzer , MassDecomposition , MatchedIterator< CONT_T, TRAIT, CONST_T > , Histogram< ValueType, BinSizeType > , Matrix< Value > , MetaInfo , MetaInfoDescription , MetaInfoInterface , MinimumDistance , MobilityPeak1D , MobilityPeak2D , Mobilogram , ModelDescription< D > , Modification , ModificationDefinition , ModificationDefinitionsSet , MRMFeatureQC::ComponentGroupQCs , MRMFeatureQC::ComponentQCs , MSChromatogram , MSExperiment , MSQuantifications , MSSpectrum , MzTabDouble , NASequence::ConstIterator , NASequence::Iterator , NASequence , OnDiscMSExperiment , OPXLDataStructs::ProteinProteinCrossLink , Param , Param::ParamEntry , Param::ParamIterator , Param::ParamNode , ParamValue , Peak1D , Peak2D , PeakGroup , PeakIndex , PeakShape , PepNovoInfile , PepNovoOutfile , PeptideEvidence , PeptideHit , PeptideHit::PeakAnnotation , PeptideHit::PepXMLAnalysisResult , PeptideIdentification , Precursor , Product , ProteinHit , ProteinIdentification , ProteinIdentification::ProteinGroup , ProteinIdentification::SearchParameters , QcMLFile::Attachment , QcMLFile::QualityParameter , RangeBase , RangeManager< RangeBases > , RangeStatsType , ReactionMonitoringTransition , Residue , ResidueModification , Ribonucleotide , RichPeak2D , Sample , SampleTreatment , ScanWindow , SequestInfile , SequestOutfile , Software , SourceFile , SpectrumIdentification , SpectrumSettings , StopWatch , StopWatch::TimeDiff_ , StringView , Tagging , TargetedExperiment , Compound , Contact , CV , Instrument , Interpretation , Peptide , PeptideCompound , Prediction , Protein , Publication , RetentionTime , TraMLProduct , TIC::Result , TransformationModel::DataPoint , UniqueIdInterface , VersionInfo::VersionDetails
• operator>() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT > , DataValue , DPosition< D, TCoordinateType > , FLASHDeconvHelperStructs::LogMzPeak , GridBasedCluster , MinimumDistance , ParamValue , PeakGroup , QcMLFile::Attachment , QcMLFile::QualityParameter , StopWatch , VersionInfo::VersionDetails
• operator>=() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType > , StopWatch
• operator>> : AASequence
• operator[]() : AASequence , ConstRefVector< ContainerT > , ContinuousWaveletTransform , DataFilters , DeconvolvedSpectrum , DPosition< D, TCoordinateType > , ExposedVector< VectorElement > , Weights , IntensityIteratorWrapper< IteratorT > , IsotopeDistribution , KDTreeFeatureNode , MassTrace , Histogram< ValueType, BinSizeType > , Mobilogram , MSExperiment , NASequence , OnDiscMSExperiment , PeakGroup , TOPPASVertex::TOPPASFilenames
• operator|() : FlagSet< ENUM >
• operator|=() : FlagSet< ENUM >
• opt_ : MzTabMSmallMoleculeEvidenceSectionRow , MzTabMSmallMoleculeFeatureSectionRow , MzTabMSmallMoleculeSectionRow , MzTabNucleicAcidSectionRow , MzTabOligonucleotideSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• OPTIMAL : LPWrapper
• optimal_threshold : MRMFeatureSelector::SelectorParameters
• optimise() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• optimization_ : PeakPickerCWT
• optimization_method_ : AbsoluteQuantitation
• optimize() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , MRMFeatureSelector , MRMFeatureSelectorQMIP , MRMFeatureSelectorScore , OptimizePeakDeconvolution , OptimizePick , TwoDOptimization
• optimize_() : LevMarqFitter1D , TraceFitter
• optimizeAnnotations_() : QTCluster
• optimizeCalibrationCurveIterative() : AbsoluteQuantitation
• optimizeCalibrationCurves() : AbsoluteQuantitation
• optimizeParameters_() : SimpleSVM
• OptimizePeakDeconvolution() : OptimizePeakDeconvolution
• OptimizePick() : OptimizePick
• optimizeRegions_() : TwoDOptimization
• optimizeRegionsScanwise_() : TwoDOptimization
• optimizeSingleCalibrationCurve() : AbsoluteQuantitation
• optimizeTree() : KDTreeFeatureMaps
• optional_begin : FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern
• optional_end : FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern
• optional_fit_improvement_ : FeatureFinderAlgorithmPicked
• optionalAttributeAsDouble_() : XMLHandler
• optionalAttributeAsDoubleList_() : XMLHandler
• optionalAttributeAsInt_() : XMLHandler
• optionalAttributeAsIntList_() : XMLHandler
• optionalAttributeAsString_() : XMLHandler
• optionalAttributeAsStringList_() : XMLHandler
• optionalAttributeAsUInt_() : XMLHandler
• options_ : ConsensusXMLFile , DTA2DFile , FeatureXMLFile , FileHandler , IndexedMzMLFileLoader , ConsensusXMLHandler , FeatureXMLHandler , MzDataHandler , MzMLHandler , MzXMLHandler , MzDataFile , MzMLFile , MzXMLFile
• OptPeakFunctor() : OptimizePick::OptPeakFunctor
• OR : CVMappingRule
• Orange : ColorBrewer::Distinct
• ORBITRAP : MassAnalyzer
• order_ : IonDetector , IonDetectorVisualizer , IonSource , IonSourceVisualizer , MassAnalyzer , MassAnalyzerVisualizer , SavitzkyGolayFilter
• orderBest_() : PeptideAndProteinQuant
• ordinal : Interpretation
• organism_ : Sample
• organizeMapWithSameIdentifier() : TargetedSpectraExtractor
• origin : ProteinResolver::PeptideEntry
• origin_ : ResidueModification , Ribonucleotide
• origin_fullname : IDRipper::RipFileIdentifier
• original_mz : RNPxlReportRow
• OriginAnnotationFormat : IDRipper
• os_ : OpenMSOSInfo , XMLValidator
• os_version_ : OpenMSOSInfo
• OSChromatogram() : OSChromatogram
• OSChromatogramMeta() : OSChromatogramMeta
• osm_data_ : MzTab
• osm_search_engine_score : MzTabMetaData
• OSSpectrum() : OSSpectrum
• OSSpectrumMeta() : OSSpectrumMeta
• OSW : FileTypes
• osw_result_files_ : SwathTabWidget
• OSWDataSharedPtrType : LayerDataDefs
• OSWFile() : OSWFile
• OSWLevel : OSWFile
• OSWPeakGroup() : OSWPeakGroup
• OSWPeptidePrecursor() : OSWPeptidePrecursor
• OSWProtein() : OSWProtein
• OSWTransition() : OSWTransition
• OTHER : DataValue , ResidueModification
• OTHER_GLYCOSYLATION : ResidueModification
• out_basename : IDRipper::RipFileIdentifier
• out_dir_ : TOPPASScene
• out_edges_ : TOPPASVertex
• outcome : SimpleSVM::Prediction
• outEdgeHasChanged() : TOPPASInputFileListVertex , TOPPASToolVertex , TOPPASVertex
• outEdgesBegin() : TOPPASVertex
• outEdgesEnd() : TOPPASVertex
• outer_points_ : ConvexHull2D
• outfile_ : FASTAFile
• outgoingEdgesCount() : TOPPASVertex
• outlier_detection_method_ : AbsoluteQuantitation
• OutOfGrid() : OutOfGrid
• OutOfMemory() : OutOfMemory
• OutOfRange() : OutOfRange
• output_combo_ : ToolsDialog
• output_delay : LPWrapper::SolverParam
• OUTPUT_FILE : ListEditor , ParameterInformation
• OUTPUT_FILE_LIST : ParameterInformation
• output_filename_ : OpenSwathOSWWriter , XTandemInfile
• output_files_ : TOPPASVertex
• output_folder_name_ : TOPPASOutputFileListVertex
• output_freq : LPWrapper::SolverParam
• output_lines_ : SequestInfile
• OUTPUT_PREFIX : ParameterInformation
• output_results_ : XTandemInfile
• OutputDirectory() : OutputDirectory
• outputFileWritable_() : TOPPBase
• outputFileWritten() : TOPPASOutputFileListVertex
• outputFolderNameChanged() : TOPPASOutputFileListVertex
• outputToStream_() : Colorizer
• outputVertexFinished() : TOPPASBase
• outside_ : LinearInterpolation< Key, Value >
• outside_0_ : BilinearInterpolation< Key, Value >
• outside_1_ : BilinearInterpolation< Key, Value >
• outsideExtractionWindow_() : ChromatogramExtractor
• overall_data_range_ : PlotCanvas
• overall_data_range_1d_ : Plot1DCanvas
• overall_quality_l : MRMFeatureQC::ComponentGroupQCs , MRMFeatureQC::ComponentQCs
• overall_quality_u : MRMFeatureQC::ComponentGroupQCs , MRMFeatureQC::ComponentQCs
• overall_values_ : Plot3DOpenGLCanvas
• OverallQualityLess : Feature
• overflow() : LogStreamBuf
• OverlapDetector() : OverlapDetector
• overlaps_() : PrecursorCorrection
• override_group_label_check_ : TransitionTSVFile
• overview_count_data_ : LayerStatistics
• overview_range_data_ : LayerStatistics
• oxidation : MQExporterHelper::MQCommonOutputs