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
• 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_ : 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
• oneNB() : NeighborSeq::NeighborStats
• only_fully_quantified_ : TopDownIsobaricQuantification
• op : DataFilters::DataFilter
• op_changed_() : DataFilterDialog
• open() : Bzip2Ifstream, GzipIfstream
• open_precursor_window_lower_ : FragmentIndex
• open_precursor_window_upper_ : FragmentIndex
• open_tag_ : PTMXMLHandler
• open_tags_ : SemanticValidator, XMLHandler
• openAsNewWindow() : TOPPViewOpenDialog
• openContainingFolder() : TOPPASInputFileListVertex, TOPPASOutputVertex, 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
• OpenMSLineEdit() : OpenMSLineEdit
• OpenMSOSInfo() : OpenMSOSInfo
• openOnlinePipelineRepository() : TOPPASBase
• OpenPepXLAlgorithm() : OpenPepXLAlgorithm
• openPreferences() : PlotWidget
• OpenSearchModificationAnalysis() : OpenSearchModificationAnalysis
• OpenSwath_Ind_Scores() : OpenSwath_Ind_Scores
• OpenSwath_Scores() : OpenSwath_Scores
• OpenSwathCalibrationWorkflow() : OpenSwathCalibrationWorkflow
• OpenSwathOSWWriter() : OpenSwathOSWWriter
• OpenSwathScoring() : OpenSwathScoring
• OpenSwathWorkflow() : OpenSwathWorkflow
• OpenSwathWorkflowBase() : OpenSwathWorkflowBase
• 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, AnnotatedMSRun, AnnotatedMSRun::PairIterator< T1, T2 >, 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, FloatDataArray, IntegerDataArray, StringDataArray, DataFilters::DataFilter, DataProcessing, DataValue, DateTime, DigestionEnzyme, DigestionEnzymeProtein, DimMapper< N_DIM >, DPosition< D, TCoordinateType >, Element, EmpiricalFormula, ExperimentalSettings, ExposedVector< VectorElement >, FeatureHandle, FeatureMap, Gradient, HashGrid< Cluster >::ConstIterator, HashGrid< Cluster >::Iterator, HPLC, ObservationMatchGroup, IMSElement, IMSIsotopeDistribution, IncludeExcludeTarget, Instrument, InstrumentSettings, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >, DIntervalBase< D >, Identification, IdentificationHit, IntensityIteratorWrapper< IteratorT >, SpectrumIdentification, IonDetector, IonSource, IsotopeDistribution, MassAnalyzer, MatchedIterator< CONT_T, TRAIT, CONST_T >, Histogram< ValueType, BinSizeType >, Matrix< Value >, MetaInfo, MetaInfoDescription, MetaInfoInterface, MobilityPeak1D, MobilityPeak2D, Mobilogram, ModelDescription< D >, ModificationDefinition, ModificationDefinitionsSet, MRMFeatureQC::ComponentGroupQCs, MRMFeatureQC::ComponentQCs, MSChromatogram, MSExperiment, MSSpectrum, NASequence::ConstIterator, NASequence::Iterator, NASequence, OnDiscMSExperiment, Param::ParamIterator, ParamValue, Peak1D, Peak2D, PeakIndex, PeptideEvidence, PeptideHit, PeptideIdentification, Precursor, Product, ProteinHit, ProteinIdentification, ProteinIdentification::SearchParameters, RangeManager< RangeBases >, ReactionMonitoringTransition, Residue, ResidueModification, RichPeak2D, ScanWindow, Software, SourceFile, SpectrumSettings, StopWatch, TargetedExperiment, Interpretation, VersionInfo::VersionDetails, LightCompound, LightModification, LightProtein, LightTransition
• 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, ControlledVocabulary::FNV1aHasher, 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::HasMetaValue< HitType >, IDFilter::HasMinMetaValue< 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, Looper< grid_size, grid_size, EvalResult, Tuple, TupleTypes... >, Looper< param_index, grid_size, EvalResult, Tuple, FirstTupleType, TupleTypes... >, IsEmptySpectrum< SpectrumType >, IsInCollisionEnergyRange< SpectrumType >, IsInIsolationWindow< SpectrumType >, IsInIsolationWindowSizeRange< SpectrumType >, IsZoomSpectrum< SpectrumType >, LevMarqFitter1D::GenericFunctor, ListUtils::DoubleTolerancePredicate_, ROCCurve::simsortdec, Matrix< Value >, MobilityPeak1D::IntensityLess, MobilityPeak1D::MobilityLess, MobilityPeak1D::PositionLess, MobilityPeak2D::IMLess, MobilityPeak2D::IntensityLess, MobilityPeak2D::MZLess, MobilityPeak2D::PositionLess, Mobilogram::RTLess, MSChromatogram::MZLess, MSExperiment::SumIntensityReduction, MSSpectrum::IMLess, MSSpectrum::RTLess, MultiplexClustering::MultiplexDistance, MzTabNucleicAcidSectionRow::RowCompare, MzTabOligonucleotideSectionRow::RowCompare, MzTabOSMSectionRow::RowCompare, MzTabPeptideSectionRow::RowCompare, MzTabProteinSectionRow::RowCompare, MzTabPSMSectionRow::RowCompare, MZTrafoModel::RTLess, NuXLModificationMassesResult::MyStringLengthCompare, OpenSearchModificationAnalysis::FuzzyDoubleComparator, OPXLDataStructs::AASeqWithMassComparator, OPXLDataStructs::CLSMScoreComparator, OPXLDataStructs::XLPrecursorComparator, OPXLHelper::PeptideIDScoreComparator, Peak1D::IntensityLess, Peak1D::MZLess, Peak1D::PositionLess, Peak2D::IntensityLess, Peak2D::MZLess, Peak2D::PositionLess, Peak2D::RTLess, PeakAlignment, PeakSpectrumCompareFunctor, PeptideHit::RankLess, PeptideHit::ScoreLess, PeptideHit::ScoreMore, PeptideHit::SequenceChargeEqual, PeptideHit::SequenceChargeHash, 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, ZhangSimilarityScore, mean_and_stddev, OSSpectrumMeta::RTLess, pair_hash, hash< OpenMS::AASequence >, hash< OpenMS::Adduct >, hash< OpenMS::AnnotatedMSRun >, hash< OpenMS::ChargePair >, hash< OpenMS::ChromatogramPeak >, hash< OpenMS::ChromatogramSettings >, hash< OpenMS::Compomer >, hash< OpenMS::ConvexHull2D >, hash< OpenMS::CVTerm >, hash< OpenMS::CVTerm::Unit >, hash< OpenMS::CVTermList >, hash< OpenMS::CVTermListInterface >, hash< OpenMS::DataValue >, hash< OpenMS::DateTime >, hash< OpenMS::DBoundingBox< D > >, hash< OpenMS::DigestionEnzyme >, hash< OpenMS::DPosition< D, TCoordinateType > >, hash< OpenMS::DRange< D > >, hash< OpenMS::Element >, hash< OpenMS::EmpiricalFormula >, hash< OpenMS::FeatureHandle >, hash< OpenMS::FLASHHelperClasses::LogMzPeak >, hash< OpenMS::FLASHHelperClasses::MassFeature >, hash< OpenMS::IncludeExcludeTarget >, hash< OpenMS::Index >, hash< OpenMS::IonDetector >, hash< OpenMS::IonSource >, hash< OpenMS::IsotopeDistribution >, hash< OpenMS::MassAnalyzer >, hash< OpenMS::MetaInfo >, hash< OpenMS::MetaInfoInterface >, hash< OpenMS::MobilityPeak1D >, hash< OpenMS::MobilityPeak2D >, hash< OpenMS::ModificationDefinition >, hash< OpenMS::NASequence >, hash< OpenMS::NuXLFragmentAdductDefinition >, hash< OpenMS::OPXLDataStructs::ProteinProteinCrossLink >, hash< OpenMS::ParamValue >, hash< OpenMS::Peak1D >, hash< OpenMS::Peak2D >, hash< OpenMS::PeakGroup >, hash< OpenMS::PeptideEvidence >, hash< OpenMS::PeptideHit >, hash< OpenMS::PeptideHit::PeakAnnotation >, hash< OpenMS::PeptideIdentification >, hash< OpenMS::Precursor >, hash< OpenMS::Product >, hash< OpenMS::ProteinHit >, hash< OpenMS::ProteinIdentification >, hash< OpenMS::ProteinIdentification::ProteinGroup >, hash< OpenMS::ProteinIdentification::SearchParameters >, hash< OpenMS::ReactionMonitoringTransition >, hash< OpenMS::Residue >, hash< OpenMS::ResidueModification >, hash< OpenMS::Ribonucleotide >, hash< OpenMS::Software >, hash< OpenMS::SpectrumSettings >, hash< OpenMS::String >, hash< OpenMS::TargetedExperimentHelper::Compound >, hash< OpenMS::TargetedExperimentHelper::Contact >, hash< OpenMS::TargetedExperimentHelper::CV >, hash< OpenMS::TargetedExperimentHelper::Instrument >, hash< OpenMS::TargetedExperimentHelper::Interpretation >, hash< OpenMS::TargetedExperimentHelper::Peptide >, hash< OpenMS::TargetedExperimentHelper::PeptideCompound >, hash< OpenMS::TargetedExperimentHelper::Prediction >, hash< OpenMS::TargetedExperimentHelper::Protein >, hash< OpenMS::TargetedExperimentHelper::Publication >, hash< OpenMS::TargetedExperimentHelper::RetentionTime >, hash< OpenMS::TargetedExperimentHelper::TraMLProduct >, hash< OpenSwath::LightCompound >, hash< OpenSwath::LightModification >, hash< OpenSwath::LightProtein >, hash< OpenSwath::LightTransition >
• operator*() : _Iterator< _Val, _Ref, _Ptr >, AASequence::ConstIterator, AASequence::Iterator, Adduct, AnnotatedMSRun::PairIterator< T1, T2 >, 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, AnnotatedMSRun::PairIterator< T1, T2 >, 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 >, FragmentIndex::SpectrumMatchesTopN, DIntervalBase< D >, MassDecomposition, MetaInfo, 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 >, FloatDataArray, IntegerDataArray, StringDataArray, DataValue, DateTime, DeconvolvedSpectrum, DigestionEnzyme, DigestionEnzymeProtein, DPosition< D, TCoordinateType >, Element, EmpiricalFormula, ExposedVector< VectorElement >, FeatureFinderAlgorithmPickedHelperStructs::Seed, FLASHHelperClasses::LogMzPeak, FLASHHelperClasses::MassFeature, GridBasedCluster, DBSearchParam, IteratorWrapper< Iterator >, ParentMatch, ProcessingStep, ScoreType, ToolDescriptionInternal, IsotopeDistribution, MassDecomposition, MetaInfoDescription, MinimumDistance, ModificationDefinition, MSstatsFile::MSstatsLine_, MSstatsFile::MSstatsTMTLine_, MzTabDouble, NASequence, NuXLFragmentAdductDefinition, NuXLFragmentAnnotationHelper::FragmentAnnotationDetail_, 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, Bitset, 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<<=() : Bitset
• operator<=() : AA, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >, ConstRefVector< ContainerT >, FloatDataArray, IntegerDataArray, StringDataArray, DPosition< D, TCoordinateType >, ExposedVector< VectorElement >, MetaInfoDescription, StopWatch
• operator=() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >, AASequence::ConstIterator, AASequence::Iterator, AASequence, AccurateMassSearchResult, Acquisition, AcquisitionInfo, AnnotatedMSRun, Annotations1DContainer, AnnotationStatistics, Area< N_DIM >, AverageLinkage, BaseFeature, BaseGroupFinder, BaseModel, BaseSuperimposer, BiGaussFitter1D, BiGaussModel, BinaryTreeNode, BinnedSharedPeakCount, BinnedSpectralContrastAngle, BinnedSpectrum, BinnedSpectrumCompareFunctor, BinnedSumAgreeingIntensities, Bzip2Ifstream, Bzip2InputStream, ChargePair, ChromatogramPeak, ChromatogramSettings, ClusterAnalyzer, ClusterFunctor, ClusterProxyKD, CoarseIsotopePatternGenerator, 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, 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_, Fitter1D, FlagSet< ENUM >, FLASHDeconvAlgorithm, FLASHHelperClasses::PrecalculatedAveragine, FuzzyStringComparator, GaussFitter1D, GaussModel, GaussTraceFitter, Gradient, GUILock, GzipIfstream, GzipInputStream, HPLC, IBSpectraFile, IDDecoyProbability, IDDecoyProbability::Transformation_, IdentificationData, IDMapper, IDRipper, IMSElement, IMSIsotopeDistribution, Weights, IncludeExcludeTarget, InspectInfile, InspectOutfile, Instrument, InstrumentSettings, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::Param, CachedMzMLHandler, DIntervalBase< D >, FileMapping, Identification, IdentificationHit, MappingParam, MzDataValidator, MzIdentMLDOMHandler, MzIdentMLHandler, MzIdentMLValidator, MzMLHandlerHelper::BinaryData, MzMLValidator, SemanticValidator, shared_xerces_ptr< T >, SpectrumIdentification, ToolDescription, ToolDescriptionHandler, ToolDescriptionInternal, TraMLHandler, TraMLValidator, unique_xerces_ptr< T >, InterpolationModel, IonDetector, IonSource, IsobaricChannelExtractor, IsobaricNormalizer, IsobaricQuantifier, IsobaricQuantifierStatistics, IsotopeDistribution, IsotopeFitter1D, IsotopeModel, ItraqEightPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, KDTreeFeatureNode, LabeledPairFinder, LayerDataBase, LayerDataChrom, LayerDataConsensus, LayerDataFeature, LayerDataIdent, LayerDataIonMobility, LayerDataPeak, LevMarqFitter1D, LogConfigHandler, MapAlignmentAlgorithmIdentification, MapAlignmentAlgorithmPoseClustering, MapAlignmentAlgorithmTreeGuided, MapAlignmentEvaluationAlgorithm, MapAlignmentEvaluationAlgorithmPrecision, MapAlignmentEvaluationAlgorithmRecall, 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 >, ModificationDefinition, ModificationDefinitionsSet, ModificationsDB, MRMFeature, MRMMapping, MRMTransitionGroup< ChromatogramType, TransitionType >, MRMTransitionGroupPicker, MSChromatogram, MSExperiment, MSPFile, MSSpectrum, MultiGradient, NASequence::ConstIterator, NASequence::Iterator, NASequence, NetworkGetRequest, NLargest, Normalizer, NucleicAcidSpectrumGenerator, NuXLFragmentAdductDefinition, OMSSAXMLFile, OnDiscMSExperiment, OSWFile, OSWPeakGroup, OSWPeptidePrecursor, OSWProtein, OSWTransition, Param, Param::ParamEntry, Param::ParamNode, ParameterInformation, ParamValue, Peak1D, Peak2D, PeakAlignment, PeakFileOptions, PeakGroup, PeakPickerChromatogram, PeakSpectrumCompareFunctor, PepNovoInfile, PepNovoOutfile, PeptideEvidence, PeptideHit, PeptideIdentification, PeptideIdentificationList, PepXMLFile::AminoAcidModification, Precursor, Product, ProgressLogger, ProteinHit, ProteinIdentification, ProteinIdentification::SearchParameters, ProteinInference, QcMLFile::Attachment, QcMLFile::QualityParameter, QTCluster, RangeBase, RangeIntensity, RangeMobility, RangeMZ, RangeRT, RankScaler, ReactionMonitoringTransition, Residue, ResidueDB, ResidueModification, Ribonucleotide, RibonucleotideDB, RichPeak2D, Sample, ScanWindow, SequestInfile, SequestOutfile, SignalToNoiseEstimator< Container >, SignalToNoiseEstimatorMeanIterative< Container >, SignalToNoiseEstimatorMedian< Container >, SimpleSVM, SimpleTSGXLMS, SingleLinkage, Software, SourceFile, SpectralDeconvolution, SpectralMatch, SpectraMerger, SpectraSTSimilarityScore, SpectrumAlignment, SpectrumAlignmentScore, SpectrumAnnotator, SpectrumCheapDPCorr, SpectrumLookup, SpectrumMetaDataLookup, SpectrumMetaDataLookup::SpectrumMetaData, SpectrumPrecursorComparator, SpectrumRangeManager, SpectrumSettings, SqrtScaler, SteinScottImproveScore, StreamHandler, String, StringListUtils, StringView, TargetedExperiment, Compound, Peptide, PeptideCompound, RetentionTime, TheoreticalSpectrumGenerator, TheoreticalSpectrumGeneratorXLMS, ThresholdMower, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TopDownIsobaricQuantification, TOPPASEdge, TOPPASInputFileListVertex, TOPPASMergerVertex, TOPPASOutputVertex, TOPPASResource, TOPPASResources, TOPPASSplitterVertex, TOPPASToolVertex::IOInfo, TOPPASToolVertex, TOPPASVertex, TraceFitter, TransformationDescription, TransformationDescription::TransformationStatistics, TransformationModel, TVToolDiscovery, UnimodXMLFile, UniqueIdInterface, VersionInfo::VersionDetails, WindowMower, XTandemInfile, XTandemXMLFile, ZhangSimilarityScore
• operator== : _Iterator< _Val, _Ref, _Ptr >, AA, AASequence::ConstIterator, AASequence::Iterator, AASequence, AbsoluteQuantitationMethod, Acquisition, AcquisitionInfo, Adduct, AdductInfo, AnnotatedMSRun, AnnotatedMSRun::PairIterator< T1, T2 >, 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, FloatDataArray, IntegerDataArray, StringDataArray, DataFilters::DataFilter, DataFilters, DataProcessing, DataValue, DateTime, DBoundingBox< D >, DeconvolvedSpectrum, DecoyHelper::DecoyStatistics, DecoyHelper::Result, DefaultParamHandler, DigestionEnzyme, DigestionEnzymeProtein, DimBase, DimMapper< N_DIM >, DistanceMatrix< Value >, DocumentIdentifier, DPosition< D, TCoordinateType >, DRange< D >, Element, EmpiricalFormula, ExperimentalSettings, ExposedVector< VectorElement >, FASTAFile::FASTAEntry, Feature, FeatureHandle, FeatureMap, FeatureSummary::Result, FlagSet< ENUM >, FLASHHelperClasses::LogMzPeak, FLASHHelperClasses::MassFeature, Gradient, GridBasedCluster, HashGrid< Cluster >::ConstIterator, HashGrid< Cluster >::Iterator, Hit, HPLC, AppliedProcessingStep, DBSearchParam, ObservationMatchGroup, ParentMatch, ProcessingStep, ScoreType, IdentificationSummary::Result, IMSElement, IMSIsotopeDistribution, IMSIsotopeDistribution::Peak, IncludeExcludeTarget, Index, InspectInfile, InspectOutfile, Instrument, InstrumentSettings, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >, DIntervalBase< D >, Identification, IdentificationHit, IntensityIteratorWrapper< IteratorT >, SpectrumIdentification, 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 >, ModificationDefinition, ModificationDefinitionsSet, MRMFeatureQC::ComponentGroupQCs, MRMFeatureQC::ComponentQCs, MSChromatogram, MSExperiment, MSSpectrum, MzTabDouble, NASequence::ConstIterator, NASequence::Iterator, NASequence, NuXLFragmentAdductDefinition, NuXLFragmentAnnotationHelper::FragmentAnnotationDetail_, OnDiscMSExperiment, OPXLDataStructs::ProteinProteinCrossLink, Param, Param::ParamEntry, Param::ParamIterator, Param::ParamNode, ParamValue, Peak1D, Peak2D, PeakGroup, PeakIndex, PepNovoInfile, PepNovoOutfile, PeptideEvidence, PeptideHit, PeptideHit::PeakAnnotation, PeptideHit::PepXMLAnalysisResult, PeptideIdentification, Precursor, Product, ProteinHit, ProteinIdentification, ProteinIdentification::ProteinGroup, ProteinIdentification::SearchParameters, ProteinModificationSummary, ProteinModificationSummary::Statistics, QcMLFile::Attachment, QcMLFile::QualityParameter, RangeBase, RangeManager< RangeBases >, RangeStatsType, ReactionMonitoringTransition, Residue, ResidueModification, Ribonucleotide, RichPeak2D, Sample, ScanWindow, SequestInfile, SequestOutfile, Software, SourceFile, SpectrumSettings, StopWatch, StopWatch::TimeDiff_, StringView, TargetedExperiment, Compound, Contact, CV, Instrument, Interpretation, Peptide, PeptideCompound, Prediction, Protein, Publication, RetentionTime, TraMLProduct, TIC::Result, TOPPASToolVertex::IOInfo, TransformationModel::DataPoint, UniqueIdInterface, VersionInfo::VersionDetails, LightCompound, LightModification, LightProtein, LightTransition
• operator>() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >, ConstRefVector< ContainerT >, FloatDataArray, IntegerDataArray, StringDataArray, DataValue, DeconvolvedSpectrum, DPosition< D, TCoordinateType >, ExposedVector< VectorElement >, FLASHHelperClasses::LogMzPeak, FLASHHelperClasses::MassFeature, GridBasedCluster, MetaInfoDescription, MinimumDistance, ParamValue, PeakGroup, QcMLFile::Attachment, QcMLFile::QualityParameter, StopWatch, VersionInfo::VersionDetails
• operator>=() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >, ConstRefVector< ContainerT >, FloatDataArray, IntegerDataArray, StringDataArray, DPosition< D, TCoordinateType >, ExposedVector< VectorElement >, MetaInfoDescription, StopWatch
• operator>> : AASequence
• operator[]() : AASequence, AnnotatedMSRun, ConstRefVector< ContainerT >, 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_method_ : AbsoluteQuantitation
• optimize() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >, MRMFeatureSelector, MRMFeatureSelectorQMIP, MRMFeatureSelectorScore
• optimize_() : LevMarqFitter1D, TraceFitter
• optimizeAnnotations_() : QTCluster
• optimizeCalibrationCurveIterative() : AbsoluteQuantitation
• optimizeCalibrationCurves() : AbsoluteQuantitation
• 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, OnDiscMSExperiment
• OR : CVMappingRule
• Orange : ColorBrewer::Distinct
• ORBITRAP : MassAnalyzer
• order_ : IonDetector, IonDetectorVisualizer, IonSource, IonSourceVisualizer, MassAnalyzer, MassAnalyzerVisualizer, SavitzkyGolayFilter
• orderBest_() : PeptideAndProteinQuant
• ordinal : Interpretation
• organism_ : Sample
• organizeMapWithSameIdentifier() : TargetedSpectraExtractor
• origin_ : ResidueModification, Ribonucleotide
• origin_fullname : IDRipper::RipFileIdentifier
• original_mz : NuXLReportRow
• original_score_higher_better : IDScoreSwitcherAlgorithm::IDSwitchResult
• original_score_name : IDScoreSwitcherAlgorithm::IDSwitchResult
• original_score_type : IDScoreSwitcherAlgorithm::IDSwitchResult
• 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
• outerStride() : Matrix< Value >
• outfile_ : FASTAFile
• outgoingEdgesCount() : TOPPASVertex
• OUTLIER : MassTraceDetection
• outlier_detection_method_ : AbsoluteQuantitation
• OutOfGrid() : OutOfGrid
• OutOfMemory() : OutOfMemory
• OutOfRange() : OutOfRange
• output_combo_ : ToolsDialog
• output_delay : LPWrapper::SolverParam
• OUTPUT_DIR : ParameterInformation
• output_dir_ : FIAMSScheduler
• OUTPUT_FILE : ListEditor, ParameterInformation
• OUTPUT_FILE_LIST : ParameterInformation
• output_filename_ : OpenSwathOSWWriter, XTandemInfile
• output_files_ : TOPPASVertex
• output_folder_name_ : TOPPASOutputVertex
• output_freq : LPWrapper::SolverParam
• output_library_ : FeatureFinderIdentificationAlgorithm
• output_lines_ : SequestInfile
• OUTPUT_PREFIX : ParameterInformation
• output_results_ : XTandemInfile
• OutputDirectory() : OutputDirectory
• outputFileWritable_() : TOPPBase
• outputFileWritten() : TOPPASOutputVertex
• outputFolderNameChanged() : TOPPASOutputVertex
• 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
• OverlapMode : FeatureOverlapFilter
• overlaps_() : PrecursorCorrection
• override_group_label_check_ : TransitionTSVFile
• overview_count_data_ : LayerStatistics
• overview_range_data_ : LayerStatistics
• oxidation : MQExporterHelper::MQCommonOutputs