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

- o -

• O : ExtendedIsotopeModel , IsotopeModel , LmaIsotopeModel , LmaIsotopeFitter1D
• O18Labeler() : O18Labeler
• OBO : FileTypes
• ObservedIntensMap : SvmTheoreticalSpectrumGeneratorTrainer
• obsolete : ControlledVocabulary::CVTerm
• OFF : MassAnalyzer
• official_ : TOPPBase
• OfflinePrecursorIonSelection() : OfflinePrecursorIonSelection
• offset_ : LinearInterpolation< Key, Value >
• offset_0_ : BilinearInterpolation< Key, Value >
• offset_1_ : BilinearInterpolation< Key, Value >
• offset_max_ : TransformationModelBSpline
• offset_min_ : TransformationModelBSpline
• ok() : DBOpenDialog
• ok_() : ToolsDialog , TOPPASToolConfigDialog
• ok_button_ : ToolsDialog
• OkButton_ : ListEditor
• OLIGO : SVMWrapper
• OLIGO_COMBINED : SVMWrapper
• OLINKED_GLYCOSYLATION : ResidueModification
• OMSSACSVFile() : OMSSACSVFile
• OMSSAXML : FileTypes
• OMSSAXMLFile() : OMSSAXMLFile
• ON : MassAnalyzer
• one_letter_code_ : Residue
• one_minus_sum_post() : PosteriorErrorProbabilityModel
• op : DataFilters::DataFilter
• op1_ : BinaryComposeFunctionAdapter< OP1, OP2, OP3 > , UnaryComposeFunctionAdapter< OP1, OP2 >
• op2_ : BinaryComposeFunctionAdapter< OP1, OP2, OP3 > , UnaryComposeFunctionAdapter< OP1, OP2 >
• op3_ : BinaryComposeFunctionAdapter< OP1, OP2, OP3 >
• op_changed_() : DataFilterDialog
• open() : SuffixArray , SuffixArraySeqan , SuffixArrayTrypticCompressed , Bzip2Ifstream , GzipIfstream
• open_boxes_ : IsotopeWaveletTransform< PeakType >
• open_tag_ : PTMXMLHandler
• open_tags_ : XMLHandler , SemanticValidator
• openAsNewWindow() : TOPPViewOpenDialog
• openContainingFolder() : TOPPASInputFileListVertex , TOPPASOutputFileListVertex , TOPPASToolVertex
• openDatabaseDialog() : TOPPViewBase
• opened : Param::ParamIterator::TraceInfo
• openExampleDialog() : TOPPASBase , TOPPViewBase
• openFile() : INIFileEditorWindow
• openFileDialog() : IDEvaluationBase , TOPPASBase , TOPPViewBase
• openFilesInTOPPView() : TOPPASBase
• openglcanvas_ : Spectrum3DCanvas
• openglwidget() : Spectrum3DCanvas
• openInputFileStream_() : FuzzyStringComparator
• openInTOPPView() : TOPPASScene , TOPPASToolVertex
• OpenMSOSInfo() : OpenMSOSInfo
• OpenMSXMLFormatTarget() : OpenMSXMLFormatTarget
• openOnlinePipelineRepository() : TOPPASBase
• openPreferences() : SpectrumWidget
• openRecentFile() : TOPPViewBase
• OPENSPLIT : IonSource
• openToppasFile() : TOPPASBase
• operator double() : DataValue , SparseVector< Value >::ValueProxy
• operator DoubleList() : DataValue
• operator float() : DataValue , SparseVector< Value >::ValueProxy
• operator int() : DataValue , SparseVector< Value >::ValueProxy
• operator IntList() : DataValue
• operator long double() : DataValue
• operator long int() : DataValue
• operator long long() : DataValue
• operator PointCoordinate() : HierarchicalClustering< PointRef >::BoundingBox
• operator short int() : DataValue
• operator std::string() : DataValue
• operator StringList() : DataValue
• operator unsigned int() : DataValue
• operator unsigned long int() : DataValue
• operator unsigned long long() : DataValue
• operator unsigned short int() : DataValue
• operator void *() : FuzzyStringComparator::InputLine
• operator!=() : SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , SparseVector< Value >::SparseVectorConstReverseIterator , IntensityIteratorWrapper< IteratorT > , DataFilters::DataFilter , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , BaseFeature , ChromatogramPeak , ConsensusMap , FeatureHandle , FeatureMap< FeatureT > , MSChromatogram< PeakT > , MSExperiment< PeakT, ChromatogramPeakT > , MSSpectrum< PeakT > , Peak1D , Peak2D , PeakIndex , RangeManager< D > , RichPeak1D , RichPeak2D , Histogram< ValueType, BinSizeType > , Acquisition , AcquisitionInfo , ChromatogramSettings , ContactPerson , CVTerm::Unit , CVTerm , CVTermList , DataProcessing , DocumentIDTagger , ExperimentalSettings , Gradient , HPLC , Identification , IdentificationHit , Instrument , InstrumentSettings , IonDetector , IonSource , MassAnalyzer , MetaInfo , MetaInfoInterface , MSQuantifications , PeptideEvidence , PeptideHit , PeptideIdentification , Precursor , Product , ProteinHit , ProteinIdentification::SearchParameters , ProteinIdentification , ScanWindow , Software , SourceFile , SpectrumIdentification , SpectrumSettings , StopWatch , ModelDescription< D > , ReactionMonitoringTransition , PeakShape , FoundProteinFunctor , IncludeExcludeTarget , AASequence::ConstIterator , AASequence::Iterator , AASequence , Element , EmpiricalFormula , IsotopeDistribution , IMSElement , IMSIsotopeDistribution , ModificationDefinition , ModificationDefinitionsSet , Residue , ResidueModification , HashGrid< Cluster >::Iterator , HashGrid< Cluster >::ConstIterator , BinnedSpectrum , ChargePair , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT > , CVMappingRule , CVMappings , CVMappingTerm , CVReference , DataValue , DIntervalBase< D > , DPosition< D, TCoordinateType > , Param::ParamIterator , SparseVector< Value >::ValueProxy , SparseVector< Value >::SparseVectorIterator
• operator()() : ChromatogramPeak::RTLess , ChromatogramPeak::PositionLess , PointerComparator< Cmp > , ReverseComparator< Cmp > , LexicographicComparator< Cmp1, Cmp2 > , PairComparatorFirstElement< PairType > , PairComparatorSecondElement< PairType > , PairComparatorFirstElementMore< PairType > , PairComparatorSecondElementMore< PairType > , PairMatcherFirstElement< PairType > , PairMatcherSecondElement< PairType > , EqualInTolerance< CompareType > , ConsensusFeature::SizeLess , ConsensusFeature::MapsLess , FeatureHandle::IndexLess , MSChromatogram< PeakT >::MZLess , MSSpectrum< PeakT >::RTLess , Peak1D::IntensityLess , Peak1D::MZLess , Peak1D::PositionLess , Peak2D::IntensityLess , Peak2D::RTLess , Peak2D::MZLess , Peak2D::PositionLess , HasMetaValue< MetaContainer > , InRTRange< SpectrumType > , InMSLevelRange< SpectrumType > , HasScanMode< SpectrumType > , IsEmptySpectrum< SpectrumType > , IsZoomSpectrum< SpectrumType > , HasActivationMethod< SpectrumType > , InPrecursorMZRange< SpectrumType > , HasPrecursorCharge< SpectrumType > , InMzRange< PeakType > , InIntensityRange< PeakType > , ROCCurve::simsortdec , PeptideHit::ScoreMore , PeptideHit::ScoreLess , ProteinHit::ScoreMore , ProteinHit::ScoreLess , IntensityLess< FeaFiModuleType > , IsotopeWaveletParallelFor< PeakType, FeatureType > , PeakWidthEstimator::Result , SimpleExtender< PeakType, FeatureType >::IndexWithPriority::PriorityLess , LCMS::OPERATOR_MZ , LCMS::OPERATOR_FeatureCompare , MS1FeatureMerger::OPERATOR_FEATURE_TR , PeakShape , PeakShape::PositionLess , FoundProteinFunctor , FeatureDistance , MapAlignmentAlgorithmSpectrumAlignment::Compare , ReactionMonitoringTransition::ProductMZLess , DiaPrescore , mySqrt , mean_and_stddev , InclusionExclusionList::WindowDistance_ , PrecursorIonSelection::TotalScoreMore , PrecursorIonSelection::SeqTotalScoreMore , PSLPFormulation::IndexLess , PSLPFormulation::ScanLess , PSLPFormulation::VariableIndexLess , IMSAlphabet::MassSortingCriteria_ , AverageLinkage , ClusterFunctor , CompleteLinkage , EuclideanSimilarity , SingleLinkage , BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSpectrumCompareFunctor , BinnedSumAgreeingIntensities , CompareFouriertransform , PeakAlignment , PeakSpectrumCompareFunctor , SpectraSTSimilarityScore , SpectrumAlignmentScore , SpectrumCheapDPCorr , SpectrumPrecursorComparator , SteinScottImproveScore , ZhangSimilarityScore , BinaryComposeFunctionAdapter< OP1, OP2, OP3 > , UnaryComposeFunctionAdapter< OP1, OP2 > , DistanceMatrix< Value > , Matrix< Value > , CmpMassTraceByMZ , CmpHypothesesByScore , SILACFiltering::SpectrumInterpolation , SpectraMerger::SpectraDistance_ , BaseFeature::QualityLess , ChromatogramPeak::IntensityLess , ChromatogramPeak::RTLess
• operator*() : AASequence::ConstIterator , AASequence::Iterator , EdwardsLippertIterator , EmpiricalFormula , IsotopeDistribution , PepIterator , TrypticIterator , HashGrid< Cluster >::Iterator , HashGrid< Cluster >::ConstIterator , Adduct , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , DPosition< D, TCoordinateType > , Param::ParamIterator , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , SparseVector< Value >::SparseVectorConstReverseIterator , IntensityIteratorWrapper< IteratorT > , FastaIterator , FastaIteratorIntern , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , IntensityIterator< FeaFiModuleType > , MzIterator< FeaFiModuleType > , RtIterator< FeaFiModuleType >
• operator*=() : IsotopeDistribution , IMSIsotopeDistribution , DPosition< D, TCoordinateType >
• operator+() : TargetedExperiment , AASequence::ConstIterator , AASequence::Iterator , AASequence , EmpiricalFormula , IsotopeDistribution , MassDecomposition , Adduct , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , DPosition< D, TCoordinateType > , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , String , FeatureMap< FeatureT >
• operator++() : AASequence::ConstIterator , AASequence::Iterator , EdwardsLippertIterator , PepIterator , TrypticIterator , HashGrid< Cluster >::Iterator , HashGrid< Cluster >::ConstIterator , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , Param::ParamIterator , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , SparseVector< Value >::SparseVectorConstReverseIterator , IntensityIteratorWrapper< IteratorT > , FastaIterator , FastaIteratorIntern , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
• operator+=() : TargetedExperiment , AASequence , EmpiricalFormula , IsotopeDistribution , MassDecomposition , Adduct , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , DPosition< D, TCoordinateType > , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , String , ConsensusMap , FeatureMap< FeatureT >
• operator-() : AASequence::ConstIterator , AASequence::Iterator , EmpiricalFormula , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , DPosition< D, TCoordinateType > , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , IntensityIteratorWrapper< IteratorT >
• operator--() : AASequence::ConstIterator , AASequence::Iterator , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , SparseVector< Value >::SparseVectorConstReverseIterator
• operator-=() : EmpiricalFormula , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , DPosition< D, TCoordinateType > , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator
• operator->() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , Param::ParamIterator , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , AASequence::ConstIterator , AASequence::Iterator , HashGrid< Cluster >::Iterator , HashGrid< Cluster >::ConstIterator , LogStream
• operator/=() : DPosition< D, TCoordinateType >
• operator<() : PILISCrossValidation::Peptide , AASequence , EnzymaticDigestion::BindingSite , MassDecomposition , ModificationDefinition , SvmTheoreticalSpectrumGenerator::IonType , VersionInfo::VersionDetails , Compomer , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT > , DataValue , DPosition< D, TCoordinateType > , Matrix< Value > , QTCluster , SparseVector< Value > , SparseVector< Value >::ValueProxy , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , ToolDescriptionInternal , QcMLFile::QualityParameter , QcMLFile::Attachment , StopWatch , FeatureFinderAlgorithmPickedHelperStructs::Seed , BackgroundControl , CentroidPeak , ClusteredMS2ConsensusSpectrum , ConsensusIsotopePattern , FeatureLCProfile , FTPeakDetectController , LCElutionPeak , MS2ConsensusSpectrum , MS2Feature , MS2Fragment , MS2Info , MSPeak , ProcessData , TOPPASToolVertex::IOInfo
• operator<< : AASequence , Element , EmpiricalFormula , Residue , LogConfigHandler , StreamHandler , Adduct , Compomer , DataValue , DoubleList , IntList , StringList , ControlledVocabulary , SVOutStream , Peak2D , BasicStatistics< RealT > , RawData , DBoundingBox< D > , DistanceMatrix< Value > , Matrix< Value >
• operator<=() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType > , SparseVector< Value >::ValueProxy , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , StopWatch , BackgroundControl , ClusteredMS2ConsensusSpectrum , ConsensusIsotopePattern , FeatureLCProfile , FTPeakDetectController , LCElutionPeak , MS2ConsensusSpectrum , MS2Feature , MS2Fragment , MS2Info , MSPeak , ProcessData
• operator=() : Scaler , StreamHandler , ToolDescriptionHandler , SpectraMerger , GzipIfstream , SteinScottImproveScore , SpectrumPrecursorComparator , WindowMower , MarkerMower , SpectrumAlignment , Normalizer , BernNorm , GoodDiffFilter , CompareFouriertransform , BinnedSumAgreeingIntensities , SparseVector< Value >::ValueProxy , FileMapping , BinnedSpectrum , FeatureHypothesis , SparseVector< Value >::ValueProxy , StringList , EuclideanSimilarity , SparseVector< Value >::SparseVectorConstReverseIterator , IntList , Matrix< Value > , AverageLinkage , DIntervalBase< D > , Compomer , DataValue , SvmTheoreticalSpectrumGenerator , DataValue , DateTime , DataValue , Residue , DataValue , MassDecompositionAlgorithm , MassDecomposition , DataValue , CVMappingRule , IMSElement , FeatureDeconvolution , CompNovoIdentification , CompNovoIdentificationBase , ElementDB , Element , CompNovoIdentificationBase::Permut , CompNovoIdentificationCID , AASequence::Iterator , CompNovoIonScoring , CompNovoIonScoringBase::IonScore , CompNovoIonScoringBase , Prediction , CompNovoIonScoringCID , DeNovoAlgorithm , DeNovoIdentification , Peptide , DeNovoIonScoring::IonScore , DeNovoIonScoring , DeNovoPostScoring , Configuration , ConsensusID , FalseDiscoveryRate , HMMState , QuantitativeExperimentalDesign , HiddenMarkovModel , IDDecoyProbability , IDDecoyProbability::Transformation_ , ItraqChannelExtractor , IDMapper , IDRipper , PILISCrossValidation::Peptide , PILISCrossValidation::Option , PILISCrossValidation , PILISIdentification , PILISModel , TransformationDescription , PILISModelGenerator , PILISNeutralLossModel , PILISScoring , MapAlignmentAlgorithmSpectrumAlignment , ProtonDistributionModel , BaseGroupFinder , BaseSuperimposer , LabeledPairFinder , ConsensusMapNormalizerAlgorithmMedian , ConsensusMapNormalizerAlgorithmQuantile , FeatureFinderAlgorithmSimplest< PeakType, FeatureType > , ConsensusMapNormalizerAlgorithmThreshold , FeatureDistance , FeatureGroupingAlgorithm , FeatureGroupingAlgorithmIdentification , FeatureGroupingAlgorithmLabeled , FeatureGroupingAlgorithmQT , FeatureGroupingAlgorithmUnlabeled , MapAlignmentAlgorithm , MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering , MapAlignmentEvaluationAlgorithm , MapAlignmentEvaluationAlgorithmPrecision , MapAlignmentEvaluationAlgorithmRecall , MRMFragmentSelection , ReactionMonitoringTransition , CachedmzML , DIAScoring , MRMTransitionGroupPicker , LocalLinearMap , PeakIntensityPredictor , ItraqQuantifier , ProteinInference , ProteinResolver , IncludeExcludeTarget , PrecursorIonSelectionPreprocessing , TargetedExperiment , SuperHirnParameters , TOPPASResources , Protein , RetentionTime , Compound , Contact , Publication , Instrument , TOPPASInputFileListVertex , TraMLProduct , ParameterInformation , AASequence::ConstIterator , AASequence , EdwardsLippertIteratorTryptic , TOPPASOutputFileListVertex , TraceFitter< PeakType > , TwoDOptimization , EmpiricalFormula , IsotopeDistribution , IMSIsotopeDistribution , Weights , MultiGradient , PenaltyFactorsIntensity , ModificationDefinition , ModificationDefinitionsSet , ModificationsDB , ResidueDB , ResidueModification , SvmTheoreticalSpectrumGenerator::IonType , SimpleSeeder< PeakType, FeatureType > , LCMSCData , ProcessData , SvmTheoreticalSpectrumGeneratorSet , SvmTheoreticalSpectrumGeneratorTrainer , TheoreticalSpectrumGenerator , ClusterAnalyzer , ClusterFunctor , CompleteLinkage , MS2ConsensusSpectrum , SingleLinkage , BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSpectrum , BinnedSpectrumCompareFunctor , MS2Info , BackgroundIntensityBin , FTPeakDetectController , PeakAlignment , PeakSpectrumCompareFunctor , SpectraSTSimilarityScore , SpectrumAlignmentScore , SpectrumCheapDPCorr , LCMS , CentroidPeak , ZhangSimilarityScore , FuzzyStringComparator , LogConfigHandler , UniqueIdInterface , BinaryTreeNode , ChargePair , GaussFitter1D , ProductModel< 2 > , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT > , ConvexHull2D , CVMappings , CVMappingTerm , CVReference , LmaIsotopeModel , DataValue , ModelDescription< D > , GaussModel , LevMarqFitter1D , DataValue , LmaGaussModel , GaussTraceFitter< PeakType > , DataValue , Date , DBoundingBox< D > , DefaultParamHandler , ContactPerson , SimRandomNumberGenerator , ExtendedIsotopeModel , DistanceMatrix< Value > , DoubleList , DPosition< D, TCoordinateType > , DRange< D > , FeaFiModule< PeakType, FeatureType > , IntList , MassExplainer , Param , SparseVector< Value > , FeatureFinderAlgorithmPicked< PeakType, FeatureType > , StopWatch , EmgFitter1D , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , StringList , ExtendedIsotopeFitter1D , TOPPASResource , BaseModel< D > , TOPPASEdge , MappingParam , PeakShape , ToolDescriptionInternal , ToolDescription , SignalToNoiseEstimator< Container > , MSPeak , SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container > , Sample , FeatureLCProfile , ConsensusIsotopePattern , RawTandemMSSignalSimulation , ComplementFilter , ModelFitter< PeakType, FeatureType > , ComplementMarker , LmaIsotopeFitter1D , LmaGaussFitter1D , IsotopeModel , FilterFunctor , IntensityBalanceFilter , IsotopeDiffFilter , FeatureFinderAlgorithmSimple< PeakType, FeatureType > , IsotopeMarker , EGHFitter1D , NeutralLossDiffFilter , NeutralLossMarker , NLargest , ParentPeakMower , PeakMarker , RawMSSignalSimulation , IonizationSimulation , DigestSimulation , SampleTreatment , SpectrumSettings , SqrtMower , ThresholdMower , TICFilter , ProteinHit , Bzip2Ifstream , Bzip2InputStream , DetectabilitySimulation , MSQuantifications::AnalysisSummary , Modification , ScanWindow , CVMappingFile , IonDetector , PersistentObject , Identification , FastaIterator , GzipInputStream , MzIdentMLHandler , CVTermList , CVTerm , ChromatogramSettings , AcquisitionInfo , PosteriorErrorProbabilityModel , LinearRegression , GumbelDistributionFitter::GumbelDistributionFitResult , MzQuantMLHandler , InstrumentSettings , LinearInterpolation< Key, Value > , RichPeak2D , RichPeak1D , Peak1D , MSSpectrum< PeakT > , MSExperiment< PeakT, ChromatogramPeakT > , MetaInfo , FeatureMap< FeatureT > , FeatureHandle , ConsensusFeature , ConsensusFeature::Ratio , PeptideEvidence , XTandemXMLFile , SemanticValidator , MzQuantMLValidator , Product , UnimodXMLFile , QcMLFile::Attachment , QcMLFile::QualityParameter , PepNovoInfile , PeptideHit , ProteinHit , TraMLHandler , InspectInfile , InspectOutfile , MSPFile , OMSSAXMLFile , PeptideIdentification , PepXMLFile::AminoAcidModification , SequestOutfile , MetaInfoDescription , MSQuantifications::Assay , MzMLValidator , XTandemInfile , MetaInfoInterface , ChromatogramPeak , Feature , IonSource , MRMFeature , MRMTransitionGroup< SpectrumType, TransitionType > , MSChromatogram< PeakT > , MSExperiment< PeakT, ChromatogramPeakT > , IdentificationHit , RangeManager< D > , BilinearInterpolation< Key, Value > , ExperimentalSettings , GammaDistributionFitter , GaussFitter , Histogram< ValueType, BinSizeType > , DataProcessing , Acquisition , CVTerm::Unit , TOPPASToolVertex , Digestion , DocumentIdentifier , DocumentIDTagger , Gradient , HPLC , ROCCurve , Instrument , MassAnalyzer , BasicStatistics< RealT > , GumbelDistributionFitter , MetaInfoRegistry , MSQuantifications , GammaDistributionFitter::GammaDistributionFitResult , Precursor , ProteinIdentification , RichPeak2D , Software , SourceFile , SpectrumIdentification , Tagging , Peak2D , EGHModel , RTSimulation , BiGaussFitter1D , BiGaussModel , EGHTraceFitter< PeakType > , EmgModel , MassTrace , FeatureFinderAlgorithm< PeakType, FeatureType > , Fitter1D , CompressedInputSource , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , ConsensusMap , InterpolationModel , IsotopeFitter1D , TOPPASVertex , BaseFeature , MaxLikeliFitter1D , SimpleExtender< PeakType, FeatureType > , MzDataValidator , TraMLValidator , DeconvPeak , LCElutionPeak , MzIdentMLValidator , MS2Fragment , SHFeature , ControlledVocabulary::CVTerm , SequestInfile , OptimizePeakDeconvolution , PenaltyFactors , Annotations1DContainer , PepNovoOutfile , TOPPASMergerVertex , TOPPASToolVertex::IOInfo , MascotRemoteQuery
• operator==() : DefaultParamHandler , SparseVector< Value > , AASequence , Element , ProteinIdentification::SearchParameters , EmpiricalFormula , Tagging , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , IMSIsotopeDistribution::Peak , ModificationDefinitionsSet , SequestInfile , StopWatch , SparseVector< Value >::SparseVectorConstIterator , HashGrid< Cluster >::Iterator , FASTAFile::FASTAEntry , BinnedSpectrum , DBoundingBox< D > , Contact , RichPeak1D , Compomer , RetentionTime , BackgroundControl , PeakShape , DPosition< D, TCoordinateType > , SourceFile , DataValue , CVTerm , DIntervalBase< D > , SparseVector< Value >::ValueProxy , DRange< D > , DocumentIdentifier , Param::ParamEntry , EnzymaticDigestion::BindingSite , Sample , HPLC , SparseVector< Value >::SparseVectorIterator , Software , IsotopeDistribution , SparseVector< Value >::SparseVectorReverseIterator , Prediction , DocumentIDTagger , InspectOutfile , ClusteredMS2ConsensusSpectrum , ScanWindow , CVMappingTerm , ProteinIdentification::ProteinGroup , Compound , Modification , MassAnalyzer , ProteinHit , Precursor , PeptideIdentification , CVTerm::Unit , Acquisition , BaseFeature , ConsensusMap , InstrumentSettings , FeatureHandle , MSSpectrum< PeakT > , Peak2D , EmpiricalFormula , FoundProteinFunctor , PeptideHit , Digestion , MetaInfoInterface , Instrument , IonDetector , TraMLProduct , Publication , IonSource , SpectrumIdentification , IdentificationHit , FeatureLCProfile , MS2Feature , TargetedExperiment , IncludeExcludeTarget , AcquisitionInfo , MS2Info , SHFeature , ExperimentalSettings , Identification , Gradient , DataProcessing , ChromatogramSettings , AASequence::ConstIterator , ContactPerson , CVTermList , MS2ConsensusSpectrum , SequestOutfile , DataFilters::DataFilter , Histogram< ValueType, BinSizeType > , ChromatogramPeak , PeakIndex , RichPeak2D , Param::ParamIterator , MSExperiment< PeakT, ChromatogramPeakT > , PepNovoInfile , Peak1D , Feature , MSChromatogram< PeakT > , QcMLFile::Attachment , Instrument , Param , QcMLFile::QualityParameter , FeatureMap< FeatureT > , InspectInfile , ToolDescriptionInternal , ReactionMonitoringTransition , DBoundingBox< D > , MetaInfoDescription , MetaInfo , SampleTreatment , DRange< D > , MSQuantifications , Peptide , Param::ParamNode , PeptideEvidence , Matrix< Value > , RangeManager< D > , ProteinIdentification , CVReference , PepNovoOutfile , IntensityIteratorWrapper< IteratorT > , DistanceMatrix< Value > , VersionInfo::VersionDetails , ConsensusIsotopePattern , UniqueIdInterface , Residue , ModelDescription< D > , MassDecomposition , ChargePair , Residue , CVMappings , IMSIsotopeDistribution , ConvexHull2D , AASequence , ModificationDefinition , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , HashGrid< Cluster >::ConstIterator , ResidueModification , BinnedSpectrum , AASequence::Iterator , CVMappingRule , IMSElement , Adduct , ConstRefVector< ContainerT > , SpectrumSettings , Product , SVMData , CV , Protein , MS2Fragment
• operator>() : QcMLFile::Attachment , SparseVector< Value >::SparseVectorReverseIterator , StopWatch , FeatureLCProfile , HierarchicalClustering< PointRef >::TreeDistance , ProcessData , DPosition< D, TCoordinateType > , MSPeak , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , DataValue , MS2Fragment , ConstRefVector< ContainerT > , FTPeakDetectController , MS2Feature , LCElutionPeak , ConsensusIsotopePattern , SparseVector< Value >::SparseVectorConstIterator , SparseVector< Value >::ValueProxy , MS2Info , MS2ConsensusSpectrum , BackgroundControl , QcMLFile::QualityParameter , ClusteredMS2ConsensusSpectrum , VersionInfo::VersionDetails , SparseVector< Value >::SparseVectorIterator
• operator>=() : StopWatch , ConsensusIsotopePattern , MS2Feature , SparseVector< Value >::SparseVectorReverseIterator , SparseVector< Value >::SparseVectorConstIterator , FeatureLCProfile , LCElutionPeak , SparseVector< Value >::ValueProxy , SparseVector< Value >::SparseVectorIterator , MS2Fragment , MS2ConsensusSpectrum , ClusteredMS2ConsensusSpectrum , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , MSPeak , MS2Info , ProcessData , ConstRefVector< ContainerT > , FTPeakDetectController , DPosition< D, TCoordinateType > , BackgroundControl
• operator>> : AASequence
• operator[]() : DPosition< D, TCoordinateType > , Map< Key, T > , ConstRefVector< ContainerT > , AASequence , Weights , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator , DPosition< D, TCoordinateType > , IntensityIteratorWrapper< IteratorT > , SparseVector< Value >::SparseVectorConstIterator , Histogram< ValueType, BinSizeType > , ContinuousWaveletTransform , MassTrace , SparseVector< Value > , DataFilters
• operator|() : HierarchicalClustering< PointRef >::BoundingBox
• operator|=() : HierarchicalClustering< PointRef >::BoundingBox
• opt_ : MzTabPeptideSectionRow , MzTabSmallMoleculeSectionRow , MzTabProteinSectionRow
• OPTIMAL : LPWrapper
• optimization_ : PeakPickerCWT
• optimize() : OptimizePick , TwoDOptimization , OptimizePeakDeconvolution
• optimize_() : TraceFitter< PeakType > , LevMarqFitter1D
• optimizeAnnotations_() : QTCluster
• OptimizePeakDeconvolution() : OptimizePeakDeconvolution
• OptimizePick() : OptimizePick
• optimizeRegions_() : TwoDOptimization
• optimizeRegionsScanwise_() : TwoDOptimization
• Option() : PILISCrossValidation::Option
• optional_begin : FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern
• optional_end : FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern
• optional_fit_improvement_ : FeatureFinderAlgorithmPicked< PeakType, FeatureType >
• optionalAttributeAsDouble_() : XMLHandler
• optionalAttributeAsDoubleList_() : XMLHandler
• optionalAttributeAsInt_() : XMLHandler
• optionalAttributeAsIntList_() : XMLHandler
• optionalAttributeAsString_() : XMLHandler
• optionalAttributeAsStringList_() : XMLHandler
• optionalAttributeAsUInt_() : XMLHandler
• options_ : MzXMLHandler< MapType > , ConsensusXMLFile , DTA2DFile , FileHandler , DBAdapter , MzDataFile , FeatureXMLFile , MzXMLFile , MzMLFile , MzDataHandler< MapType > , MzMLHandler< MapType >
• OR : CVMappingRule
• ORBITRAP : MassAnalyzer
• order_ : MassAnalyzerVisualizer , IonSource , IonDetector , IonDetectorVisualizer , MassAnalyzer , SavitzkyGolayFilter , IonSourceVisualizer
• order_by_mass() : LCMS
• orderBest_() : PeptideAndProteinQuant
• organism_ : Sample
• orgIntensity_ : CentroidPeak
• origin : ProteinResolver::PeptideEntry
• origin_ : ResidueModification
• original_mz : RNPxlReportRow
• os : OpenMSOSInfo
• os_ : XMLValidator
• os_version : OpenMSOSInfo
• OTHER : ResidueModification
• OTHER_GLYCOSYLATION : ResidueModification
• out : TOPPViewBase
• out_dir_ : TOPPASScene
• out_edges_ : TOPPASVertex
• outEdgeHasChanged() : TOPPASVertex , TOPPASInputFileListVertex , TOPPASToolVertex
• outEdgesBegin() : TOPPASVertex
• outEdgesEnd() : TOPPASVertex
• outer_points_ : ConvexHull2D
• outgoingEdgesCount() : TOPPASVertex
• outlier_candidate() : MRMRTNormalizer
• OutlierAttribute : MS2Fragment
• OutOfGrid() : OutOfGrid
• OutOfMemory() : OutOfMemory
• OutOfRange() : OutOfRange
• output_combo_ : ToolsDialog
• output_delay : LPWrapper::SolverParam
• OUTPUT_DIR : FTPeakDetectController
• OUTPUT_FILE : ListEditor , ParameterInformation
• OUTPUT_FILE_LIST : ParameterInformation
• output_filename_ : XTandemInfile
• output_files_ : TOPPASVertex
• output_freq : LPWrapper::SolverParam
• output_lines_ : SequestInfile
• outputFileWritable_() : TOPPBase
• outputFileWritten() : TOPPASOutputFileListVertex
• outputVertexFinished() : TOPPASBase
• outside_ : LinearInterpolation< Key, Value >
• outside_0_ : BilinearInterpolation< Key, Value >
• outside_1_ : BilinearInterpolation< Key, Value >
• outsideExtractionWindow_() : ChromatogramExtractor
• outsideLCelutionSignals : FeatureLCProfile
• overall_data_range_ : SpectrumCanvas
• overall_values_ : Spectrum3DOpenGLCanvas
• OverallQualityLess : Feature
• overflow() : LogStreamBuf
• own_model_ : PILISIdentification
• own_sequence_db_ : PILISIdentification