- a -

• AcquisitionMode : IonDetector
• ActionMode : XMLHandler , TOPPASScene
• ActionModes : SpectrumCanvas
• ActivationMethod : Precursor
• AggregationMethod : BasicProteinInferenceAlgorithm
• Alignment : AxisPainter
• AnalyzerType : MassAnalyzer
• AnnotationState : BaseFeature
• Averagines : ExtendedIsotopeModel , IsotopeModel

- b -

• BoundaryCondition : BSpline2d
• ByteOrder : Base64

- c -

• CASE : ListUtils
• CHARGEMODE : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• ChecksumType : SourceFile
• ChromatogramType : ChromatogramSettings
• CombinationsLogic : CVMappingRule
• CopyOptions : File

- d -

• DataType : DataValue , LayerData
• DecoyTransitionType : ReactionMonitoringTransition
• DFS_COLOR : TOPPASVertex
• DimensionDescription : Peak2D
• DRangeIntersection : DRange< D >
• DrawModes : Spectrum1DCanvas
• DriftTimeUnit : Precursor

- e -

• EdgeStatus : TOPPASEdge
• ErrorUnit : XTandemInfile
• ExitCodes : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , PeptideIndexing , SimpleSearchEngineAlgorithm , TOPPBase , XFDRAlgorithm

- f -

• FilterOperation : DataFilters
• FilterType : DataFilters
• Flag : FeatureFinderDefs
• Flags : LayerData
• FLOATINDICES : PeakPickerMRM
• FragmentationType : ProtonDistributionModel

- g -

• GroupType : XTandemXMLFile

- i -

• InletType : IonSource
• IntensityModes : SpectrumCanvas
• IntensityThresholdCalculation : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• InterpolationMode : MultiGradient
• IonizationMethod : IonSource
• IONIZATIONMETHOD : RawMSSignalSimulation
• IonizationType : IonizationSimulation
• IonOpticsType : Instrument
• IOType : TOPPASToolVertex::IOInfo
• IsotopeType : CompNovoIonScoringBase
• IsotopeVariant : Tagging
• ITRAQ_TYPES : ItraqConstants

- l -

• LabelMode : Spectrum1DCanvas
• LabelType : LayerData
• LambdaScore : MRMFeatureSelector
• LOADDETAIL : XMLHandler
• LogState : TOPPASBase , TOPPViewBase
• LogType : ProgressLogger

- m -

• MassType : XTandemInfile
• Measure : IDMapper
• MissingDecoy : PeptideIndexing
• MODELTYPE : MZTrafoModel
• MT_QUANTMETHOD : MassTrace

- n -

• NASFragmentType : NASequence
• NormalizationMethod : ConsensusMapNormalizerAlgorithmMedian
• NumpressCompression : MSNumpressCoder

- p -

• ParameterTypes : ParameterInformation
• PeakMassType : ProteinIdentification
• PeptidePosition : OPXLDataStructs
• Polarity : IonSource
• ProcessingAction : DataProcessing
• PROFILESHAPE : RawMSSignalSimulation
• ProteinProteinCrossLinkType : OPXLDataStructs

- q -

• QUANT_TYPES : MSQuantifications
• QuotingMethod : String

- r -

• ReflectronState : MassAnalyzer
• RefreshStatus : TOPPASScene
• RequirementLevel : CVMappingRule
• Requires : QCBase
• ResidueType : Residue
• ResolutionMethod : MassAnalyzer
• RESOLUTIONMODEL : RawMSSignalSimulation
• ResolutionType : MassAnalyzer
• RETURN_STATUS : NonNegativeLeastSquaresSolver
• RETURNSTATE : ExternalProcess
• RTType : RetentionTime
• RTUnit : RetentionTime

- s -

• SampleState : Sample
• ScanDirection : MassAnalyzer
• ScanLaw : MassAnalyzer
• ScanMode : InstrumentSettings
• ScoreType : IDScoreSwitcherAlgorithm , PercolatorOutfile
• Sense : LPWrapper
• ShadeModes : Spectrum3DCanvas
• SIDE : Compomer
• SOLVER : LPWrapper
• SolverStatus : LPWrapper
• Sorted : IsotopeDistribution
• SourceClassification : ResidueModification
• Specificity : EnzymaticDigestion
• SpecificityType : Modification
• SpectrumType : SpectrumSettings
• SplitMeta : ConsensusMap
• StreamType : StreamHandler
• SUBSTREESTATUS : TOPPASVertex
• SVM_kernel_type : SVMWrapper
• SVM_parameter_type : SVMWrapper

- t -

• TermSpecificity : ResidueModification
• TermSpecificityNuc : Ribonucleotide
• ToleranceUnit : FragmentMassError
• TOOLSTATUS : TOPPASToolVertex
• Type : FileTypes , IonDetector , ListEditor , LPWrapper , PeakShape , PrecursorIonSelection
• type : ProteinResolver::ProteinEntry , ProteinResolver::ResolverResult

- u -

• UnitType : DataValue
• Unmatched : PeptideIndexing

- v -

• VariableType : LPWrapper , MRMFeatureSelector

- w -

• WEIGHTMODE : WeightWrapper
• WriteFormat : LPWrapper

- x -

• XRefType : ControlledVocabulary::CVTerm