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()
: BSpline2d
, FuzzyStringComparator::InputLine
- 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()
: Bzip2Ifstream
, GzipIfstream
, SuffixArray
, SuffixArraySeqan
, SuffixArrayTrypticCompressed
- open_boxes_
: IsotopeWaveletTransform< PeakType >
- open_tag_
: PTMXMLHandler
- open_tags_
: SemanticValidator
, XMLHandler
- openAsNewWindow()
: TOPPViewOpenDialog
- openContainingFolder()
: TOPPASInputFileListVertex
, TOPPASOutputFileListVertex
, TOPPASToolVertex
- opened
: Param::ParamIterator::TraceInfo
- openExampleDialog()
: TOPPASBase
, TOPPViewBase
- openFile()
: IndexedMzMLFile
, INIFileEditorWindow
, OnDiscMSExperiment< PeakT, ChromatogramPeakT >
- 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!=()
: AASequence::ConstIterator
, AASequence::Iterator
, AASequence
, Acquisition
, AcquisitionInfo
, BaseFeature
, BinnedSpectrum
, ChargePair
, ChromatogramPeak
, ChromatogramSettings
, ConsensusMap
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >
, ContactPerson
, CVMappingRule
, CVMappings
, CVMappingTerm
, CVReference
, CVTerm
, CVTerm::Unit
, CVTermList
, DataFilters::DataFilter
, DataProcessing
, DataValue
, DocumentIDTagger
, DPosition< D, TCoordinateType >
, Element
, EmpiricalFormula
, ExperimentalSettings
, FeatureHandle
, FeatureMap
, Gradient
, HashGrid< Cluster >::ConstIterator
, HashGrid< Cluster >::Iterator
, HPLC
, Identification
, IdentificationHit
, IMSElement
, IMSIsotopeDistribution
, IncludeExcludeTarget
, Instrument
, InstrumentSettings
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, DIntervalBase< D >
, IntensityIteratorWrapper< IteratorT >
, IonDetector
, IonSource
, IsotopeDistribution
, MassAnalyzer
, Histogram< ValueType, BinSizeType >
, MetaInfo
, MetaInfoInterface
, ModelDescription< D >
, ModificationDefinition
, ModificationDefinitionsSet
, MSChromatogram< PeakT >
, MSExperiment< PeakT, ChromatogramPeakT >
, MSQuantifications
, MSSpectrum< PeakT >
, OnDiscMSExperiment< PeakT, ChromatogramPeakT >
, Param::ParamIterator
, Peak1D
, Peak2D
, PeakIndex
, PeakShape
, PeptideEvidence
, PeptideHit
, PeptideIdentification
, Precursor
, Product
, ProteinHit
, ProteinIdentification
, ProteinIdentification::SearchParameters
, RangeManager< D >
, ReactionMonitoringTransition
, Residue
, ResidueModification
, RichPeak1D
, RichPeak2D
, ScanWindow
, Software
, SourceFile
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::ValueProxy
, SpectrumIdentification
, SpectrumSettings
, StopWatch
, TargetedExperiment
, FoundProteinFunctor
- operator()()
: AccurateMassSearchEngine::CompareEntryAndMass_
, AverageLinkage
, BaseFeature::QualityLess
, BinaryComposeFunctionAdapter< OP1, OP2, OP3 >
, BinnedSharedPeakCount
, BinnedSpectralContrastAngle
, BinnedSpectrumCompareFunctor
, BinnedSumAgreeingIntensities
, ChromatogramPeak::IntensityLess
, ChromatogramPeak::PositionLess
, ChromatogramPeak::RTLess
, ClusterFunctor
, CmpHypothesesByScore
, CmpMassTraceByMZ
, CompleteLinkage
, ConsensusFeature::MapsLess
, ConsensusFeature::SizeLess
, DiaPrescore
, DistanceMatrix< Value >
, EGHFitter1D::EGHFitterFunctor
, EGHTraceFitter::EGHTraceFunctor
, EmgFitter1D::EgmFitterFunctor
, EqualInTolerance< CompareType >
, EuclideanSimilarity
, FeatureDistance
, FeatureHandle::IndexLess
, FloatsWithTolLess
, GaussTraceFitter::GaussTraceFunctor
, HasActivationMethod< SpectrumType >
, HasMetaValue< MetaContainer >
, HasPrecursorCharge< SpectrumType >
, HasScanMode< SpectrumType >
, HasScanPolarity< SpectrumType >
, IMSAlphabet::MassSortingCriteria_
, InclusionExclusionList::WindowDistance_
, InIntensityRange< PeakType >
, InMSLevelRange< SpectrumType >
, InMzRange< PeakType >
, InPrecursorMZRange< SpectrumType >
, InRTRange< SpectrumType >
, IntensityLess< FeaFiModuleType >
, IntsInRangeLess
, IsEmptySpectrum< SpectrumType >
, IsInCollisionEnergyRange< SpectrumType >
, IsInIsolationWindowSizeRange< SpectrumType >
, IsZoomSpectrum< SpectrumType >
, LCMS::OPERATOR_FeatureCompare
, LCMS::OPERATOR_MZ
, LevMarqFitter1D::GenericFunctor
, LexicographicComparator< Cmp1, Cmp2 >
, ListUtils::DoubleTolerancePredicate_
, MapAlignmentAlgorithmSpectrumAlignment::Compare
, ROCCurve::simsortdec
, Matrix< Value >
, MS1FeatureMerger::OPERATOR_FEATURE_TR
, MSChromatogram< PeakT >::MZLess
, MSSpectrum< PeakT >::RTLess
, MultiplexClustering::MultiplexDistance
, OptimizePick::OptPeakFunctor
, PairComparatorFirstElement< PairType >
, PairComparatorFirstElementMore< PairType >
, PairComparatorSecondElement< PairType >
, PairComparatorSecondElementMore< PairType >
, PairMatcherFirstElement< PairType >
, PairMatcherSecondElement< PairType >
, Peak1D::IntensityLess
, Peak1D::MZLess
, Peak1D::PositionLess
, Peak2D::IntensityLess
, Peak2D::MZLess
, Peak2D::PositionLess
, Peak2D::RTLess
, PeakAlignment
, PeakShape
, PeakShape::PositionLess
, PeakSpectrumCompareFunctor
, PeptideHit::ScoreLess
, PeptideHit::ScoreMore
, PointerComparator< Cmp >
, PrecursorIonSelection::SeqTotalScoreMore
, PrecursorIonSelection::TotalScoreMore
, PrecursorMassComparator
, ProteinHit::ScoreLess
, ProteinHit::ScoreMore
, PSLPFormulation::IndexLess
, PSLPFormulation::ScanLess
, PSLPFormulation::VariableIndexLess
, ReactionMonitoringTransition::ProductMZLess
, ReverseComparator< Cmp >
, SingleLinkage
, SpectralMatchScoreComparator
, SpectraMerger::SpectraDistance_
, SpectraSTSimilarityScore
, SpectrumAlignmentScore
, SpectrumCheapDPCorr
, SpectrumPrecursorComparator
, SteinScottImproveScore
, TraceFitter::GenericFunctor
, TwoDOptimization::TwoDOptFunctor
, UnaryComposeFunctionAdapter< OP1, OP2 >
, ZhangSimilarityScore
, mean_and_stddev
, mySqrt
, FoundProteinFunctor
, SimpleSearchEngine::HasInvalidPeptideLengthPredicate
- operator*()
: AASequence::ConstIterator
, AASequence::Iterator
, Adduct
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, DPosition< D, TCoordinateType >
, EdwardsLippertIterator
, EmpiricalFormula
, FastaIterator
, FastaIteratorIntern
, HashGrid< Cluster >::ConstIterator
, HashGrid< Cluster >::Iterator
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, IntensityIterator< FeaFiModuleType >
, IntensityIteratorWrapper< IteratorT >
, MzIterator< FeaFiModuleType >
, RtIterator< FeaFiModuleType >
, IsotopeDistribution
, Param::ParamIterator
, PepIterator
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, TrypticIterator
- operator*=()
: DPosition< D, TCoordinateType >
, IMSIsotopeDistribution
, IsotopeDistribution
- operator+()
: AASequence::ConstIterator
, AASequence::Iterator
, AASequence
, Adduct
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, DPosition< D, TCoordinateType >
, EmpiricalFormula
, FeatureMap
, IsotopeDistribution
, MassDecomposition
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, String
, TargetedExperiment
- operator++()
: AASequence::ConstIterator
, AASequence::Iterator
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, EdwardsLippertIterator
, FastaIterator
, FastaIteratorIntern
, HashGrid< Cluster >::ConstIterator
, HashGrid< Cluster >::Iterator
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, IntensityIteratorWrapper< IteratorT >
, Param::ParamIterator
, PepIterator
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, TrypticIterator
- operator+=()
: AASequence
, Adduct
, AnnotationStatistics
, ConsensusMap
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, DPosition< D, TCoordinateType >
, EmpiricalFormula
, FeatureMap
, IsotopeDistribution
, MassDecomposition
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, String
, TargetedExperiment
- operator-()
: AASequence::ConstIterator
, AASequence::Iterator
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, DPosition< D, TCoordinateType >
, EmpiricalFormula
, IntensityIteratorWrapper< IteratorT >
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
- operator--()
: AASequence::ConstIterator
, AASequence::Iterator
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
- operator-=()
: ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, DPosition< D, TCoordinateType >
, EmpiricalFormula
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
- operator->()
: 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
, Param::ParamIterator
- operator/=()
: DPosition< D, TCoordinateType >
- operator<()
: AASequence
, BackgroundControl
, CentroidPeak
, ClusteredMS2ConsensusSpectrum
, Compomer
, ConsensusIsotopePattern
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >
, DataValue
, DPosition< D, TCoordinateType >
, EnzymaticDigestion::BindingSite
, FeatureFinderAlgorithmPickedHelperStructs::Seed
, FeatureLCProfile
, FTPeakDetectController
, GridBasedCluster
, ToolDescriptionInternal
, LCElutionPeak
, MassDecomposition
, Matrix< Value >
, MinimumDistance
, ModificationDefinition
, MS2ConsensusSpectrum
, MS2Feature
, MS2Fragment
, MS2Info
, MSPeak
, PILISCrossValidation::Peptide
, ProcessData
, ProteinIdentification::ProteinGroup
, QcMLFile::Attachment
, QcMLFile::QualityParameter
, QTCluster
, SparseVector< Value >
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::ValueProxy
, StopWatch
, SvmTheoreticalSpectrumGenerator::IonType
, TOPPASToolVertex::IOInfo
, VersionInfo::VersionDetails
, PeptideProteinMatchInformation
- operator<<
: AASequence
, AccurateMassSearchResult
, Adduct
, Compomer
, ControlledVocabulary
, DataValue
, DBoundingBox< D >
, DistanceMatrix< Value >
, Element
, EmpiricalFormula
, LogConfigHandler
, BasicStatistics< RealT >
, Matrix< Value >
, Peak2D
, RawData
, Residue
, StreamHandler
, SVOutStream
, TextFile
- operator<=()
: BackgroundControl
, ClusteredMS2ConsensusSpectrum
, ConsensusIsotopePattern
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >
, DPosition< D, TCoordinateType >
, FeatureLCProfile
, FTPeakDetectController
, LCElutionPeak
, MS2ConsensusSpectrum
, MS2Feature
, MS2Fragment
, MS2Info
, MSPeak
, ProcessData
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::ValueProxy
, StopWatch
- operator=()
: AASequence::ConstIterator
, AASequence::Iterator
, AASequence
, AccurateMassSearchResult
, Acquisition
, AcquisitionInfo
, Annotations1DContainer
, AnnotationStatistics
, AverageLinkage
, BackgroundIntensityBin
, BaseFeature
, BaseGroupFinder
, BaseModel< D >
, BaseSuperimposer
, BernNorm
, BiGaussFitter1D
, BiGaussModel
, BinaryTreeNode
, BinnedSharedPeakCount
, BinnedSpectralContrastAngle
, BinnedSpectrum
, BinnedSpectrumCompareFunctor
, BinnedSumAgreeingIntensities
, Bzip2Ifstream
, Bzip2InputStream
, CachedmzML
, CentroidPeak
, ChargePair
, ChromatogramPeak
, ChromatogramSettings
, ClusterAnalyzer
, ClusterFunctor
, ComplementFilter
, ComplementMarker
, CompleteLinkage
, CompNovoIdentification
, CompNovoIdentificationBase
, CompNovoIdentificationBase::Permut
, CompNovoIdentificationCID
, CompNovoIonScoring
, CompNovoIonScoringBase::IonScore
, CompNovoIonScoringBase
, CompNovoIonScoringCID
, Compomer
, CompressedInputSource
, ConsensusFeature
, ConsensusFeature::Ratio
, ConsensusID
, ConsensusIsotopePattern
, ConsensusMap
, ConsensusMapNormalizerAlgorithmMedian
, ConsensusMapNormalizerAlgorithmQuantile
, ConsensusMapNormalizerAlgorithmThreshold
, ConsoleUtils
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >
, ContactPerson
, ControlledVocabulary::CVTerm
, ConvexHull2D
, CVMappingFile
, CVMappingRule
, CVMappings
, CVMappingTerm
, CVReference
, CVTerm
, CVTerm::Unit
, CVTermList
, DataProcessing
, DataValue
, Date
, DateTime
, DBoundingBox< D >
, DeconvPeak
, DefaultParamHandler
, DeNovoAlgorithm
, DeNovoIdentification
, DeNovoIonScoring::IonScore
, DeNovoIonScoring
, DeNovoPostScoring
, DetectabilitySimulation
, DIAScoring
, Digestion
, DigestSimulation
, DistanceMatrix< Value >
, DocumentIdentifier
, DocumentIDTagger
, DPosition< D, TCoordinateType >
, DRange< D >
, EdwardsLippertIteratorTryptic
, EGHFitter1D
, EGHModel
, EGHTraceFitter
, Element
, ElementDB
, EmgFitter1D
, EmgModel
, EmpiricalFormula
, EnzymaticDigestion
, EuclideanSimilarity
, ExperimentalSettings
, ExtendedIsotopeFitter1D
, ExtendedIsotopeModel
, FalseDiscoveryRate
, FastaIterator
, FeaFiModule< PeakType >
, Feature
, FeatureDeconvolution
, FeatureDistance
, FeatureFinderAlgorithm
, FeatureFinderAlgorithmPicked
, FeatureGroupingAlgorithm
, FeatureGroupingAlgorithmIdentification
, FeatureGroupingAlgorithmLabeled
, FeatureGroupingAlgorithmQT
, FeatureGroupingAlgorithmUnlabeled
, FeatureHandle
, FeatureHypothesis
, FeatureLCProfile
, FeatureMap
, FilterFunctor
, Fitter1D
, FTPeakDetectController
, FuzzyStringComparator
, GaussFitter1D
, GaussModel
, GaussTraceFitter
, GoodDiffFilter
, Gradient
, GzipIfstream
, GzipInputStream
, HiddenMarkovModel
, HMMState
, HPLC
, IBSpectraFile
, IDDecoyProbability
, IDDecoyProbability::Transformation_
, Identification
, IdentificationHit
, IDMapper
, IDRipper
, IMSElement
, IMSIsotopeDistribution
, Weights
, IncludeExcludeTarget
, InspectInfile
, InspectOutfile
, Instrument
, InstrumentSettings
, IntensityBalanceFilter
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, DIntervalBase< D >
, FileMapping
, MappingParam
, MzDataValidator
, MzIdentMLDOMHandler
, MzIdentMLHandler
, MzIdentMLValidator
, MzMLValidator
, MzQuantMLHandler
, MzQuantMLValidator
, SemanticValidator
, ToolDescription
, ToolDescriptionHandler
, ToolDescriptionInternal
, TraMLHandler
, TraMLValidator
, InterpolationModel
, IonDetector
, IonizationSimulation
, IonSource
, IsobaricChannelExtractor
, IsobaricNormalizer
, IsobaricQuantifier
, IsobaricQuantifierStatistics
, IsotopeDiffFilter
, IsotopeDistribution
, IsotopeFitter1D
, IsotopeMarker
, IsotopeModel
, ItraqChannelExtractor
, ItraqEightPlexQuantitationMethod
, ItraqFourPlexQuantitationMethod
, ItraqQuantifier
, LabeledPairFinder
, LCElutionPeak
, LCMS
, LCMSCData
, LevMarqFitter1D
, LocalLinearMap
, LogConfigHandler
, MapAlignmentAlgorithm
, MapAlignmentAlgorithmIdentification
, MapAlignmentAlgorithmPoseClustering
, MapAlignmentAlgorithmSpectrumAlignment
, MapAlignmentEvaluationAlgorithm
, MapAlignmentEvaluationAlgorithmPrecision
, MapAlignmentEvaluationAlgorithmRecall
, MarkerMower
, MascotRemoteQuery
, MassAnalyzer
, MassDecomposition
, MassDecompositionAlgorithm
, MassExplainer
, MassTrace
, BasicStatistics< RealT >
, BilinearInterpolation< Key, Value >
, GammaDistributionFitter
, GaussFitter
, GumbelDistributionFitter
, Histogram< ValueType, BinSizeType >
, LinearInterpolation< Key, Value >
, LinearRegression
, PosteriorErrorProbabilityModel
, ROCCurve
, Matrix< Value >
, MaxLikeliFitter1D
, MetaInfo
, MetaInfoDescription
, MetaInfoInterface
, MetaInfoRegistry
, ModelDescription< D >
, Modification
, ModificationDefinition
, ModificationDefinitionsSet
, ModificationsDB
, MRMFeature
, MRMFragmentSelection
, MRMTransitionGroup< SpectrumType, TransitionType >
, MRMTransitionGroupPicker
, MS2ConsensusSpectrum
, MS2Fragment
, MS2Info
, MSChromatogram< PeakT >
, MSExperiment< PeakT, ChromatogramPeakT >
, MSPeak
, MSPFile
, MSQuantifications::AnalysisSummary
, MSQuantifications::Assay
, MSQuantifications
, MSSpectrum< PeakT >
, MultiGradient
, NeutralLossDiffFilter
, NeutralLossMarker
, NLargest
, Normalizer
, OMSSAXMLFile
, OnDiscMSExperiment< PeakT, ChromatogramPeakT >
, PenaltyFactors
, PenaltyFactorsIntensity
, OptimizePeakDeconvolution
, Param
, ParameterInformation
, ParentPeakMower
, Peak1D
, Peak2D
, PeakAlignment
, PeakIntensityPredictor
, PeakMarker
, PeakPickerMRM
, PeakShape
, PeakSpectrumCompareFunctor
, PepNovoInfile
, PepNovoOutfile
, PeptideEvidence
, PeptideHit
, PeptideIdentification
, PepXMLFile::AminoAcidModification
, PILISCrossValidation
, PILISCrossValidation::Option
, PILISCrossValidation::Peptide
, PILISIdentification
, PILISModel
, PILISModelGenerator
, PILISNeutralLossModel
, PILISScoring
, Precursor
, PrecursorIonSelectionPreprocessing
, ProcessData
, Product
, ProductModel< 2 >
, ProgressLogger
, ProteinHit
, ProteinIdentification
, ProteinInference
, ProteinResolver
, ProtonDistributionModel
, QcMLFile::Attachment
, QcMLFile::QualityParameter
, QuantitativeExperimentalDesign
, RangeManager< D >
, RawMSSignalSimulation
, RawTandemMSSignalSimulation
, ReactionMonitoringTransition
, Residue
, ResidueDB
, ResidueModification
, RichPeak1D
, RichPeak2D
, RTSimulation
, Sample
, SampleTreatment
, Scaler
, ScanWindow
, SequestInfile
, SequestOutfile
, SHFeature
, SignalToNoiseEstimator< Container >
, SignalToNoiseEstimatorMeanIterative< Container >
, SignalToNoiseEstimatorMedian< Container >
, SingleLinkage
, Software
, SourceFile
, SparseVector< Value >
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::ValueProxy
, SpectralMatch
, SpectraMerger
, SpectraSTSimilarityScore
, SpectrumAlignment
, SpectrumAlignmentScore
, SpectrumCheapDPCorr
, SpectrumIdentification
, SpectrumPrecursorComparator
, SpectrumSettings
, SqrtMower
, SteinScottImproveScore
, StopWatch
, StreamHandler
, StringListUtils
, SuperHirnParameters
, SvmTheoreticalSpectrumGenerator::IonType
, SvmTheoreticalSpectrumGenerator
, SvmTheoreticalSpectrumGeneratorSet
, SvmTheoreticalSpectrumGeneratorTrainer
, Tagging
, TargetedExperiment
, Compound
, Configuration
, Contact
, Instrument
, Peptide
, Prediction
, Protein
, Publication
, RetentionTime
, TraMLProduct
, TheoreticalSpectrumGenerator
, ThresholdMower
, TICFilter
, TMTSixPlexQuantitationMethod
, TMTTenPlexQuantitationMethod
, TOPPASEdge
, TOPPASInputFileListVertex
, TOPPASMergerVertex
, TOPPASOutputFileListVertex
, TOPPASResource
, TOPPASResources
, TOPPASToolVertex::IOInfo
, TOPPASToolVertex
, TOPPASVertex
, TraceFitter
, TransformationDescription
, TwoDOptimization
, UnimodXMLFile
, UniqueIdInterface
, WindowMower
, XTandemInfile
, XTandemXMLFile
, ZhangSimilarityScore
- operator==()
: AASequence::ConstIterator
, AASequence::Iterator
, AASequence
, Acquisition
, AcquisitionInfo
, Adduct
, AnnotationStatistics
, BackgroundControl
, BaseFeature
, BinnedSpectrum
, ChargePair
, ChromatogramPeak
, ChromatogramSettings
, ClusteredMS2ConsensusSpectrum
, Compomer
, ConsensusIsotopePattern
, ConsensusMap
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >
, ContactPerson
, ConvexHull2D
, CVMappingRule
, CVMappings
, CVMappingTerm
, CVReference
, CVTerm
, CVTerm::Unit
, CVTermList
, DataFilters::DataFilter
, DataProcessing
, DataValue
, DBoundingBox< D >
, DefaultParamHandler
, Digestion
, DistanceMatrix< Value >
, DocumentIdentifier
, DocumentIDTagger
, DPosition< D, TCoordinateType >
, DRange< D >
, Element
, EmpiricalFormula
, EnzymaticDigestion::BindingSite
, ExperimentalSettings
, FASTAFile::FASTAEntry
, Feature
, FeatureHandle
, FeatureLCProfile
, FeatureMap
, Gradient
, GridBasedCluster
, HashGrid< Cluster >::ConstIterator
, HashGrid< Cluster >::Iterator
, HPLC
, Identification
, IdentificationHit
, IMSElement
, IMSIsotopeDistribution
, IMSIsotopeDistribution::Peak
, IncludeExcludeTarget
, InspectInfile
, InspectOutfile
, Instrument
, InstrumentSettings
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, DIntervalBase< D >
, IntensityIteratorWrapper< IteratorT >
, ToolDescriptionInternal
, IonDetector
, IonSource
, IsotopeDistribution
, MassAnalyzer
, MassDecomposition
, Histogram< ValueType, BinSizeType >
, Matrix< Value >
, MetaInfo
, MetaInfoDescription
, MetaInfoInterface
, MinimumDistance
, ModelDescription< D >
, Modification
, ModificationDefinition
, ModificationDefinitionsSet
, MS2ConsensusSpectrum
, MS2Feature
, MS2Fragment
, MS2Info
, MSChromatogram< PeakT >
, MSExperiment< PeakT, ChromatogramPeakT >
, MSQuantifications
, MSSpectrum< PeakT >
, OnDiscMSExperiment< PeakT, ChromatogramPeakT >
, Param
, Param::ParamEntry
, Param::ParamIterator
, Param::ParamNode
, Peak1D
, Peak2D
, PeakIndex
, PeakShape
, PepNovoInfile
, PepNovoOutfile
, PeptideEvidence
, PeptideHit
, PeptideIdentification
, Precursor
, Product
, ProteinHit
, ProteinIdentification
, ProteinIdentification::ProteinGroup
, ProteinIdentification::SearchParameters
, QcMLFile::Attachment
, QcMLFile::QualityParameter
, RangeManager< D >
, ReactionMonitoringTransition
, Residue
, ResidueModification
, RichPeak1D
, RichPeak2D
, Sample
, SampleTreatment
, ScanWindow
, SequestInfile
, SequestOutfile
, SHFeature
, Software
, SourceFile
, SparseVector< Value >
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::ValueProxy
, SpectrumIdentification
, SpectrumSettings
, StopWatch
, SVMData
, Tagging
, TargetedExperiment
, Compound
, Contact
, CV
, Instrument
, Peptide
, Prediction
, Protein
, Publication
, RetentionTime
, TraMLProduct
, UniqueIdInterface
, VersionInfo::VersionDetails
, PeptideProteinMatchInformation
, FoundProteinFunctor
- operator>()
: BackgroundControl
, ClusteredMS2ConsensusSpectrum
, ConsensusIsotopePattern
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >
, DataValue
, DPosition< D, TCoordinateType >
, FeatureLCProfile
, FTPeakDetectController
, GridBasedCluster
, LCElutionPeak
, MinimumDistance
, MS2ConsensusSpectrum
, MS2Feature
, MS2Fragment
, MS2Info
, MSPeak
, ProcessData
, QcMLFile::Attachment
, QcMLFile::QualityParameter
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::ValueProxy
, StopWatch
, VersionInfo::VersionDetails
- operator>=()
: BackgroundControl
, ClusteredMS2ConsensusSpectrum
, ConsensusIsotopePattern
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >
, DPosition< D, TCoordinateType >
, FeatureLCProfile
, FTPeakDetectController
, LCElutionPeak
, MS2ConsensusSpectrum
, MS2Feature
, MS2Fragment
, MS2Info
, MSPeak
, ProcessData
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::ValueProxy
, StopWatch
- operator>>
: AASequence
- operator[]()
: AASequence
, ConstRefVector< ContainerT >
, ContinuousWaveletTransform
, DataFilters
, DPosition< D, TCoordinateType >
, Weights
, IntensityIteratorWrapper< IteratorT >
, Map< Key, T >
, MassTrace
, Histogram< ValueType, BinSizeType >
, MSExperiment< PeakT, ChromatogramPeakT >
, OnDiscMSExperiment< PeakT, ChromatogramPeakT >
, SparseVector< Value >
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
- opt_
: MzTabPeptideSectionRow
, MzTabProteinSectionRow
, MzTabPSMSectionRow
, MzTabSmallMoleculeSectionRow
- OPTIMAL
: LPWrapper
- optimization_
: PeakPickerCWT
- optimize()
: OptimizePeakDeconvolution
, OptimizePick
, TwoDOptimization
- optimize_()
: LevMarqFitter1D
, TraceFitter
- 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_
: ConsensusXMLFile
, DTA2DFile
, FeatureXMLFile
, FileHandler
, IndexedMzMLFileLoader
, MzDataHandler< MapType >
, MzMLHandler< MapType >
, MzXMLHandler< MapType >
, MzDataFile
, MzMLFile
, MzXMLFile
- OptPeakFunctor()
: OptimizePick::OptPeakFunctor
- OR
: CVMappingRule
- ORBITRAP
: MassAnalyzer
- order_
: IonDetector
, IonDetectorVisualizer
, IonSource
, IonSourceVisualizer
, MassAnalyzer
, MassAnalyzerVisualizer
, SavitzkyGolayFilter
- 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()
: TOPPASInputFileListVertex
, TOPPASToolVertex
, TOPPASVertex
- 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