Class Hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

• AAIndex
• AASequence
• FuzzyStringComparator::AbortComparison
• AcqusHandler
• Adduct
• PepXMLFile::AminoAcidModification
• MSQuantifications::AnalysisSummary
• Annotation1DItem
  • Annotation1DDistanceItem
  • Annotation1DPeakItem
  • Annotation1DTextItem
• Annotations1DContainer
• AScore
• MSQuantifications::Assay
• QcMLFile::Attachment
• AveragePosition< D >
• AxisPainter
• AxisTickCalculator
• BackgroundControl
• BackgroundIntensityBin
• Base64
• BaseException
  • BinnedSpectrum::NoSpectrumIntegrated
  • BinnedSpectrumCompareFunctor::IncompatibleBinning
  • ClusterFunctor::InsufficientInput
  • DBConnection::InvalidQuery
  • DBConnection::NotConnected
  • BufferOverflow
  • ConversionError
  • DepletedIDPool
  • DivisionByZero
  • ElementNotFound
  • FailedAPICall
  • FileEmpty
  • FileNotFound
  • FileNotReadable
  • FileNotWritable
  • IllegalArgument
  • IllegalPosition
  • IllegalSelfOperation
  • IllegalTreeOperation
  • IncompatibleIterators
  • IndexOverflow
  • IndexUnderflow
  • InvalidIterator
  • InvalidParameter
  • InvalidRange
  • InvalidSize
  • InvalidValue
  • IOException
  • MissingInformation
  • NotImplemented
  • NullPointer
  • OutOfGrid
  • OutOfMemory
  • OutOfRange
  • ParseError
  • Postcondition
  • Precondition
  • RequiredParameterNotGiven
  • SizeUnderflow
  • UnableToCalibrate
  • UnableToCreateFile
  • UnableToFit
  • UnregisteredParameter
  • WrongParameterType
  • FeatureFinderDefs::NoSuccessor
  • XMLHandler::EndParsingSoftly
  • Map< Key, T >::IllegalKey
  • UnnormalizedComparator
• BaseVisualizer< ObjectType >
• BaseVisualizer< Acquisition >
  • AcquisitionVisualizer
• BaseVisualizer< AcquisitionInfo >
  • AcquisitionInfoVisualizer
• BaseVisualizer< ContactPerson >
  • ContactPersonVisualizer
• BaseVisualizer< DataProcessing >
  • DataProcessingVisualizer
• BaseVisualizer< Digestion >
  • DigestionVisualizer
• BaseVisualizer< DocumentIdentifier >
  • DocumentIdentifierVisualizer
• BaseVisualizer< ExperimentalSettings >
  • ExperimentalSettingsVisualizer
• BaseVisualizer< Gradient >
  • GradientVisualizer
• BaseVisualizer< HPLC >
  • HPLCVisualizer
• BaseVisualizer< Instrument >
  • InstrumentVisualizer
• BaseVisualizer< InstrumentSettings >
  • InstrumentSettingsVisualizer
• BaseVisualizer< IonDetector >
  • IonDetectorVisualizer
• BaseVisualizer< IonSource >
  • IonSourceVisualizer
• BaseVisualizer< MassAnalyzer >
  • MassAnalyzerVisualizer
• BaseVisualizer< MetaInfoDescription >
  • MetaInfoDescriptionVisualizer
• BaseVisualizer< MetaInfoInterface >
  • MetaInfoVisualizer
• BaseVisualizer< Modification >
  • ModificationVisualizer
• BaseVisualizer< PeptideHit >
  • PeptideHitVisualizer
• BaseVisualizer< PeptideIdentification >
  • PeptideIdentificationVisualizer
• BaseVisualizer< Precursor >
  • PrecursorVisualizer
• BaseVisualizer< Product >
  • ProductVisualizer
• BaseVisualizer< ProteinHit >
  • ProteinHitVisualizer
• BaseVisualizer< ProteinIdentification >
  • ProteinIdentificationVisualizer
• BaseVisualizer< Sample >
  • SampleVisualizer
• BaseVisualizer< ScanWindow >
  • ScanWindowVisualizer
• BaseVisualizer< Software >
  • SoftwareVisualizer
• BaseVisualizer< SourceFile >
  • SourceFileVisualizer
• BaseVisualizer< SpectrumSettings >
  • SpectrumSettingsVisualizer
• BaseVisualizer< Tagging >
  • TaggingVisualizer
• BasicStatistics< RealT >
• BasicStatistics< Real >
  • AsymmetricStatistics< Real >
• BigString
• BilinearInterpolation< Key, Value >
• binary_function
  • BaseFeature::QualityLess
  • BinaryComposeFunctionAdapter< OP1, OP2, OP3 >
  • ChromatogramPeak::IntensityLess
  • ChromatogramPeak::PositionLess
  • ChromatogramPeak::RTLess
  • ConsensusFeature::MapsLess
  • ConsensusFeature::SizeLess
  • EqualInTolerance< CompareType >
  • FeatureHandle::IndexLess
  • IntensityLess< FeaFiModuleType >
  • LexicographicComparator< Cmp1, Cmp2 >
  • MSChromatogram< PeakT >::MZLess
  • MSSpectrum< PeakT >::RTLess
  • 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
  • PointerComparator< Cmp >
  • PrecursorIonSelection::SeqTotalScoreMore
  • PrecursorIonSelection::TotalScoreMore
  • PSLPFormulation::IndexLess
  • PSLPFormulation::ScanLess
  • PSLPFormulation::VariableIndexLess
  • ReactionMonitoringTransition::ProductMZLess
  • ReverseComparator< Cmp >
• MzMLHandler< MapType >::BinaryData
• BinaryDataArray
• BinaryTreeNode
• EnzymaticDigestion::BindingSite
• BinInputStream
  • Bzip2InputStream
  • GzipInputStream
• SILACFiltering::BlacklistEntry
• FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::BoxElement
• IsotopeWaveletTransform< PeakType >::BoxElement
• Bzip2Ifstream
• CentroidData
• CentroidPeak
  • DeconvPeak
• ItraqConstants::ChannelInfo
• IsotopeCluster::ChargedIndexSet
• ChargePair
• Chromatogram
• ChromatogramMeta
• ChromatogramPeak
• ChromatogramTools
• EnzymaticDigestion::CleavageModel
• ClusterAnalyzer
• ClusterFunctor
  • AverageLinkage
  • CompleteLinkage
  • SingleLinkage
• ClusterHierarchical
• CmpHypothesesByScore
• CmpMassTraceByMZ
• MapAlignmentAlgorithmSpectrumAlignment::Compare
• Compomer
• ConsensusIsotopePattern
• ConsensusMapNormalizerAlgorithmMedian
• ConsensusMapNormalizerAlgorithmQuantile
• ConsensusMapNormalizerAlgorithmThreshold
• AASequence::ConstIterator
• ConstRefVector< ContainerT >
• ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
  • ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
• RawMSSignalSimulation::ContaminantInfo
• ContinuousWaveletTransform
  • ContinuousWaveletTransformNumIntegration
• ControlledVocabulary
• ConvexHull2D
• cudaHelp
• CV
• CVMappingRule
• CVMappings
• CVMappingTerm
• CVReference
• SemanticValidator::CVTerm
• CVTerm
• ControlledVocabulary::CVTerm
• EGHFitter1D::Data
• EmgFitter1D::Data
• LmaGaussFitter1D::Data
• LmaIsotopeFitter1D::Data
• OptimizePeakDeconvolution::Data
• OptimizePick::Data
• TwoDOptimization::Data
• DataFilters::DataFilter
• DataFilterDialogTemplate
  • DataFilterDialog
• DataFilters
• DataValue
• DBAdapter
• DBConnection
• DefaultHandler
  • XMLHandler
    • ConsensusXMLFile
    • CVMappingFile
    • FeatureXMLFile
    • IdXMLFile
    • MascotXMLHandler
    • MzDataHandler< MapType >
    • MzIdentMLHandler
    • MzMLHandler< MapType >
    • MzQuantMLHandler
    • MzXMLHandler< MapType >
    • ParamXMLHandler
      • ToolDescriptionHandler
    • PTMXMLHandler
    • SemanticValidator
      • MzDataValidator
      • MzIdentMLValidator
      • MzMLValidator
      • MzQuantMLValidator
      • TraMLValidator
    • TraMLHandler
    • UnimodXMLHandler
    • XTandemInfileXMLHandler
    • OMSSAXMLFile
    • PepXMLFile
    • PepXMLFileMascot
    • ProtXMLFile
    • QcMLFile
    • TransformationXMLFile
    • XTandemXMLFile
• DefaultParamHandler
  • BaseModel< 1 >
    • InterpolationModel
      • BiGaussModel
      • EGHModel
      • EmgModel
      • ExtendedIsotopeModel
      • GaussModel
      • IsotopeModel
      • LmaGaussModel
      • LmaIsotopeModel
  • BaseModel< 2 >
    • ProductModel< 2 >
  • BaseGroupFinder
    • LabeledPairFinder
    • QTClusterFinder
    • SimplePairFinder
    • StablePairFinder
  • BaseLabeler
    • ICPLLabeler
    • ITRAQLabeler
    • LabelFreeLabeler
    • O18Labeler
    • SILACLabeler
  • BaseModel< D >
  • BaseSuperimposer
    • PoseClusteringAffineSuperimposer
    • PoseClusteringShiftSuperimposer
  • BernNorm
  • BinnedSpectrumCompareFunctor
    • BinnedSharedPeakCount
    • BinnedSpectralContrastAngle
    • BinnedSumAgreeingIntensities
  • CompNovoIdentificationBase
    • CompNovoIdentification
    • CompNovoIdentificationCID
  • CompNovoIonScoringBase
    • CompNovoIonScoring
    • CompNovoIonScoringCID
  • ConsensusID
  • DeNovoAlgorithm
  • DeNovoIdentification
  • DeNovoIonScoring
  • DeNovoPostScoring
  • DetectabilitySimulation
  • DiaPrescore
  • DIAScoring
  • DigestSimulation
  • ElutionPeakDetection
  • FalseDiscoveryRate
  • FeaFiModule< PeakType, FeatureType >
    • ModelFitter< PeakType, FeatureType >
    • SimpleExtender< PeakType, FeatureType >
    • SimpleSeeder< PeakType, FeatureType >
  • FeatureDeconvolution
  • FeatureDistance
  • FeatureFinderAlgorithm< PeakType, FeatureType >
    • FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >
    • FeatureFinderAlgorithmMRM< PeakType, FeatureType >
    • FeatureFinderAlgorithmPicked< PeakType, FeatureType >
    • FeatureFinderAlgorithmSH< PeakType, FeatureType >
    • FeatureFinderAlgorithmSimple< PeakType, FeatureType >
    • FeatureFinderAlgorithmSimplest< PeakType, FeatureType >
  • FeatureFindingMetabo
  • FeatureGroupingAlgorithm
    • FeatureGroupingAlgorithmIdentification
    • FeatureGroupingAlgorithmLabeled
    • FeatureGroupingAlgorithmQT
    • FeatureGroupingAlgorithmUnlabeled
  • FilterFunctor
    • ComplementFilter
    • GoodDiffFilter
    • IntensityBalanceFilter
    • IsotopeDiffFilter
    • NeutralLossDiffFilter
    • TICFilter
  • Fitter1D
    • LevMarqFitter1D
      • EGHFitter1D
      • EmgFitter1D
      • LmaGaussFitter1D
      • LmaIsotopeFitter1D
    • MaxLikeliFitter1D
      • BiGaussFitter1D
      • ExtendedIsotopeFitter1D
      • GaussFitter1D
      • IsotopeFitter1D
  • GaussFilter
  • IDDecoyProbability
  • IDEvaluationBase
  • IDMapper
  • IDRipper
  • InclusionExclusionList
  • InternalCalibration
  • IonizationSimulation
  • ItraqChannelExtractor
  • ItraqQuantifier
  • LinearResampler
    • LinearResamplerAlign
  • LowessSmoothing
  • MapAlignmentAlgorithm
    • MapAlignmentAlgorithmIdentification
    • MapAlignmentAlgorithmPoseClustering
    • MapAlignmentAlgorithmSpectrumAlignment
  • MarkerMower
  • MascotGenericFile
  • MascotRemoteQuery
  • MassDecompositionAlgorithm
  • MassTraceDetection
  • PosteriorErrorProbabilityModel
  • MorphologicalFilter
  • MRMFeatureFinderScoring
  • MRMFragmentSelection
  • MRMTransitionGroupPicker
  • MSPFile
  • MSSim
  • NLargest
  • Normalizer
  • OfflinePrecursorIonSelection
  • OptimizePeakDeconvolution
  • ParentPeakMower
  • PeakMarker
    • ComplementMarker
    • IsotopeMarker
    • NeutralLossMarker
  • PeakPickerCWT
  • PeakPickerHiRes
  • PeakPickerSH
  • PeakSpectrumCompareFunctor
    • CompareFouriertransform
    • PeakAlignment
    • SpectraSTSimilarityScore
    • SpectrumAlignmentScore
    • SpectrumCheapDPCorr
    • SpectrumPrecursorComparator
    • SteinScottImproveScore
    • ZhangSimilarityScore
  • PeptideAndProteinQuant
  • PILISCrossValidation
  • PILISIdentification
  • PILISModel
  • PILISModelGenerator
  • PILISNeutralLossModel
  • PILISScoring
  • PrecursorIonSelection
  • PrecursorIonSelectionPreprocessing
  • ProteinResolver
  • ProtonDistributionModel
  • PSLPFormulation
  • QuantitativeExperimentalDesign
  • RawMSSignalSimulation
  • RawTandemMSSignalSimulation
  • RTSimulation
  • SavitzkyGolayFilter
  • Scaler
  • SignalToNoiseEstimator< Container >
    • SignalToNoiseEstimatorMeanIterative< Container >
    • SignalToNoiseEstimatorMedian< Container >
  • SpectraIdentificationViewWidget
  • SpectraMerger
  • SpectraMerger::SpectraDistance_
  • SpectrumAlignment
  • SpectrumCanvas
    • Spectrum1DCanvas
    • Spectrum2DCanvas
    • Spectrum3DCanvas
  • SqrtMower
  • SvmTheoreticalSpectrumGenerator
  • SvmTheoreticalSpectrumGeneratorTrainer
  • TheoreticalSpectrumGenerator
  • ThresholdMower
  • TOFCalibration
  • TOPPASBase
  • TOPPViewBase
  • TraceFitter< PeakType >
    • EGHTraceFitter< PeakType >
    • GaussTraceFitter< PeakType >
  • TwoDOptimization
  • WindowMower
• Deisotoper
• SvmTheoreticalSpectrumGenerator::DescriptorSet
• DIntervalBase< D >
  • DRange< 1 >
  • DBoundingBox< D >
  • DRange< D >
• DistanceMatrix< Value >
• FeatureDistance::DistanceParams_
• DocumentIdentifier
  • ConsensusMap
  • ExperimentalSettings
    • MSExperiment< PeakT, ChromatogramPeakT >
    • MSQuantifications
  • FeatureMap< FeatureT >
• DocumentIDTagger
• DoubleList
• DPeak< dimensions >
• DPosition< D, TCoordinateType >
• DRichPeak< dimensions >
• DTAFile
• EDTAFile
• Element
• ElementDB
• EmgScoring
• EmpiricalFormula
• EnhancedTabBarWidgetInterface
  • SpectrumWidget
    • Spectrum1DWidget
    • Spectrum2DWidget
    • Spectrum3DWidget
  • TOPPASWidget
• EnzymaticDigestion
• EquivalenceClassAA_< T >
• ErrorHandler
  • XMLValidator
• EuclideanSimilarity
• FactoryBase
  • Factory< FactoryProduct >
• FASTAFile::FASTAEntry
• FASTAFile
• FeatureEditDialogTemplate
  • FeatureEditDialog
• FeatureFileOptions
• FeatureFinderAlgorithmPickedHelperStructs
• FeatureFinderAlgorithmSHCtrl
• FeatureFinderDefs
  • FeatureFinder
  • FeatureFinderAlgorithmMRM< PeakType, FeatureType >
  • FeatureFinderAlgorithmPicked< PeakType, FeatureType >
  • FeatureFinderAlgorithmSH< PeakType, FeatureType >
  • FeatureFinderAlgorithmSimple< PeakType, FeatureType >
  • FeatureFinderAlgorithmSimplest< PeakType, FeatureType >
  • Fitter1D
  • ModelFitter< PeakType, FeatureType >
  • SimpleExtender< PeakType, FeatureType >
  • SimpleSeeder< PeakType, FeatureType >
• FeatureHypothesis
• FeatureLCProfile
• IsotopeWavelet::fi_
• FidHandler
• File
• FileHandler
• FileMapping
• FileTypes
• FoundProteinFunctor
• FTPeakDetectController
• FuzzyStringComparator
• GammaDistributionFitter::GammaDistributionFitResult
• GammaDistributionFitter
• GaussFitter::GaussFitResult
• GaussFitter
• SignalToNoiseEstimator< Container >::GaussianEstimate
• GlobalExceptionHandler
• glp_prob
• Gradient
• GridFeature
• GumbelDistributionFitter::GumbelDistributionFitResult
• GumbelDistributionFitter
• GzipIfstream
• HashGrid< Cluster >
• HiddenMarkovModel
• HierarchicalClustering< PointRef >
• HierarchicalClustering< SILACPattern * >
  • SILACClustering
• Histogram< ValueType, BinSizeType >
• HMMState
• HPLC
• IDataFrameWriter
  • CSVWriter
  • DataMatrix
• IDFilter
• InclusionExclusionList::IEWindow
• IFeature
  • FeatureOpenMS
  • MockFeature
• ILPDCWrapper
• IMRMFeature
  • MRMFeatureOpenMS
  • MockMRMFeature
• IMSAlphabet
• IMSAlphabetParser< AlphabetElementType, Container, InputSource >
• IMSAlphabetParser<>
  • IMSAlphabetTextParser
• IMSElement
• IMSIsotopeDistribution
• PSLPFormulation::IndexTriple
• SimpleExtender< PeakType, FeatureType >::IndexWithPriority
• INIUpdater
• FuzzyStringComparator::InputLine
• InputSource
  • CompressedInputSource
• InspectInfile
• InspectOutfile
• IntensityIterator< FeaFiModuleType >
• IntList
• TOPPASToolVertex::IOInfo
• CompNovoIonScoringBase::IonScore
• DeNovoIonScoring::IonScore
• SvmTheoreticalSpectrumGenerator::IonType
• ProteinResolver::ISDGroup
• ISignalToNoise
  • SignalToNoiseOpenMS< PeakT >
  • MockSignalToNoise
• IsotopeCluster
• IsotopeDistribution
• IsotopeDistributionCache
• FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern
• IsotopeWavelet
• IsotopeWaveletParallelFor< PeakType, FeatureType >
• IsotopeWaveletTransform< PeakType >
• IsotopicDist
• ISpectrumAccess
  • SpectrumAccessOpenMS
  • SpectrumAccessOpenMSCached
• AASequence::Iterator
• iterator
  • HashGrid< Cluster >::ConstIterator
  • HashGrid< Cluster >::Iterator
  • AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
  • IntensityIteratorWrapper< IteratorT >
• ITransitionGroup
  • TransitionGroupOpenMS< SpectrumT, TransitionT >
  • MockTransitionGroup
• ItraqConstants
  • ItraqChannelExtractor
  • ItraqQuantifier
• ItraqQuantifier::ItraqQuantifierStats
• KroenikFile
• LayerData
• LayerStatisticsDialogTemplate
  • LayerStatisticsDialog
• LCElutionPeak
• LCMS
• LCMSCData
• LibSVMEncoder
• LightModification
• LightPeptide
• LightProtein
• LightTargetedExperiment
• LightTransition
• LinearInterpolation< Key, Value >
• LinearRegression
• LocalLinearMap::LLMParam
• LocalLinearMap
• LogStreamBuf::LogCacheStruct
• LogConfigHandler
• LogStream
• LogStreamNotifier
• LPWrapper
• Map< Key, T >
• MapAlignmentEvaluationAlgorithm
  • MapAlignmentEvaluationAlgorithmPrecision
  • MapAlignmentEvaluationAlgorithmRecall
• MapAlignmentTransformer
• MappingParam
• MarkerIonExtractor
• MassDecomposer< ValueType, DecompositionValueType >
  • IntegerMassDecomposer< ValueType, DecompositionValueType >
• MassDecomposition
• MassExplainer
• IMSAlphabet::MassSortingCriteria_
• MassTrace
• FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >
• FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >
• Matrix< Value >
• mean_and_stddev
• MetaInfo
• MetaInfoInterface
  • Acquisition
  • AcquisitionInfo
  • ChromatogramSettings
    • MSChromatogram< PeakT >
  • ConsensusMap
  • ConsensusMap::FileDescription
  • ContactPerson
  • CVTermList
    • IncludeExcludeTarget
    • Precursor
    • Product
    • ReactionMonitoringTransition
    • Software
    • SourceFile
    • Compound
    • Configuration
    • Contact
    • Instrument
    • Peptide
    • Peptide::Modification
    • Prediction
    • Protein
    • Publication
    • RetentionTime
    • TraMLProduct
  • DataProcessing
  • ExperimentalSettings
  • Identification
  • IdentificationHit
  • Instrument
  • InstrumentSettings
  • IonDetector
  • IonSource
  • MassAnalyzer
  • MetaInfoDescription
    • MSChromatogram< PeakT >::FloatDataArray
    • MSChromatogram< PeakT >::IntegerDataArray
    • MSChromatogram< PeakT >::StringDataArray
    • MSSpectrum< PeakT >::FloatDataArray
    • MSSpectrum< PeakT >::IntegerDataArray
    • MSSpectrum< PeakT >::StringDataArray
  • PeptideEvidence
  • PeptideHit
  • PeptideIdentification
  • ProteinHit
  • ProteinIdentification
  • ProteinIdentification::SearchParameters
  • RichPeak1D
  • RichPeak2D
    • BaseFeature
      • ConsensusFeature
      • Feature
        • MRMFeature
  • Sample
  • SampleTreatment
    • Digestion
    • Modification
      • Tagging
  • ScanWindow
  • SpectrumIdentification
  • SpectrumSettings
    • MSSpectrum<>
      • BinnedSpectrum
    • MSSpectrum< PeakT >
• MetaInfoRegistry
• LayerStatisticsDialog::MetaStatsValue_
• ModelDescription< D >
• ModificationDefinition
• ModificationDefinitionsSet
• ModificationMassesResult
• ModificationsDB
• ModifierRep
• MRMRTNormalizer
• MRMScoring
• MRMTransitionGroup< SpectrumType, TransitionType >
• MS1FeatureMerger
• MS1Signal
• MS2ConsensusSpectrum
  • ClusteredMS2ConsensusSpectrum
    • MS2Feature
• MS2Fragment
• MS2Info
• ProteinResolver::MSDGroup
• MsInspectFile
• MSPeak
• MultiGradient
• MzIterator< FeaFiModuleType >
• MzTab
• MzTabFile
• MzTabNAAbleInterface
  • MzTabModification
  • MzTabNAAbleBase
    • MzTabBoolean
    • MzTabDouble
    • MzTabDoubleList
    • MzTabInteger
    • MzTabModificationList
  • MzTabParameter
  • MzTabParameterList
  • MzTabSpectraRef
  • MzTabString
  • MzTabStringList
• MzTabPeptideSectionRow
• MzTabProteinSectionRow
• MzTabSmallMoleculeSectionRow
• MzTabSubIdMetaData
• MzTabUnitIdMetaData
• NonNegativeLeastSquaresSolver
• OMSSACSVFile
• OpenMSOSInfo
• OpenSwath_Scores
• OpenSwathDataAccessHelper
• OpenSwathHelper
• MS1FeatureMerger::OPERATOR_FEATURE_TR
• LCMS::OPERATOR_FeatureCompare
• LCMS::OPERATOR_MZ
• OptimizePick
• PILISCrossValidation::Option
• pair
  • HierarchicalClustering< PointRef >::BoundingBox
• Param
• ParamEditorTemplate
  • ParamEditor
• Param::ParamEntry
• ParameterInformation
• Param::ParamIterator
• Param::ParamNode
• IMSIsotopeDistribution::Peak
• Peak1D
  • Precursor
  • RichPeak1D
• Peak2D
  • FeatureHandle
    • FeatureHandle::FeatureHandleMutable_
  • RichPeak2D
• PeakPickerCWT::PeakArea_
• PeakFileOptions
• PeakIndex
• PeakIntensityPredictor
• PeakShape
• PeakTypeEstimator
• PeakWidthEstimator
• PenaltyFactors
  • PenaltyFactorsIntensity
• PepIterator
  • EdwardsLippertIterator
    • EdwardsLippertIteratorTryptic
  • FastaIterator
  • FastaIteratorIntern
  • TrypticIterator
• PepNovoInfile
• PepNovoOutfile
• PILISCrossValidation::Peptide
• Peptide
• PeptideAndProteinQuant::PeptideData
• ProteinResolver::PeptideEntry
• CompNovoIdentificationBase::Permut
• PersistentObject
  • MSSpectrum<>
  • MSChromatogram< PeakT >
  • MSExperiment< PeakT, ChromatogramPeakT >
  • MSSpectrum< PeakT >
• PeakShape::PositionLess
• PrecisionWrapper< FloatingPointType >
• FuzzyStringComparator::PrefixInfo_
• SimpleExtender< PeakType, FeatureType >::IndexWithPriority::PriorityLess
• ProbablePhosphoSites
• ProcessData
• ProgressLogger
  • AverageLinkage
  • BaseGroupFinder
  • BaseSuperimposer
  • CachedmzML
  • ChromatogramExtractor
  • CompleteLinkage
  • ConsensusXMLFile
  • DTA2DFile
  • ElutionPeakDetection
  • FeatureFinder
  • FeatureFindingMetabo
  • FeatureXMLFile
  • GaussFilter
  • InternalCalibration
  • IonizationSimulation
  • LinearResampler
  • MapAlignmentAlgorithm
  • MascotGenericFile
  • MascotInfile
  • MassTraceDetection
  • MorphologicalFilter
  • MRMDecoy
  • MRMFeatureFinderScoring
  • MS2File
  • MSSim
  • MzDataFile
  • MzIdentMLFile
  • MzMLFile
  • MzQuantMLFile
  • MzXMLFile
  • PeakPickerCWT
  • PeakPickerHiRes
  • PeakPickerSH
  • QcMLFile
  • RawMSSignalSimulation
  • SavitzkyGolayFilter
  • SignalToNoiseEstimator< Container >
  • SILACFiltering
  • SingleLinkage
  • SVMWrapper
  • TOFCalibration
  • ToolDescriptionFile
  • TraMLFile
  • TransitionTSVReader
  • XMassFile
• Protein
• PeptideAndProteinQuant::ProteinData
• ProteinResolver::ProteinEntry
• ProteinIdentification::ProteinGroup
• ProteinInference
• PSProteinInference
• QApplication
  • QApplicationTOPP
• QDate
  • Date
• QDateTime
  • DateTime
• QDialog
  • DataFilterDialog
  • DBOpenDialog
  • FeatureEditDialog
  • HistogramDialog
  • Spectrum1DPrefDialog
  • Spectrum2DPrefDialog
  • Spectrum3DPrefDialog
  • TOPPViewPrefDialog
  • LayerStatisticsDialog
  • ListEditor
  • MetaDataBrowser
  • SaveImageDialog
  • Spectrum1DGoToDialog
  • Spectrum2DGoToDialog
  • SpectrumAlignmentDialog
  • TheoreticalSpectrumGenerationDialog
  • ToolsDialog
  • TOPPASInputFileDialog
  • TOPPASInputFilesDialog
  • TOPPASIOMappingDialog
  • TOPPASOutputFilesDialog
  • TOPPASToolConfigDialog
  • TOPPASVertexNameDialog
  • TOPPViewOpenDialog
• QFileSystemWatcher
  • FileWatcher
• QGLWidget
  • Spectrum3DOpenGLCanvas
• QGraphicsItem
  • TOPPASEdge
  • TOPPASVertex
    • TOPPASInputFileListVertex
    • TOPPASMergerVertex
    • TOPPASOutputFileListVertex
    • TOPPASToolVertex
• QGraphicsScene
  • TOPPASScene
• QGraphicsView
  • TOPPASWidget
• QItemDelegate
  • ListEditorDelegate
  • ParamEditorDelegate
• QListWidget
  • ListTable
• QMainWindow
  • IDEvaluationBase
  • INIFileEditorWindow
  • TOPPASBase
  • TOPPViewBase
• QObject
  • MascotRemoteQuery
  • TOPPASEdge
  • TOPPASResource
  • TOPPASResources
  • TOPPASVertex
  • TOPPViewBehaviorInterface
    • TOPPViewIdentificationViewBehavior
    • TOPPViewSpectraViewBehavior
• QProcess
  • FakeProcess
• QTabBar
  • EnhancedTabBar
  • TOPPASTabBar
• QTCluster
• QTextEdit
  • TOPPASLogWindow
• QTreeWidget
  • ParamTree
  • TOPPASTreeView
• QcMLFile::QualityParameter
• QWidget
  • AxisWidget
  • BaseVisualizerGUI
    • AcquisitionInfoVisualizer
    • AcquisitionVisualizer
    • ContactPersonVisualizer
    • DataProcessingVisualizer
    • DigestionVisualizer
    • DocumentIdentifierVisualizer
    • ExperimentalSettingsVisualizer
    • GradientVisualizer
    • HPLCVisualizer
    • InstrumentSettingsVisualizer
    • InstrumentVisualizer
    • IonDetectorVisualizer
    • IonSourceVisualizer
    • MassAnalyzerVisualizer
    • MetaInfoDescriptionVisualizer
    • MetaInfoVisualizer
    • ModificationVisualizer
    • PeptideHitVisualizer
    • PeptideIdentificationVisualizer
    • PrecursorVisualizer
    • ProductVisualizer
    • ProteinHitVisualizer
    • ProteinIdentificationVisualizer
    • SampleVisualizer
    • ScanWindowVisualizer
    • SoftwareVisualizer
    • SourceFileVisualizer
    • SpectrumSettingsVisualizer
    • TaggingVisualizer
  • ColorSelector
  • HistogramWidget
  • MultiGradientSelector
  • ParamEditor
  • SpectraIdentificationViewWidget
  • SpectraViewWidget
  • SpectrumCanvas
  • SpectrumWidget
• QWorkspace
  • EnhancedWorkspace
• RangeManager< D >
• RangeManager< 1 >
  • MSSpectrum<>
  • MSChromatogram< PeakT >
  • MSSpectrum< PeakT >
• RangeManager< 2 >
  • ConsensusMap
  • FeatureMap< FeatureT >
  • MSExperiment< PeakT, ChromatogramPeakT >
• ConsensusFeature::Ratio
• RawData
• RealMassDecomposer
• Base64::Reinterpreter32_
• Base64::Reinterpreter64_
• Residue
• ResidueDB
• ResidueModification
• ProteinResolver::ResolverResult
• PeakWidthEstimator::Result
• RNPxlReportRow
• RNPxlReportRowHeader
• ROCCurve
• RtIterator< FeaFiModuleType >
• SAValue< Index< StringSet< Peptide >, IndexWotd<> > >
• ProteinHit::ScoreLess
• PeptideHit::ScoreLess
• ProteinHit::ScoreMore
• PeptideHit::ScoreMore
• FeatureFinderAlgorithmPickedHelperStructs::Seed
• SeedListGenerator
• SequestInfile
• SequestOutfile
• SHFeature
• SILACFilter
• SILACPoint
  • SILACPattern
• SimpleOpenMSSpectraFactory
• SimRandomNumberGenerator
• ROCCurve::simsortdec
• SingletonRegistry
• LPWrapper::SolverParam
• SparseVector< Value >
• SparseVector< Value >::SparseVectorConstIterator
• SparseVector< Value >::SparseVectorConstReverseIterator
• SparseVector< Value >::SparseVectorIterator
• SparseVector< Value >::SparseVectorReverseIterator
• SpecArrayFile
• Spectrum
• Spectrum1DGoToDialogTemplate
  • Spectrum1DGoToDialog
• Spectrum1DPrefDialogTemplate
  • Spectrum1DPrefDialog
• Spectrum2DGoToDialogTemplate
  • Spectrum2DGoToDialog
• Spectrum2DPrefDialogTemplate
  • Spectrum2DPrefDialog
• Spectrum3DPrefDialogTemplate
  • Spectrum3DPrefDialog
• SpectrumAddition
• SpectrumAlignmentDialogTemplate
  • SpectrumAlignmentDialog
• SILACFiltering::SpectrumInterpolation
• SpectrumMeta
• PeptideAndProteinQuant::Statistics
• StopWatch
• streambuf
  • LogStreamBuf
• FuzzyStringComparator::StreamElement_
• StreamHandler
• LogStreamBuf::StreamStruct
• String
• StringList
  • TextFile
    • CsvFile
• StringManager
• SuffixArray
  • SuffixArraySeqan
    • SuffixArrayTrypticSeqan
  • SuffixArrayTrypticCompressed
• Summary
• SuperHirnParameters
• SuperHirnUtil
• SVMData
• SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• SvmTheoreticalSpectrumGeneratorSet
• SVOutStream
• TargetedExperiment
• TargetedExperiment
• FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern
• TheoreticalSpectrumGenerationDialogTemplate
  • TheoreticalSpectrumGenerationDialog
• ToolDescriptionInternal
  • ToolDescription
• ToolExternalDetails
• ToolHandler
• TOPPASInputFileDialogTemplate
  • TOPPASInputFileDialog
• TOPPASInputFilesDialogTemplate
  • TOPPASInputFilesDialog
• TOPPASIOMappingDialogTemplate
  • TOPPASIOMappingDialog
• TOPPASOutputFilesDialogTemplate
  • TOPPASOutputFilesDialog
• TOPPASVertexNameDialogTemplate
  • TOPPASVertexNameDialog
• TOPPBase
  • TOPPRNPxl
  • TOPPRNPxlXICFilter
• TOPPASScene::TOPPProcess
• TOPPViewOpenDialogTemplate
  • TOPPViewOpenDialog
• TOPPViewPrefDialogTemplate
  • TOPPViewPrefDialog
• Param::ParamIterator::TraceInfo
• IDDecoyProbability::Transformation_
• TransformationDescription
• TransformationModel
  • TransformationModelBSpline
  • TransformationModelInterpolated
  • TransformationModelLinear
• TransitionHelper
• IsotopeWaveletTransform< PeakType >::TransSpectrum
• HierarchicalClustering< PointRef >::TreeDistance
• HierarchicalClustering< PointRef >::TreeNode
• TransitionTSVReader::TSVTransition
• unary_function
  • HasActivationMethod< SpectrumType >
  • HasMetaValue< MetaContainer >
  • HasPrecursorCharge< SpectrumType >
  • HasScanMode< SpectrumType >
  • InIntensityRange< PeakType >
  • InMSLevelRange< SpectrumType >
  • InMzRange< PeakType >
  • InPrecursorMZRange< SpectrumType >
  • InRTRange< SpectrumType >
  • IsEmptySpectrum< SpectrumType >
  • IsZoomSpectrum< SpectrumType >
  • UnaryComposeFunctionAdapter< OP1, OP2 >
  • mySqrt
• UniqueIdGenerator
• UniqueIdIndexer< RandomAccessContainer >
• UniqueIdIndexer< ConsensusMap >
  • ConsensusMap
• UniqueIdIndexer< FeatureMap< FeatureT > >
  • FeatureMap< FeatureT >
• UniqueIdInterface
  • ConsensusMap
  • FeatureHandle
  • FeatureMap< FeatureT >
  • RichPeak2D
• CVTerm::Unit
• unordered_multimap
  • HierarchicalClustering< PointRef >::Cluster
• SparseVector< Value >::ValueProxy
• VersionInfo::VersionDetails
• VersionInfo
• TOPPASVertex::VertexRoundPackage
• Weights
• WeightWrapper
  • SuffixArrayPeptideFinder
  • SuffixArraySeqan
  • SuffixArrayTrypticCompressed
• InclusionExclusionList::WindowDistance_
• XMLFile
  • ConsensusXMLFile
  • CVMappingFile
  • FeatureXMLFile
  • IdXMLFile
  • SemanticValidator
  • MascotXMLFile
  • MzDataFile
  • MzIdentMLFile
  • MzMLFile
  • MzQuantMLFile
  • MzXMLFile
  • OMSSAXMLFile
  • ParamXMLFile
  • PepXMLFile
  • PepXMLFileMascot
  • ProtXMLFile
  • PTMXMLFile
  • QcMLFile
  • ToolDescriptionFile
  • TraMLFile
  • TransformationXMLFile
  • UnimodXMLFile
  • XTandemInfile
  • XTandemXMLFile
• XMLFormatTarget
  • OpenMSXMLFormatTarget
• XTandemInfileNote
• double
• FeatureT
• FloatDataArray
• Int
• IntegerDataArray
• MassTrace< PeakType >
• MSSpectrum< PeakT >
• PeakT
• Real
• StringDataArray
• unsigned int