Here is a list of all class members with links to the classes they belong to:
- o -
- O
: ExtendedIsotopeModel
, IsotopeModel
- O18Labeler()
: O18Labeler
- OBO
: FileTypes
- observed_intensity_
: AccurateMassSearchResult
- observed_mz_
: AccurateMassSearchResult
- observed_precursor_mass_
: SpectralMatch
- observed_precursor_rt_
: SpectralMatch
- observed_rt_
: AccurateMassSearchResult
- observed_spectrum_idx_
: SpectralMatch
- 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
- OffsetVector
: IndexedMzMLDecoder
- ofs
: OpenSwathTSVWriter
- ofs_
: MSDataCachedConsumer
, MSDataWritingConsumer
- ok()
: FuzzyStringComparator::InputLine
, BSpline2d
- ok_()
: ToolsDialog
, TOPPASToolConfigDialog
- ok_button_
: ToolsDialog
- OkButton_
: ListEditor
- OLIGO
: SVMWrapper
- OLIGO_COMBINED
: SVMWrapper
- OLINKED_GLYCOSYLATION
: ResidueModification
- OMSSACSVFile()
: OMSSACSVFile
- OMSSAXML
: FileTypes
- OMSSAXMLFile()
: OMSSAXMLFile
- ON
: MassAnalyzer
- OnDiscMSExperiment()
: OnDiscMSExperiment< PeakT, ChromatogramPeakT >
- 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
- opened
: Param::ParamIterator::TraceInfo
- openExampleDialog()
: TOPPASBase
, TOPPViewBase
- openFile()
: IndexedMzMLFile
, OnDiscMSExperiment< PeakT, ChromatogramPeakT >
, INIFileEditorWindow
- openFileDialog()
: IDEvaluationBase
, TOPPASBase
, TOPPViewBase
- openFilesInTOPPView()
: TOPPASBase
- openglcanvas_
: Spectrum3DCanvas
- openglwidget()
: Spectrum3DCanvas
- openInputFileStream_()
: FuzzyStringComparator
- openInTOPPView()
: TOPPASScene
, TOPPASToolVertex
- OpenMSLineEdit()
: OpenMSLineEdit
- OpenMSOSInfo()
: OpenMSOSInfo
- openOnlinePipelineRepository()
: TOPPASBase
- openPreferences()
: SpectrumWidget
- openRecentFile()
: TOPPViewBase
- OPENSPLIT
: IonSource
- OpenSwath_Scores()
: OpenSwath_Scores
- OpenSwath_Scores_Usage()
: OpenSwath_Scores_Usage
- OpenSwathScoring()
: OpenSwathScoring
- OpenSwathTSVWriter()
: OpenSwathTSVWriter
- OpenSwathWorkflow()
: OpenSwathWorkflow
- 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 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!=()
: 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
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, IntensityIteratorWrapper< IteratorT >
, DataFilters::DataFilter
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, BaseFeature
, ChromatogramPeak
, ConsensusMap
, FeatureHandle
, FeatureMap
, MSChromatogram< PeakT >
, MSExperiment< PeakT, ChromatogramPeakT >
, MSSpectrum< PeakT >
, OnDiscMSExperiment< PeakT, ChromatogramPeakT >
, 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 >
, PeakShape
, FoundProteinFunctor
, ReactionMonitoringTransition
, IncludeExcludeTarget
, TargetedExperiment
, AASequence::ConstIterator
, AASequence::Iterator
, AASequence
, Element
, EmpiricalFormula
, IsotopeDistribution
, IMSElement
, IMSIsotopeDistribution
, ModificationDefinition
, ModificationDefinitionsSet
, Residue
, ResidueModification
, HashGrid< Cluster >::Iterator
, HashGrid< Cluster >::ConstIterator
, BinnedSpectrum
- operator()()
: ListUtils::DoubleTolerancePredicate_
, Matrix< Value >
, FloatsWithTolLess
, IntsInRangeLess
, CmpMassTraceByMZ
, CmpHypothesesByScore
, SpectraMerger::SpectraDistance_
, BaseFeature::QualityLess
, ChromatogramPeak::IntensityLess
, 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 >
, HasScanPolarity< SpectrumType >
, IsEmptySpectrum< SpectrumType >
, IsZoomSpectrum< SpectrumType >
, HasActivationMethod< SpectrumType >
, InPrecursorMZRange< SpectrumType >
, HasPrecursorCharge< SpectrumType >
, InMzRange< PeakType >
, InIntensityRange< PeakType >
, IsInCollisionEnergyRange< SpectrumType >
, IsInIsolationWindowSizeRange< SpectrumType >
, ROCCurve::simsortdec
, PeptideHit::ScoreMore
, PeptideHit::ScoreLess
, ProteinHit::ScoreMore
, ProteinHit::ScoreLess
, EGHFitter1D::EGHFitterFunctor
, EGHTraceFitter::EGHTraceFunctor
, EmgFitter1D::EgmFitterFunctor
, IntensityLess< FeaFiModuleType >
, GaussTraceFitter::GaussTraceFunctor
, LevMarqFitter1D::GenericFunctor
, MultiplexClustering::MultiplexDistance
, TraceFitter::GenericFunctor
, OptimizePick::OptPeakFunctor
, PeakShape
, PeakShape::PositionLess
, TwoDOptimization::TwoDOptFunctor
, LCMS::OPERATOR_MZ
, LCMS::OPERATOR_FeatureCompare
, MS1FeatureMerger::OPERATOR_FEATURE_TR
, FoundProteinFunctor
, SimpleSearchEngine::HasInvalidPeptideLengthPredicate
, mySqrt
, mean_and_stddev
, AccurateMassSearchEngine::CompareEntryAndMass_
, PrecursorMassComparator
, SpectralMatchScoreComparator
, FeatureDistance
, MapAlignmentAlgorithmSpectrumAlignment::Compare
, ReactionMonitoringTransition::ProductMZLess
, DiaPrescore
, InclusionExclusionList::WindowDistance_
, PrecursorIonSelection::TotalScoreMore
, PrecursorIonSelection::SeqTotalScoreMore
, PSLPFormulation::IndexLess
, PSLPFormulation::ScanLess
, PSLPFormulation::VariableIndexLess
, IMSAlphabet::MassSortingCriteria_
, AverageLinkage
, ClusterFunctor
, CompleteLinkage
, EuclideanSimilarity
, SingleLinkage
, BinnedSharedPeakCount
, BinnedSpectralContrastAngle
, BinnedSpectrumCompareFunctor
, BinnedSumAgreeingIntensities
, PeakAlignment
, PeakSpectrumCompareFunctor
, SpectraSTSimilarityScore
, SpectrumAlignmentScore
, SpectrumCheapDPCorr
, SpectrumPrecursorComparator
, SteinScottImproveScore
, ZhangSimilarityScore
, BinaryComposeFunctionAdapter< OP1, OP2, OP3 >
, UnaryComposeFunctionAdapter< OP1, OP2 >
, DistanceMatrix< Value >
- 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
- 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
, AnnotationStatistics
, FeatureMap
- 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--()
: SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, AASequence::ConstIterator
, AASequence::Iterator
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
- operator-=()
: EmpiricalFormula
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, DPosition< D, TCoordinateType >
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::SparseVectorConstIterator
- operator->()
: AASequence::ConstIterator
, AASequence::Iterator
, HashGrid< Cluster >::Iterator
, HashGrid< Cluster >::ConstIterator
, LogStream
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, Param::ParamIterator
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
- operator/=()
: DPosition< D, TCoordinateType >
- operator<()
: PILISCrossValidation::Peptide
, AASequence
, EnzymaticDigestion::BindingSite
, MassDecomposition
, ModificationDefinition
, SvmTheoreticalSpectrumGenerator::IonType
, GridBasedCluster
, MinimumDistance
, 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
, ProteinIdentification::ProteinGroup
, StopWatch
, FeatureFinderAlgorithmPickedHelperStructs::Seed
, BackgroundControl
, CentroidPeak
, ClusteredMS2ConsensusSpectrum
, ConsensusIsotopePattern
, FeatureLCProfile
, FTPeakDetectController
, LCElutionPeak
, MS2ConsensusSpectrum
, MS2Feature
, MS2Fragment
, MS2Info
, MSPeak
, ProcessData
, TOPPASToolVertex::IOInfo
, PeptideProteinMatchInformation
- operator<<
: AccurateMassSearchResult
, AASequence
, Element
, EmpiricalFormula
, Residue
, LogConfigHandler
, StreamHandler
, Adduct
, Compomer
, DataValue
, ControlledVocabulary
, SVOutStream
, TextFile
, 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=()
: TheoreticalSpectrumGenerator
, ComplementFilter
, ToolDescriptionHandler
, SvmTheoreticalSpectrumGenerator::IonType
, IBSpectraFile
, GaussModel
, TICFilter
, ModificationsDB
, MzIdentMLHandler
, SqrtMower
, Scaler
, MassDecomposition
, FilterFunctor
, IsotopeMarker
, IsotopeDiffFilter
, IsotopeDistribution
, DataValue
, ToolDescription
, SignalToNoiseEstimatorMedian< Container >
, Element
, SignalToNoiseEstimatorMeanIterative< Container >
, SparseVector< Value >::SparseVectorIterator
, StringListUtils
, AASequence::ConstIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, DRange< D >
, SparseVector< Value >::ValueProxy
, Prediction
, Param
, Date
, DefaultParamHandler
, DBoundingBox< D >
, FuzzyStringComparator
, DataValue
, Configuration
, DataValue
, TMTTenPlexQuantitationMethod
, DataValue
, CVReference
, ProgressLogger
, ProteinInference
, ChargePair
, UniqueIdInterface
, BinaryTreeNode
, SpectrumAlignment
, SteinScottImproveScore
, BinnedSpectralContrastAngle
, BinnedSumAgreeingIntensities
, IsobaricChannelExtractor
, BinnedSpectrumCompareFunctor
, CompleteLinkage
, SingleLinkage
, MRMTransitionGroupPicker
, FeatureDeconvolution
, CompNovoIdentification
, CompNovoIdentificationBase
, TransformationDescription
, CompNovoIdentificationBase::Permut
, CompNovoIdentificationCID
, CompNovoIonScoring
, CompNovoIonScoringBase::IonScore
, CompNovoIonScoringBase
, CompNovoIonScoringCID
, DeNovoAlgorithm
, LabeledPairFinder
, DeNovoIdentification
, DeNovoIonScoring::IonScore
, DeNovoIonScoring
, FeatureGroupingAlgorithmIdentification
, GaussTraceFitter
, DeNovoPostScoring
, AccurateMassSearchResult
, ConsensusMapNormalizerAlgorithmQuantile
, ConsensusID
, FalseDiscoveryRate
, HMMState
, HiddenMarkovModel
, IDDecoyProbability
, IDDecoyProbability::Transformation_
, IDMapper
, IDRipper
, SpectralMatch
, PILISCrossValidation::Peptide
, PILISCrossValidation::Option
, PILISCrossValidation
, PILISIdentification
, PILISModel
, PILISModelGenerator
, PILISNeutralLossModel
, PILISScoring
, ProtonDistributionModel
, BaseGroupFinder
, BaseSuperimposer
, ConsensusMapNormalizerAlgorithmMedian
, ConsensusMapNormalizerAlgorithmThreshold
, FeatureDistance
, FeatureGroupingAlgorithm
, FeatureGroupingAlgorithmLabeled
, FeatureGroupingAlgorithmQT
, FeatureGroupingAlgorithmUnlabeled
, MapAlignmentAlgorithm
, MapAlignmentAlgorithmIdentification
, MapAlignmentAlgorithmPoseClustering
, MapAlignmentAlgorithmSpectrumAlignment
, MapAlignmentEvaluationAlgorithm
, MapAlignmentEvaluationAlgorithmPrecision
, MapAlignmentEvaluationAlgorithmRecall
, MRMFragmentSelection
, ReactionMonitoringTransition
, DIAScoring
, PeakPickerMRM
, LocalLinearMap
, PeakIntensityPredictor
, IsobaricNormalizer
, IsobaricQuantifier
, IsobaricQuantifierStatistics
, ItraqChannelExtractor
, ItraqEightPlexQuantitationMethod
, ItraqFourPlexQuantitationMethod
, ItraqQuantifier
, ProteinResolver
, QuantitativeExperimentalDesign
, TMTSixPlexQuantitationMethod
, IncludeExcludeTarget
, PrecursorIonSelectionPreprocessing
, TargetedExperiment
, FeatureLCProfile
, Protein
, RetentionTime
, Compound
, Peptide
, Contact
, Publication
, Instrument
, TraMLProduct
, ConsoleUtils
, ParameterInformation
, AASequence::Iterator
, AASequence
, EdwardsLippertIteratorTryptic
, FTPeakDetectController
, ElementDB
, EmpiricalFormula
, EnzymaticDigestion
, IMSElement
, IMSIsotopeDistribution
, Weights
, LCElutionPeak
, MassDecompositionAlgorithm
, ModificationDefinition
, ModificationDefinitionsSet
, Residue
, ResidueDB
, ResidueModification
, IsotopeFitter1D
, DeconvPeak
, SvmTheoreticalSpectrumGenerator
, SvmTheoreticalSpectrumGeneratorSet
, SvmTheoreticalSpectrumGeneratorTrainer
, AverageLinkage
, ClusterAnalyzer
, ClusterFunctor
, PeakShape
, CentroidPeak
, EuclideanSimilarity
, BinnedSharedPeakCount
, BinnedSpectrum
, BackgroundIntensityBin
, IsotopeModel
, TraceFitter
, PeakAlignment
, PeakSpectrumCompareFunctor
, SpectraSTSimilarityScore
, SpectrumAlignmentScore
, SpectrumCheapDPCorr
, SpectrumPrecursorComparator
, LevMarqFitter1D
, ProductModel< 2 >
, ZhangSimilarityScore
, LogConfigHandler
, MaxLikeliFitter1D
, StreamHandler
, ModelDescription< D >
, Bzip2InputStream
, CVTerm::Unit
, BaseModel< D >
, FeatureFinderAlgorithm
, Compomer
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >
, ConvexHull2D
, CVMappingRule
, CVMappings
, CVMappingTerm
, FeatureFinderAlgorithmPicked
, LCMS
, DataValue
, GaussFitter1D
, BiGaussFitter1D
, ExtendedIsotopeFitter1D
, DataValue
, BiGaussModel
, EmgModel
, DataValue
, DateTime
, DBoundingBox< D >
, EmgFitter1D
, SampleTreatment
, RTSimulation
, DIntervalBase< D >
, DistanceMatrix< Value >
, DPosition< D, TCoordinateType >
, DRange< D >
, MassExplainer
, Matrix< Value >
, EGHModel
, MSPeak
, TOPPASInputFileListVertex
, RawTandemMSSignalSimulation
, SparseVector< Value >
, SparseVector< Value >::ValueProxy
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::SparseVectorConstIterator
, RawMSSignalSimulation
, Annotations1DContainer
, Tagging
, MS2Fragment
, FileMapping
, MappingParam
, ToolDescriptionInternal
, FeatureHypothesis
, SignalToNoiseEstimator< Container >
, TOPPASMergerVertex
, InterpolationModel
, DigestSimulation
, Software
, TOPPASResource
, SpectrumSettings
, BernNorm
, ComplementMarker
, TOPPASToolVertex::IOInfo
, GoodDiffFilter
, TOPPASEdge
, IonizationSimulation
, IntensityBalanceFilter
, SpectrumIdentification
, MetaInfoDescription
, ProteinIdentification
, ScanWindow
, Sample
, MarkerMower
, NeutralLossDiffFilter
, PeptideIdentification
, NeutralLossMarker
, RangeManager< D >
, NLargest
, MetaInfoInterface
, Normalizer
, TOPPASVertex
, ParentPeakMower
, IdentificationHit
, PeakMarker
, Precursor
, ProteinHit
, DataProcessing
, CVTerm
, SpectraMerger
, ThresholdMower
, ROCCurve
, WindowMower
, ChromatogramSettings
, GaussFitter
, LinearInterpolation< Key, Value >
, RichPeak2D
, RichPeak1D
, Peak2D
, Bzip2Ifstream
, ProteinHit
, DocumentIDTagger
, MRMTransitionGroup< SpectrumType, TransitionType >
, FeatureMap
, FeatureHandle
, ConsensusMap
, ConsensusFeature
, BaseFeature
, MSQuantifications
, IonDetector
, SemanticValidator
, MzIdentMLValidator
, UnimodXMLFile
, SequestInfile
, QcMLFile::Attachment
, PepNovoOutfile
, CompressedInputSource
, MSQuantifications::AnalysisSummary
, InspectOutfile
, TraMLHandler
, MzQuantMLHandler
, ControlledVocabulary::CVTerm
, CVMappingFile
, GzipIfstream
, GzipInputStream
, MzIdentMLDOMHandler
, MetaInfoRegistry
, MSQuantifications::Assay
, InspectInfile
, CVTermList
, MassAnalyzer
, OMSSAXMLFile
, PepNovoInfile
, QcMLFile::QualityParameter
, Instrument
, IonSource
, MzQuantMLValidator
, Gradient
, XTandemXMLFile
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, ConsensusFeature::Ratio
, Digestion
, ExperimentalSettings
, MRMFeature
, CachedmzML
, BilinearInterpolation< Key, Value >
, LCMSCData
, MSExperiment< PeakT, ChromatogramPeakT >
, MSSpectrum< PeakT >
, OnDiscMSExperiment< PeakT, ChromatogramPeakT >
, TOPPASToolVertex
, Acquisition
, ContactPerson
, GammaDistributionFitter
, Histogram< ValueType, BinSizeType >
, LinearRegression
, PosteriorErrorProbabilityModel
, AcquisitionInfo
, BasicStatistics< RealT >
, GumbelDistributionFitter
, DocumentIdentifier
, AnnotationStatistics
, RichPeak2D
, HPLC
, Identification
, InstrumentSettings
, Peak1D
, MetaInfo
, Modification
, MSExperiment< PeakT, ChromatogramPeakT >
, PeptideEvidence
, PeptideHit
, Product
, MassTrace
, MSChromatogram< PeakT >
, SourceFile
, MzDataValidator
, Feature
, TOPPASResources
, DetectabilitySimulation
, EGHFitter1D
, MS2ConsensusSpectrum
, ChromatogramPeak
, StopWatch
, EGHTraceFitter
, XTandemInfile
, ExtendedIsotopeModel
, FeaFiModule< PeakType >
, Fitter1D
, MzMLValidator
, TraMLValidator
, TOPPASOutputFileListVertex
, SequestOutfile
, PenaltyFactorsIntensity
, OptimizePeakDeconvolution
, PenaltyFactors
, TwoDOptimization
, PepXMLFile::AminoAcidModification
, ConsensusIsotopePattern
, MultiGradient
, MSPFile
, MS2Info
, SHFeature
, SuperHirnParameters
, FastaIterator
, MascotRemoteQuery
, ProcessData
- operator==()
: SparseVector< Value >::SparseVectorReverseIterator
, ExperimentalSettings
, ReactionMonitoringTransition
, SVMData
, IncludeExcludeTarget
, PeptideIdentification
, CV
, ScanWindow
, Peptide
, Contact
, ResidueModification
, AASequence
, Element
, EmpiricalFormula
, PepNovoOutfile
, IsotopeDistribution
, DataFilters::DataFilter
, MassDecomposition
, SourceFile
, MS2Info
, BinnedSpectrum
, HashGrid< Cluster >::Iterator
, ConsensusMap
, HashGrid< Cluster >::ConstIterator
, BinnedSpectrum
, UniqueIdInterface
, Param::ParamEntry
, SpectrumSettings
, Compomer
, AASequence::ConstIterator
, DPosition< D, TCoordinateType >
, MSSpectrum< PeakT >
, DataValue
, DBoundingBox< D >
, PeakShape
, ProteinIdentification::SearchParameters
, DIntervalBase< D >
, DRange< D >
, ProteinHit
, Param::ParamIterator
, VersionInfo::VersionDetails
, PeptideEvidence
, CVTerm::Unit
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorConstIterator
, Gradient
, Digestion
, DataProcessing
, MS2ConsensusSpectrum
, Adduct
, Tagging
, SpectrumIdentification
, ProteinIdentification
, InspectOutfile
, Instrument
, IdentificationHit
, IonDetector
, QcMLFile::Attachment
, MassAnalyzer
, CVTermList
, ChromatogramSettings
, Acquisition
, BaseFeature
, ChromatogramPeak
, MSQuantifications
, FeatureHandle
, MSExperiment< PeakT, ChromatogramPeakT >
, MetaInfoInterface
, Modification
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, RichPeak2D
, Histogram< ValueType, BinSizeType >
, ConstRefVector< ContainerT >
, Identification
, InstrumentSettings
, MetaInfoDescription
, SequestInfile
, DocumentIDTagger
, Product
, ProteinIdentification::ProteinGroup
, RangeManager< D >
, Software
, BackgroundControl
, DocumentIdentifier
, SHFeature
, RichPeak1D
, ContactPerson
, GridBasedCluster
, AcquisitionInfo
, DBoundingBox< D >
, CVReference
, Peak2D
, SequestOutfile
, MSChromatogram< PeakT >
, PeakIndex
, Peak1D
, DistanceMatrix< Value >
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, Matrix< Value >
, AnnotationStatistics
, Feature
, DRange< D >
, Param
, FASTAFile::FASTAEntry
, CVMappings
, SparseVector< Value >
, InspectInfile
, SparseVector< Value >::ValueProxy
, QcMLFile::QualityParameter
, PepNovoInfile
, ToolDescriptionInternal
, CVMappingTerm
, Param::ParamNode
, FeatureMap
, OnDiscMSExperiment< PeakT, ChromatogramPeakT >
, ClusteredMS2ConsensusSpectrum
, DefaultParamHandler
, CVMappingRule
, ChargePair
, ConvexHull2D
, FeatureLCProfile
, CVTerm
, ModelDescription< D >
, StopWatch
, IonSource
, MinimumDistance
, HPLC
, IntensityIteratorWrapper< IteratorT >
, Instrument
, TraMLProduct
, FoundProteinFunctor
, MetaInfo
, PeptideHit
, Precursor
, IMSIsotopeDistribution::Peak
, PeptideProteinMatchInformation
, IMSIsotopeDistribution
, SampleTreatment
, RetentionTime
, Residue
, ConsensusIsotopePattern
, Publication
, ModificationDefinition
, Prediction
, ModificationDefinitionsSet
, Residue
, AASequence::Iterator
, IMSElement
, EnzymaticDigestion::BindingSite
, TargetedExperiment
, MS2Feature
, Compound
, MS2Fragment
, Protein
, Sample
- operator>()
: FeatureLCProfile
, MS2Info
, LCElutionPeak
, MS2ConsensusSpectrum
, ProcessData
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::ValueProxy
, DataValue
, MS2Feature
, FTPeakDetectController
, ClusteredMS2ConsensusSpectrum
, MSPeak
, StopWatch
, SparseVector< Value >::SparseVectorConstIterator
, QcMLFile::Attachment
, DPosition< D, TCoordinateType >
, SparseVector< Value >::SparseVectorIterator
, QcMLFile::QualityParameter
, MinimumDistance
, BackgroundControl
, VersionInfo::VersionDetails
, MS2Fragment
, ConsensusIsotopePattern
, GridBasedCluster
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >
- operator>=()
: StopWatch
, MS2Info
, SparseVector< Value >::SparseVectorConstIterator
, ConsensusIsotopePattern
, SparseVector< Value >::SparseVectorIterator
, ClusteredMS2ConsensusSpectrum
, FeatureLCProfile
, ProcessData
, MS2ConsensusSpectrum
, MSPeak
, MS2Fragment
, FTPeakDetectController
, BackgroundControl
, MS2Feature
, LCElutionPeak
, SparseVector< Value >::ValueProxy
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, DPosition< D, TCoordinateType >
, ConstRefVector< ContainerT >
, SparseVector< Value >::SparseVectorReverseIterator
- operator>>
: AASequence
- operator[]()
: DPosition< D, TCoordinateType >
, Histogram< ValueType, BinSizeType >
, Map< Key, T >
, MassTrace
, SparseVector< Value >
, ContinuousWaveletTransform
, SparseVector< Value >::SparseVectorConstIterator
, DPosition< D, TCoordinateType >
, ContinuousWaveletTransform
, SparseVector< Value >
, MassTrace
, AASequence
, SparseVector< Value >::SparseVectorIterator
, AASequence
, IntensityIteratorWrapper< IteratorT >
, SparseVector< Value >::SparseVectorReverseIterator
, MSExperiment< PeakT, ChromatogramPeakT >
, ConstRefVector< ContainerT >
, DataFilters
, OnDiscMSExperiment< PeakT, ChromatogramPeakT >
, Weights
- opt_
: MzTabProteinSectionRow
, MzTabPSMSectionRow
, MzTabPeptideSectionRow
, MzTabSmallMoleculeSectionRow
- OPTIMAL
: LPWrapper
- optimization_
: PeakPickerCWT
- optimize()
: TwoDOptimization
, OptimizePick
, OptimizePeakDeconvolution
- optimize_()
: TraceFitter
, 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
- optionalAttributeAsDouble_()
: XMLHandler
- optionalAttributeAsDoubleList_()
: XMLHandler
- optionalAttributeAsInt_()
: XMLHandler
- optionalAttributeAsIntList_()
: XMLHandler
- optionalAttributeAsString_()
: XMLHandler
- optionalAttributeAsStringList_()
: XMLHandler
- optionalAttributeAsUInt_()
: XMLHandler
- options_
: MzXMLHandler< MapType >
, FeatureXMLFile
, IndexedMzMLFileLoader
, DTA2DFile
, MzMLFile
, MzXMLFile
, MzDataFile
, FileHandler
, MzMLHandler< MapType >
, ConsensusXMLFile
, MzDataHandler< MapType >
- OptPeakFunctor()
: OptimizePick::OptPeakFunctor
- OR
: CVMappingRule
- ORBITRAP
: MassAnalyzer
- order_
: SavitzkyGolayFilter
, IonDetector
, IonSource
, MassAnalyzer
, IonSourceVisualizer
, MassAnalyzerVisualizer
, IonDetectorVisualizer
- 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
- OSChromatogram()
: OSChromatogram
- OSChromatogramMeta()
: OSChromatogramMeta
- OSSpectrum()
: OSSpectrum
- OSSpectrumMeta()
: OSSpectrumMeta
- OTHER
: ResidueModification
- OTHER_GLYCOSYLATION
: ResidueModification
- out
: TOPPViewBase
- out_dir_
: TOPPASScene
- out_edges_
: TOPPASVertex
- outEdgeHasChanged()
: TOPPASVertex
, TOPPASToolVertex
, TOPPASInputFileListVertex
- outEdgesBegin()
: TOPPASVertex
- outEdgesEnd()
: TOPPASVertex
- outer_points_
: ConvexHull2D
- outgoingEdgesCount()
: TOPPASVertex
- 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
- output_results_
: XTandemInfile
- 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
- override_group_label_check_
: TransitionTSVReader
- own_model_
: PILISIdentification
- own_sequence_db_
: PILISIdentification