 AAIndex | Representation of selected AAIndex properties |
 AASequence | Representation of a peptide/protein sequence |
 FuzzyStringComparator::AbortComparison | Internal exception class |
 AccurateMassSearchResult | |
 AcqusHandler | Read-only acqus File handler for XMass Analysis |
 Adduct | |
 AdductInfo | |
 PepXMLFile::AminoAcidModification | |
 MzIdentMLDOMHandler::AnalysisSoftware | |
 MSQuantifications::AnalysisSummary | |
 Annotation1DItem | An abstract class acting as an interface for the different 1D annotation items |
  Annotation1DCaret | An annotation item which paints a set of carets on the canvas |
  Annotation1DDistanceItem | An annotation item which represents a measured distance between two peaks |
  Annotation1DPeakItem | A peak annotation item |
  Annotation1DTextItem | An annotation item which represents an arbitrary text on the canvas |
 AnnotationStatistics | |
 AScore | Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the most probable phosphorylation-site(s). For each phosphorylation site a probability score is calculated. The algorithm is implemented according to Beausoleil et al |
 MSQuantifications::Assay | |
 QcMLFile::Attachment | Representation of an attachment |
 AveragePosition< D > | Maintain an average position by summing up positions with weights |
 AxisPainter | Draws a coordinate axis. It has only static methods, that's why the constructor is private |
 AxisTickCalculator | Calculates ticks for a given value range |
 BackgroundControl | |
 BackgroundIntensityBin | |
 Base64 | Class to encode and decode Base64 |
 BaseVisualizer< ObjectType > | A base class for all visualizer classes |
 BaseVisualizer< Acquisition > | |
  AcquisitionVisualizer | Class that displays all meta information for Acquisition objects |
 BaseVisualizer< AcquisitionInfo > | |
  AcquisitionInfoVisualizer | Class that displays all meta information for AcquisitionInfo objects |
 BaseVisualizer< ContactPerson > | |
  ContactPersonVisualizer | Class that displays all meta information for ContactPerson objects |
 BaseVisualizer< DataProcessing > | |
  DataProcessingVisualizer | Class that displays all meta information for DataProcessing objects |
 BaseVisualizer< Digestion > | |
  DigestionVisualizer | Class that displays all meta information of digestion objects |
 BaseVisualizer< DocumentIdentifier > | |
  DocumentIdentifierVisualizer | Class that displays all meta information for DocumentIdentifier objects |
 BaseVisualizer< ExperimentalSettings > | |
  ExperimentalSettingsVisualizer | Class that displays all meta information for ExperimentalSettings objects |
 BaseVisualizer< Gradient > | |
  GradientVisualizer | GradientVisualizer is a visualizer class for objects of type gradient |
 BaseVisualizer< HPLC > | |
  HPLCVisualizer | Class that displays all meta information for HPLC objects |
 BaseVisualizer< Instrument > | |
  InstrumentVisualizer | Class that displays all meta information for an MS instrument |
 BaseVisualizer< InstrumentSettings > | |
  InstrumentSettingsVisualizer | Class that displays all meta information for InstrumentSettings objects |
 BaseVisualizer< IonDetector > | |
  IonDetectorVisualizer | Class that displays all meta information for IonDetector objects |
 BaseVisualizer< IonSource > | |
  IonSourceVisualizer | Class that displays all meta information for IonSource objects |
 BaseVisualizer< MassAnalyzer > | |
  MassAnalyzerVisualizer | Class that displays all meta information for MassAnalyzer objects |
 BaseVisualizer< MetaInfoDescription > | |
  MetaInfoDescriptionVisualizer | Class that displays all meta information for MetaInfoDescription objects |
 BaseVisualizer< MetaInfoInterface > | |
  MetaInfoVisualizer | MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member |
 BaseVisualizer< Modification > | |
  ModificationVisualizer | Class that displays all meta information of modification objects |
 BaseVisualizer< PeptideHit > | |
  PeptideHitVisualizer | Class that displays all meta information for PeptideHit objects |
 BaseVisualizer< PeptideIdentification > | |
  PeptideIdentificationVisualizer | Class that displays all meta information for PeptideIdentification objects |
 BaseVisualizer< Precursor > | |
  PrecursorVisualizer | Class that displays all meta information for Precursor objects |
 BaseVisualizer< Product > | |
  ProductVisualizer | Class that displays all meta information for Product objects |
 BaseVisualizer< ProteinHit > | |
  ProteinHitVisualizer | Class that displays all meta information for ProteinHit objects |
 BaseVisualizer< ProteinIdentification > | |
  ProteinIdentificationVisualizer | Class that displays all meta information for ProteinIdentification objects |
 BaseVisualizer< Sample > | |
  SampleVisualizer | Class that displays all meta information of sample objects |
 BaseVisualizer< ScanWindow > | |
  ScanWindowVisualizer | Class that displays all meta information for ScanWindow objects |
 BaseVisualizer< Software > | |
  SoftwareVisualizer | Class that displays all meta information for Software objects |
 BaseVisualizer< SourceFile > | |
  SourceFileVisualizer | Class that displays all meta information for SourceFile objects |
 BaseVisualizer< SpectrumSettings > | |
  SpectrumSettingsVisualizer | Class that displays all meta information for SpectrumSettings objects |
 BaseVisualizer< Tagging > | |
  TaggingVisualizer | Class that displays all meta information of tagging objects |
 basic_string< Char > | STL class |
  string | STL class |
   String | A more convenient string class |
 BasicStatistics< RealT > | Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation |
  AsymmetricStatistics< RealT > | Internal class for asymmetric distributions |
 BasicStatistics< CoordinateType > | |
 BigString | Concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $) |
 BilinearInterpolation< Key, Value > | Provides access to bilinearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero |
 binary_function | |
  BaseFeature::QualityLess | Compare by quality |
  BinaryComposeFunctionAdapter< OP1, OP2, OP3 > | Represents the binary compose function object adapter |
  ChromatogramPeak::IntensityLess | Comparator by intensity |
  ChromatogramPeak::PositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for RTLess |
  ChromatogramPeak::RTLess | Comparator by RT position |
  ConsensusFeature::MapsLess | Compare by the sets of consensus elements (lexicographically) |
  ConsensusFeature::SizeLess | Compare by size(), the number of consensus elements |
  EqualInTolerance< CompareType > | Struct for binary predicate to consider equality with a certain tolerance |
  FeatureHandle::IndexLess | Comparator by map and unique id |
  FloatsWithTolLess | Comparator for two doubles with a tolerance value |
  IntensityLess< FeaFiModuleType > | Comparator that allows to compare the indices of two peaks by their intensity |
  IntsInRangeLess | Comparator for two doubles with a tolerance value |
  LexicographicComparator< Cmp1, Cmp2 > | A wrapper class that combines two comparators lexicographically. Normally you should use the make-function lexicographicComparator() because then you do not need to specify the template arguments |
  MSChromatogram< PeakT >::MZLess | Comparator for the retention time |
  MSSpectrum< PeakT >::RTLess | Comparator for the retention time |
  PairComparatorFirstElement< PairType > | Class for comparison of std::pair using first ONLY e.g. for use with std::sort |
  PairComparatorFirstElementMore< PairType > | Class for comparison of std::pair using first ONLY e.g. for use with std::sort |
  PairComparatorSecondElement< PairType > | Class for comparison of std::pair using second ONLY e.g. for use with std::sort |
  PairComparatorSecondElementMore< PairType > | Class for comparison of std::pair using second ONLY e.g. for use with std::sort |
  PairMatcherFirstElement< PairType > | Class for comparison of std::pair using first ONLY e.g. for use with std::sort |
  PairMatcherSecondElement< PairType > | Struct for comparison of std::pair using second ONLY e.g. for use with std::sort |
  Peak1D::IntensityLess | |
  Peak1D::MZLess | Comparator by m/z position |
  Peak1D::PositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for MZLess |
  Peak2D::IntensityLess | |
  Peak2D::MZLess | Comparator by m/z position |
  Peak2D::PositionLess | Comparator by position. Lexicographical comparison (first RT then m/z) is done |
  Peak2D::RTLess | Comparator by RT position |
  PointerComparator< Cmp > | Wrapper that takes a comparator for `something' and makes a comparator for pointers to `something' out of it. Normally you should use the make-function pointerComparator() because then you do not need to specify the template arguments |
  PrecursorIonSelection::SeqTotalScoreMore | Compare by score |
  PrecursorIonSelection::TotalScoreMore | Compare by score |
  PSLPFormulation::IndexLess | |
  PSLPFormulation::ScanLess | |
  PSLPFormulation::VariableIndexLess | |
  ReactionMonitoringTransition::ProductMZLess | Comparator by Product ion MZ |
  ReverseComparator< Cmp > | Wrapper that reverses (exchanges) the two arguments of a comparator. Normally you should use the make-function reverseComparator() because then you do not need to specify the template arguments |
 MzMLHandlerHelper::BinaryData | Binary data representation |
 BinaryDataArray | The datastructures used by the OpenSwath interfaces |
 BinaryTreeNode | Elements of a binary tree used to represent a hierarchical clustering process |
 EnzymaticDigestion::BindingSite | |
 BinInputStream | |
  Bzip2InputStream | Implements the BinInputStream class of the xerces-c library in order to read bzip2 compressed XML files |
  GzipInputStream | Implements the BinInputStream class of the xerces-c library in order to read gzip compressed XML files |
 BinnedSpectrum | This is a binned representation of a PeakSpectrum |
 MultiplexFiltering::BlackListEntry | Structure for peak blacklisting |
 FeatureFinderAlgorithmIsotopeWavelet::BoxElement | Internally used data structure for the sweep line algorithm |
 IsotopeWaveletTransform< PeakType >::BoxElement | Internally used data structure |
 BSpline< T > | |
 BSpline2d | B spline interpolation |
 BSpline< double > | |
 Bzip2Ifstream | Decompresses files which are compressed in the bzip2 format (*.bz2) |
 CentroidData | |
 CentroidPeak | |
  DeconvPeak | |
 ItraqConstants::ChannelInfo | Stores information on an iTRAQ channel |
 ChargePair | Representation of a (putative) link between two Features, which stem from the same compound but have different charge (including different adduct ions (H+, Na+, ..) |
 Chromatogram | A single chromatogram |
 MzMLHandler< MapType >::ChromatogramData | Data necessary to generate a single chromatogram |
 ChromatogramMeta | Identifying information for a chromatogram |
 ChromatogramPeak | A 1-dimensional raw data point or peak for chromatograms |
 ChromatogramTools | Conversion class to convert chromatograms |
 OpenSwathWorkflow::ChromExtractParams | ChromatogramExtractor parameters |
 EnzymaticDigestion::CleavageModel | |
 ClusterAnalyzer | Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's) |
 ClusterFunctor | Base class for cluster functors |
  AverageLinkage | AverageLinkage ClusterMethod |
  CompleteLinkage | CompleteLinkage ClusterMethod |
  SingleLinkage | SingleLinkage ClusterMethod |
 ClusterHierarchical | Hierarchical clustering with generic clustering functions |
 ClusteringGrid | Data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering |
 CmpHypothesesByScore | |
 CmpMassTraceByMZ | Method for the assembly of mass traces belonging to the same isotope pattern, i.e., that are compatible in retention times, mass-to-charge ratios, and isotope abundances |
 MapAlignmentAlgorithmSpectrumAlignment::Compare | Innerclass necessary for using the sort algo |
 AccurateMassSearchEngine::CompareEntryAndMass_ | |
 Compomer | Holds information on an edge connecting two features from a (putative) charge ladder |
 ConsensusIsotopePattern | |
 ConsensusMapNormalizerAlgorithmMedian | Algorithms of ConsensusMapNormalizer |
 ConsensusMapNormalizerAlgorithmQuantile | Algorithms of ConsensusMapNormalizer |
 ConsensusMapNormalizerAlgorithmThreshold | Algorithms of ConsensusMapNormalizer |
 ConsoleUtils | |
 set< K >::const_iterator | STL iterator class |
  IntensityIterator< FeaFiModuleType > | Intensity iterator for a FeatureFinderDefs::IndexSet |
  MzIterator< FeaFiModuleType > | M/z iterator for a FeatureFinderDefs::IndexSet |
  RtIterator< FeaFiModuleType > | Retention time iterator for a FeatureFinderDefs::IndexSet |
 AASequence::ConstIterator | ConstIterator for AASequence |
 ConstRefVector< ContainerT > | This vector holds pointer to the elements of another container |
 ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > | ConstIterator for the ConstRefVector |
  ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > | Mutable iterator for the ConstRefVector |
 MSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, addMassTraces > | Helper class to add either general data points in set2DData or use mass traces from meta values |
 MSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, false > | |
 MSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, true > | |
 RawMSSignalSimulation::ContaminantInfo | |
 ContinuousWaveletTransform | This class is the base class of the continuous wavelet transformation |
  ContinuousWaveletTransformNumIntegration | This class computes the continuous wavelet transformation using a marr wavelet |
 ControlledVocabulary | Representation of a controlled vocabulary |
 ConvexHull2D | A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling |
 CubicSpline2d | Cubic spline interpolation as described in R.L. Burden, J.D. Faires, Numerical Analysis, 4th ed. PWS-Kent, 1989, ISBN 0-53491-585-X, pp. 126-131 |
 CV | |
 CVMappingRule | Representation of a CV Mapping rule used by CVMappings |
 CVMappings | Representation of controlled vocabulary mapping rules (for PSI formats) |
 CVMappingTerm | Representation of controlled vocabulary term |
 CVReference | Controlled Vocabulary Reference |
 ControlledVocabulary::CVTerm | Representation of a CV term |
 SemanticValidator::CVTerm | Representation of a parsed CV term |
 CVTerm | Representation of controlled vocabulary term |
 TwoDOptimization::Data | Helper struct (contains the size of an area and a raw data container) |
 EGHFitter1D::Data | Helper struct (contains the size of an area and a raw data container) |
 EmgFitter1D::Data | Helper struct (contains the size of an area and a raw data container) |
 OptimizePeakDeconvolution::Data | Class containing the data needed for optimization |
 OptimizePick::Data | |
 MzIdentMLDOMHandler::DatabaseInput | |
 DataFilters::DataFilter | Representation of a peak/feature filter combining FilterType, FilterOperation and a value |
 DataFilterDialogTemplate | |
  DataFilterDialog | Dialog for creating and changing a DataFilter |
 DataFilters | DataFilter array providing some convenience functions |
 DataValue | Class to hold strings, numeric values, lists of strings and lists of numeric values |
 MzIdentMLDOMHandler::DBSequence | |
 DefaultHandler | |
  XMLHandler | Base class for XML handlers |
   MzMLHandler< MSExperiment<> > | |
    MSDataWritingConsumer | Consumer class that writes MS data to disk using the mzML format |
     NoopMSDataWritingConsumer | Consumer class that perform no operation |
     PlainMSDataWritingConsumer | Consumer class that writes MS data to disk using the mzML format |
   ConsensusXMLFile | This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation |
   CVMappingFile | Used to load CvMapping files |
   FeatureXMLFile | This class provides Input/Output functionality for feature maps |
   IdXMLFile | Used to load and store idXML files |
   MascotXMLHandler | Handler that is used for parsing MascotXML data |
   MzDataHandler< MapType > | XML handler for MzDataFile |
   MzIdentMLHandler | XML STREAM handler for MzIdentMLFile |
   MzMLHandler< MapType > | XML handler for MzMLFile |
   MzQuantMLHandler | XML handler for MzQuantMLFile |
   MzXMLHandler< MapType > | XML handlers for MzXMLFile |
   ParamXMLHandler | XML Handler for Param files |
    ToolDescriptionHandler | XML handler for ToolDescriptionFile |
   PTMXMLHandler | Handler that is used for parsing PTMXML data |
   SemanticValidator | Semantically validates XML files using CVMappings and a ControlledVocabulary |
    MzDataValidator | Semantically validates MzXML files |
    MzIdentMLValidator | Semantically validates MzXML files |
    MzMLValidator | Semantically validates MzXML files |
    MzQuantMLValidator | Semantically validates MzQuantML files |
    TraMLValidator | Semantically validates MzXML files |
   TraMLHandler | XML handler for TraMLFile |
   UnimodXMLHandler | Handler that is used for parsing XTandemXML data |
   XTandemInfileXMLHandler | Handler that is used for parsing XTandemXML data |
   OMSSAXMLFile | Used to load OMSSAXML files |
   PepXMLFile | Used to load and store PepXML files |
   PepXMLFileMascot | Used to load Mascot PepXML files |
   ProtXMLFile | Used to load (storing not supported, yet) ProtXML files |
   QcMLFile | File adapter for QcML files |
   TransformationXMLFile | Used to load and store TransformationXML files |
   XTandemXMLFile | Used to load XTandemXML files |
 DefaultParamHandler | A base class for all classes handling default parameters |
  BaseModel< 1 > | |
   InterpolationModel | Abstract class for 1D-models that are approximated using linear interpolation |
    BiGaussModel | BiGaussian distribution approximated using linear interpolation |
    EGHModel | Exponential-Gaussian hybrid distribution model for elution profiles |
    EmgModel | Exponentially modified gaussian distribution model for elution profiles |
    ExtendedIsotopeModel | Extended isotope distribution approximated using linear interpolation |
    GaussModel | Normal distribution approximated using linear interpolation |
    IsotopeModel | Isotope distribution approximated using linear interpolation |
  BaseModel< 2 > | |
   ProductModel< 2 > | The class template is only implemented for D=2 because we use Peak2D here |
  AccurateMassSearchEngine | An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB) |
  BaseGroupFinder | The base class of all element group finding algorithms |
   LabeledPairFinder | The LabeledPairFinder allows the matching of labeled features (features with a fixed distance) |
   QTClusterFinder | A variant of QT clustering for the detection of feature groups |
   SimplePairFinder | This class implements a simple point pair finding algorithm |
   StablePairFinder | This class implements a pair finding algorithm for consensus features |
  BaseLabeler | Abstract base class for all kinds of labeling techniques |
   ICPLLabeler | Simulate ICPL experiments |
   ITRAQLabeler | Simulate iTRAQ experiments |
   LabelFreeLabeler | Abstract base class for all kinds of labeling techniques |
   O18Labeler | Simulate O-18 experiments |
   SILACLabeler | Simulate SILAC experiments |
  BaseModel< D > | Abstract base class for all D-dimensional models |
  BaseSuperimposer | The base class of all superimposer algorithms |
   PoseClusteringAffineSuperimposer | A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation |
   PoseClusteringShiftSuperimposer | A superimposer that uses a voting scheme, also known as pose clustering, to find a good shift transformation |
  BernNorm | BernNorm scales the peaks by ranking them and then scaling them according to rank |
  BinnedSpectrumCompareFunctor | Base class for compare functors of BinnedSpectra |
   BinnedSharedPeakCount | Compare functor scoring the shared peaks for similarity measurement |
   BinnedSpectralContrastAngle | Compare functor scoring the spectral contrast angle for similarity measurement |
   BinnedSumAgreeingIntensities | Compare functor scoring the sum of agreeing intensities for similarity measurement |
  CompNovoIdentificationBase | Run with CompNovoIdentificationBase |
   CompNovoIdentification | Run with CompNovoIdentification |
   CompNovoIdentificationCID | Run with CompNovoIdentificationCID |
  CompNovoIonScoringBase | Run with CompNovoIonScoringBase |
   CompNovoIonScoring | Run with CompNovoIonScoring |
   CompNovoIonScoringCID | Run with CompNovoIonScoringCID |
  ConsensusID | Calculates a consensus ID from several ID runs |
  DeNovoAlgorithm | Base class for ion scoring implementation for de novo algorithms |
  DeNovoIdentification | Base class for de novo identification |
  DeNovoIonScoring | Base class for ion scoring implementation for de novo algorithms |
  DeNovoPostScoring | Base class for ion scoring implementation for de novo algorithms |
  DetectabilitySimulation | Simulates peptide detectability |
  DiaPrescore | Scoring of an spectrum given library intensities of a transition group |
  DIAScoring | Scoring of an spectrum at the peak apex of an chromatographic elution peak |
  DigestSimulation | Simulates protein digestion |
  ElutionPeakDetection | Extracts chromatographic peaks from a mass trace |
  FalseDiscoveryRate | Calculates an FDR from identifications |
  FeaFiModule< PeakType > | Implements a module of the FeatureFinder algorithm |
  FeatureDeconvolution | An algorithm to decharge features (i.e. as found by FeatureFinder) |
  FeatureDistance | A functor class for the calculation of distances between features or consensus features |
  FeatureFinderAlgorithm | Abstract base class for FeatureFinder algorithms |
   FeatureFinderAlgorithmIsotopeWavelet | Implements the isotope wavelet feature finder |
   FeatureFinderAlgorithmMRM | FeatureFinderAlgorithm for MRM experiments |
   FeatureFinderAlgorithmPicked | FeatureFinderAlgorithm for picked peaks |
   FeatureFinderAlgorithmSH | The Superhirn FeatureFinderAlgorithm |
  FeatureFindingMetabo | |
  FeatureGroupingAlgorithm | Base class for all feature grouping algorithms |
   FeatureGroupingAlgorithmIdentification | A map feature grouping algorithm for identified features |
   FeatureGroupingAlgorithmLabeled | A map feature grouping algorithm for labeling techniques with two labels |
   FeatureGroupingAlgorithmQT | A feature grouping algorithm for unlabeled data |
   FeatureGroupingAlgorithmUnlabeled | A map feature grouping algorithm for unlabeled data |
  FilterFunctor | A FilterFunctor extracts some spectrum characteristics for quality assessment |
   ComplementFilter | Total intensity of peak pairs that could result from complementing fragments of charge state 1 |
   GoodDiffFilter | GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss |
   IntensityBalanceFilter | IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions |
   IsotopeDiffFilter | IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks |
   NeutralLossDiffFilter | NeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained by a neutral loss |
   TICFilter | TICFilter calculates TIC |
  Fitter1D | Abstract base class for all 1D-dimensional model fitter |
   LevMarqFitter1D | Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization |
    EGHFitter1D | Exponential-Gaussian hybrid distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization |
    EmgFitter1D | Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization |
   MaxLikeliFitter1D | Abstract base class for all 1D-model fitters using maximum likelihood optimization |
    BiGaussFitter1D | BiGaussian distribution fitter (1-dim.) approximated using linear interpolation |
    ExtendedIsotopeFitter1D | Extended isotope distribution fitter (1-dim.) approximated using linear interpolation |
    GaussFitter1D | Gaussian distribution fitter (1-dim.) approximated using linear interpolation |
    IsotopeFitter1D | Isotope distribution fitter (1-dim.) approximated using linear interpolation |
  GaussFilter | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data |
  IDDecoyProbability | IDDecoyProbability calculates probabilities using decoy approach |
  IDEvaluationBase | Main window of the IDEvaluation tool |
  IDMapper | Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications |
  IDRipper | Ripping protein/peptide identification according their file origin |
  InclusionExclusionList | Provides functionality for writing inclusion or exclusion lists |
  InternalCalibration | A simple calibration method using linear interpolation of given reference masses |
  IonizationSimulation | Simulates Protein ionization |
  IsobaricChannelExtractor | Extracts individual channels from MS/MS spectra for isobaric labeling experiments |
  IsobaricQuantifier | Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing |
  IsobaricQuantitationMethod | Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix |
   ItraqEightPlexQuantitationMethod | ITRAQ 8 plex quantitation to be used with the IsobaricQuantitation |
   ItraqFourPlexQuantitationMethod | ITRAQ 4 plex quantitation to be used with the IsobaricQuantitation |
   TMTSixPlexQuantitationMethod | TMT 6plex quantitation to be used with the IsobaricQuantitation |
   TMTTenPlexQuantitationMethod | TMT 10plex quantitation to be used with the IsobaricQuantitation |
  ItraqChannelExtractor | [experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map |
  ItraqQuantifier | Does post-processing on raw iTRAQ channel quantitation |
  LinearResampler | Linear Resampling of raw data |
   LinearResamplerAlign | Linear Resampling of raw data with alignment |
  LowessSmoothing | LOWESS (locally weighted scatterplot smoothing) |
  MapAlignmentAlgorithm | Base class for all map-alignment algorithms |
   MapAlignmentAlgorithmIdentification | A map alignment algorithm based on peptide identifications from MS2 spectra |
   MapAlignmentAlgorithmPoseClustering | A map alignment algorithm based on pose clustering |
   MapAlignmentAlgorithmSpectrumAlignment | A map alignment algorithm based on spectrum similarity (dynamic programming) |
  MarkerMower | MarkerMower uses PeakMarker to find peaks, those that are not marked get removed |
  MascotGenericFile | Mascot input file adapter |
  MascotRemoteQuery | Class which handles the communication between OpenMS and the Mascot server |
  MassDecompositionAlgorithm | Mass decomposition algorithm, given a mass it suggests possible compositions |
  MassTraceDetection | A mass trace extraction method that gathers peaks similar in m/z and moving along retention time |
  PosteriorErrorProbabilityModel | Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture |
  MetaboliteSpectralMatching | |
  MorphologicalFilter | This class implements baseline filtering operations using methods from mathematical morphology |
  MRMFeatureFinderScoring | The MRMFeatureFinder finds and scores peaks of transitions that co-elute |
  MRMFragmentSelection | This class can select appropriate fragment ions of an MS/MS spectrum of a peptide |
  MRMTransitionGroupPicker | The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors |
  MSPFile | File adapter for MSP files (NIST spectra library) |
  MSSim | Central class for simulation of mass spectrometry experiments |
  NLargest | NLargest removes all but the n largest peaks |
  Normalizer | Normalizer normalizes the peak intensities |
  OfflinePrecursorIonSelection | Implements different algorithms for precursor ion selection |
  OptimizePeakDeconvolution | This class provides the deconvolution of peak regions using non-linear optimization |
  ParentPeakMower | ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions |
  PeakMarker | PeakMarker marks peaks that seem to fulfill some criterion |
   ComplementMarker | ComplementMarker marks peak pairs which could represent y - b ion pairs |
   IsotopeMarker | IsotopeMarker marks peak pairs which could represent an ion and its isotope |
   NeutralLossMarker | NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water, ammonia) |
  PeakPickerCWT | This class implements a peak picking algorithm using wavelet techniques |
  PeakPickerHiRes | This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width |
  PeakPickerIterative | This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data) |
  PeakPickerMRM | The PeakPickerMRM finds peaks a single chromatogram |
  PeakPickerSH | |
  PeakSpectrumCompareFunctor | Base class for compare functors of spectra, that return a similarity value for two spectra |
   PeakAlignment | Make a PeakAlignment of two PeakSpectra |
   SpectraSTSimilarityScore | Similarity score of SpectraST |
   SpectrumAlignmentScore | Similarity score via spectra alignment |
   SpectrumCheapDPCorr | SpectrumCheapDPCorr calculates an optimal alignment on stick spectra |
   SpectrumPrecursorComparator | SpectrumPrecursorComparator compares just the parent mass of two spectra |
   SteinScottImproveScore | Similarity score based of Stein & Scott |
   ZhangSimilarityScore | Similarity score of Zhang |
  PeptideAndProteinQuant | Helper class for peptide and protein quantification based on feature data annotated with IDs |
  PILISCrossValidation | Implementation of a cross validation training for the PILIS model |
  PILISIdentification | This class actually implements a complete ProteinIdentification run with PILIS |
  PILISModel | This class implements the simulation of the spectra from PILIS |
  PILISModelGenerator | This class implements the simulation of the spectra from PILIS |
  PILISNeutralLossModel | This class implements the simulation of the spectra from PILIS |
  PILISScoring | This class actually implements the E-value based scoring of PILIS |
  PrecursorIonSelection | This class implements different precursor ion selection strategies |
  PrecursorIonSelectionPreprocessing | This class implements the database preprocessing needing for precursor ion selection |
  ProteinResolver | Helper class for peptide and protein quantification based on feature data annotated with IDs |
  ProtonDistributionModel | A proton distribution model to calculate the proton distribution over charged peptides |
  PSLPFormulation | Implements ILP formulation of precursor selection problems |
  QuantitativeExperimentalDesign | Merge files according to experimental design |
  RawMSSignalSimulation | Simulates MS signals for a given set of peptides |
  RawTandemMSSignalSimulation | Simulates tandem MS signals for a given set of peptides |
  RTSimulation | Simulates/Predicts retention times for peptides or peptide separation |
  SavitzkyGolayFilter | Computes the Savitzky-Golay filter coefficients using QR decomposition |
  Scaler | Scaler scales the peak by ranking the peaks and assigning intensity according to rank |
  SignalToNoiseEstimator< Container > | This class represents the abstract base class of a signal to noise estimator |
   SignalToNoiseEstimatorMeanIterative< Container > | Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities |
   SignalToNoiseEstimatorMedian< Container > | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) |
  SpectraIdentificationViewWidget | Tabular visualization / selection of identified spectra |
  SpectraMerger | Merges blocks of MS or MS2 spectra |
  SpectraMerger::SpectraDistance_ | |
  SpectrumAlignment | Aligns the peaks of two spectra |
  SpectrumCanvas | Base class for visualization canvas classes |
   Spectrum1DCanvas | Canvas for visualization of one or several spectra |
   Spectrum2DCanvas | Canvas for 2D-visualization of peak map, feature map and consensus map data |
   Spectrum3DCanvas | Canvas for 3D-visualization of peak map data |
  SqrtMower | Scales the intensity of peaks to the sqrt |
  SvmTheoreticalSpectrumGenerator | Simulates MS2 spectra with support vector machines |
  SvmTheoreticalSpectrumGeneratorTrainer | Train SVM models that are used by SvmTheoreticalSpectrumGenerator |
  TheoreticalSpectrumGenerator | Generates theoretical spectra with various options |
  ThresholdMower | ThresholdMower removes all peaks below a threshold |
  TOFCalibration | This class implements an external calibration for TOF data using external calibrant spectra |
  TOPPASBase | Main window of the TOPPAS tool |
  TOPPViewBase | Main window of TOPPView tool |
  TraceFitter | Abstract fitter for RT profile fitting |
   EGHTraceFitter | A RT Profile fitter using an Exponential Gaussian Hybrid background model |
   GaussTraceFitter | Fitter for RT profiles using a Gaussian background model |
  TransitionTSVReader | This class can convert TraML and TSV files into each other |
  TwoDOptimization | This class provides the two-dimensional optimization of the picked peak parameters |
  WindowMower | WindowMower augments the highest peaks in a sliding or jumping window |
  SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > > | |
   SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > > | |
 Deisotoper | |
 SvmTheoreticalSpectrumGenerator::DescriptorSet | A set of descriptors for a single training row |
 DIntervalBase< D > | A base class for D-dimensional interval |
  DBoundingBox< 2 > | |
  DRange< 1 > | |
  DRange< 2 > | |
  DRange< 3 > | |
  DBoundingBox< D > | A D-dimensional bounding box |
  DRange< D > | A D-dimensional half-open interval |
 DistanceMatrix< Value > | A two-dimensional distance matrix, similar to OpenMS::Matrix |
 FeatureDistance::DistanceParams_ | Structure for storing distance parameters |
 DocumentIdentifier | Manage source document information |
  ConsensusMap | A container for consensus elements |
  ExperimentalSettings | Description of the experimental settings |
   MSExperiment< OpenMS::Peak1D > | |
   MSExperiment< Peak1D > | |
   MSExperiment< SimPointType > | |
   MSExperiment<> | |
   MSExperiment< PeakT, ChromatogramPeakT > | In-Memory representation of a mass spectrometry experiment |
   MSQuantifications | |
  FeatureMap | A container for features |
 DocumentIDTagger | Tags OpenMS file containers with a DocumentID |
 ListUtils::DoubleTolerancePredicate_ | Predicate to check double equality with a given tolerance |
 DPeak< dimensions > | Metafunction to choose among Peak1D respectively Peak2D through a template argument |
 DPosition< D, TCoordinateType > | Representation of a coordinate in D-dimensional space |
 DPosition< 1 > | |
 DPosition< 2 > | |
 DPosition< 2, Int64 > | |
 DPosition< D > | |
 DPosition< DIMENSION > | |
 DRichPeak< dimensions > | Metafunction to choose among RichPeak1D respectively RichPeak2D through a template argument |
 DTAFile | File adapter for DTA files |
 EDTAFile | File adapter for Enhanced DTA files |
 Element | Representation of an element |
 ElementDB | Stores elements |
 EmgScoring | Scoring of an elution peak using an exponentially modified gaussian distribution model |
 EmpiricalFormula | Representation of an empirical formula |
 EnhancedTabBarWidgetInterface | Widgets that are placed into an EnhancedTabBar must implement this interface |
  SpectrumWidget | Base class for spectrum widgets |
   Spectrum1DWidget | Widget for visualization of several spectra |
   Spectrum2DWidget | Widget for 2D-visualization of peak map and feature map data |
   Spectrum3DWidget | Widget for 3D-visualization of map data |
  TOPPASWidget | Widget visualizing and allowing to edit TOPP pipelines |
 EnzymaticDigestion | Class for the enzymatic digestion of proteins |
 EquivalenceClassAA_< T > | |
 ErrorHandler | |
  XMLValidator | Validator for XML files |
 EuclideanSimilarity | CompareFunctor for 2Dpoints |
 exception | STL class |
  BaseException | Exception base class |
   BinnedSpectrum::NoSpectrumIntegrated | Exception which is thrown if BinnedSpectrum bins are accessed and no PeakSpektrum has been integrated yet i.e. bins_ is empty |
   BinnedSpectrumCompareFunctor::IncompatibleBinning | Exception thrown if compared spectra are incompatible |
   ClusterFunctor::InsufficientInput | Exception thrown if not enough data (<2) is used |
   BufferOverflow | Buffer overflow exception |
   ConversionError | Invalid conversion exception |
   DepletedIDPool | Exception used if no more unique document ID's can be drawn from ID pool |
   DivisionByZero | Division by zero error exception |
   ElementNotFound | Element could not be found exception |
   FailedAPICall | A call to an external library (other than OpenMS) went wrong |
   FileEmpty | File is empty |
   FileNotFound | File not found exception |
   FileNotReadable | File not readable exception |
   FileNotWritable | File not writable exception |
   IllegalArgument | A method or algorithm argument contains illegal values |
   IllegalPosition | Invalid 3-dimensional position exception |
   IllegalSelfOperation | Illegal self operation exception |
   IllegalTreeOperation | Illegal tree operation exception |
   IncompatibleIterators | Incompatible iterator exception |
   IndexOverflow | Int overflow exception |
   IndexUnderflow | Int underflow exception |
   InvalidIterator | Invalid iterator exception |
   InvalidParameter | Exception indicating that an invalid parameter was handed over to an algorithm |
   InvalidRange | Invalid range exception |
   InvalidSize | Invalid UInt exception |
   InvalidValue | Invalid value exception |
   IOException | General IOException |
   MissingInformation | Not all required information provided |
   NotImplemented | Not implemented exception |
   NullPointer | Null pointer argument is invalid exception |
   OutOfGrid | Out of grid exception |
   OutOfMemory | Out of memory exception |
   OutOfRange | Out of range exception |
   ParseError | Parse Error exception |
   Postcondition | Postcondition failed exception |
   Precondition | Precondition failed exception |
   RequiredParameterNotGiven | A required parameter was not given |
   SizeUnderflow | UInt underflow exception |
   UnableToCalibrate | Exception used if an error occurred while calibrating a dataset |
   UnableToCreateFile | Unable to create file exception |
   UnableToFit | Exception used if an error occurred while fitting a model to a given dataset |
   UnregisteredParameter | An unregistered parameter was accessed |
   WrongParameterType | A parameter was accessed with the wrong type |
   FeatureFinderDefs::NoSuccessor | Exception that is thrown if a method an invalid IndexPair is given |
   XMLHandler::EndParsingSoftly | Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file is needed) |
   Map< Key, T >::IllegalKey | Map illegal key exception |
   UnnormalizedComparator | Exception thrown if clustering is attempted without a normalized compare functor |
  bad_alloc | STL class |
   OutOfMemory | Out of memory exception |
 ChromatogramExtractorAlgorithm::ExtractionCoordinates | |
 FactoryBase | Base class for Factory<T> |
  Factory< FactoryProduct > | Returns FactoryProduct* based on the name of the desired concrete FactoryProduct |
 FASTAFile::FASTAEntry | FASTA entry type (identifier, description and sequence) |
 FASTAFile | This class serves for reading in FASTA files |
 FeatureEditDialogTemplate | |
  FeatureEditDialog | Dialog for editing a feature |
 FeatureFileOptions | Options for loading files containing features |
 FeatureFinderAlgorithmPickedHelperStructs | Wrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes |
 FeatureFinderAlgorithmSHCtrl | A facade for various Superhirn FeatureFinder classes. Use FeatureFinderAlgorithmSH instead |
 FeatureFinderDefs | The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes |
  FeatureFinder | The main feature finder class |
  FeatureFinderAlgorithmMRM | FeatureFinderAlgorithm for MRM experiments |
  FeatureFinderAlgorithmPicked | FeatureFinderAlgorithm for picked peaks |
  FeatureFinderAlgorithmSH | The Superhirn FeatureFinderAlgorithm |
  Fitter1D | Abstract base class for all 1D-dimensional model fitter |
 FeatureHypothesis | |
 FeatureLCProfile | |
 IsotopeWavelet::fi_ | Internal union for fast computation of the power function |
 File | Basic file handling operations |
 FileHandler | Facilitates file handling by file type recognition |
 FileMapping | Maps input/output files to filenames for the external program |
 FileTypes | Centralizes the file types recognized by FileHandler |
 FoundProteinFunctor | |
 FTPeakDetectController | |
 FuzzyStringComparator | Fuzzy comparison of strings, tolerates numeric differences |
 GammaDistributionFitter::GammaDistributionFitResult | Struct to represent the parameters of a gamma distribution |
 GammaDistributionFitter | Implements a fitter for the Gamma distribution |
 GaussFilterAlgorithm | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data |
 GaussFitter::GaussFitResult | Struct of parameters of a gaussian distribution |
 GaussFitter | Implements a fitter for gaussian functions |
 SignalToNoiseEstimator< Container >::GaussianEstimate | Protected struct to store parameters my, sigma for a Gaussian distribution |
 LevMarqFitter1D::GenericFunctor | |
  EGHFitter1D::EGHFitterFunctor | |
  EmgFitter1D::EgmFitterFunctor | |
 TraceFitter::GenericFunctor | |
  EGHTraceFitter::EGHTraceFunctor | |
  GaussTraceFitter::GaussTraceFunctor | |
 GlobalExceptionHandler | OpenMS global exception handler |
 glp_prob | |
 Gradient | Representation of a HPLC gradient |
 GridBasedCluster | Basic data structure for clustering |
 GridFeature | Representation of a feature in a hash grid |
 GumbelDistributionFitter::GumbelDistributionFitResult | Struct to represent the parameters of a gumbel distribution |
 GumbelDistributionFitter | Implements a fitter for the Gumbel distribution |
 GzipIfstream | Decompresses files which are compressed in the gzip format (*.gzip) |
 HashGrid< Cluster > | Container for (2-dimensional coordinate, value) pairs |
 SimpleSearchEngine::HasInvalidPeptideLengthPredicate | |
 HiddenMarkovModel | Hidden Markov Model implementation of PILIS |
 Histogram< ValueType, BinSizeType > | Representation of a histogram |
 HMMState | Hidden Markov Model State class for the Hidden Markov Model |
 HPLC | Representation of a HPLC experiment |
 IBSpectraFile | Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results |
 IChromatogramsReader | The interface of read-access to a list of chromatograms |
 IChromatogramsWriter | |
 IDataFrameWriter | |
  CSVWriter | |
  DataMatrix | |
 IDFilter | Used to filter identifications by different criteria |
 InclusionExclusionList::IEWindow | |
 IFeature | |
  FeatureOpenMS | An implementation of the OpenSWATH Feature Access interface using OpenMS |
  MockFeature | Mock object implementing IFeature |
 ILPDCWrapper | |
 IMRMFeature | |
  MRMFeatureOpenMS | An implementation of the OpenSWATH MRM Feature Access interface using OpenMS |
  MockMRMFeature | Mock object implementing IMRMFeature |
 IMSAlphabet | Holds an indexed list of bio-chemical elements |
 IMSAlphabetParser< AlphabetElementType, Container, InputSource > | An abstract templatized parser to load the data that is used to initialize Alphabet objects |
 IMSAlphabetParser<> | |
  IMSAlphabetTextParser | Implements abstract AlphabetParser to read data from the plain text format |
 IMSDataConsumer< MapType > | The interface of a consumer of spectra and chromatograms |
 IMSDataConsumer< MSExperiment<> > | |
  MSDataChainingConsumer | Consumer class that passes all operations on to a set of consumers |
  MSDataWritingConsumer | Consumer class that writes MS data to disk using the mzML format |
  NoopMSDataConsumer | Consumer class that perform no operation |
 IMSDataConsumer<> | |
  FullSwathFileConsumer | Abstract base class which can consume spectra coming from SWATH experiment stored in a single file |
   CachedSwathFileConsumer | On-disk cached implementation of FullSwathFileConsumer |
   RegularSwathFileConsumer | In-memory implementation of FullSwathFileConsumer |
  MSDataCachedConsumer | Transforming and cached writing consumer of MS data |
  MSDataTransformingConsumer | Transforming consumer of MS data |
 IMSElement | Represents a chemical atom with name and isotope distribution |
 IMSIsotopeDistribution | Represents a distribution of isotopes restricted to the first K elements |
 IndexedMzMLDecoder | A class to analyze indexedmzML files and extract the offsets of individual tags |
 IndexedMzMLFile | A class to read an indexedmzML file |
 IndexedMzMLFileLoader | A class to load an indexedmzML file |
 PSLPFormulation::IndexTriple | Struct that holds the indices of the precursors in the feature map and the ilp formulation |
 INIUpdater | |
 FuzzyStringComparator::InputLine | Stores information about the current input line (i.e., stream for the line and the current position in the stream) |
 InputSource | |
  CompressedInputSource | This class is based on xercesc::LocalFileInputSource |
 InspectInfile | Inspect input file adapter |
 InspectOutfile | Representation of an Inspect outfile |
 TransformationModelInterpolated::Interpolator | The class defines a generic interpolation technique used in the TransformationModelInterpolated |
 TOPPASToolVertex::IOInfo | Stores the information for input/output files/lists |
 CompNovoIonScoringBase::IonScore | |
 DeNovoIonScoring::IonScore | IonScore |
 SvmTheoreticalSpectrumGenerator::IonType | Nested class |
 ios_base | STL class |
  basic_ios< Char > | STL class |
   basic_istream< Char > | STL class |
    basic_ifstream< Char > | STL class |
     ifstream | STL class |
      FidHandler | Read-only fid File handler for XMass Analysis |
   basic_ostream< Char > | STL class |
    ostream | STL class |
     LogStream | Log Stream Class |
     SVOutStream | Stream class for writing to comma/tab/...-separated values files |
 ProteinResolver::ISDGroup | |
 ISignalToNoise | |
  SignalToNoiseOpenMS< PeakT > | An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS |
  MockSignalToNoise | Mock object implementing ISignalToNoise |
 IsobaricQuantitationMethod::IsobaricChannelInformation | Summary of an isobaric quantitation channel |
 IsobaricIsotopeCorrector | Performs isotope impurity correction on the intensities extracted from an isobaric labeling experiment |
 IsobaricNormalizer | Performs median normalization on the extracted ratios of isobaric labeling experiment |
 IsobaricQuantifierStatistics | Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion) |
 IsotopeCluster | Stores information about an isotopic cluster (i.e. potential peptide charge variants) |
 IsotopeDistribution | Isotope distribution class |
 IsotopeDistributionCache | Pre-calculate isotope distributions for interesting mass ranges |
 FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern | Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked |
 IsotopeWavelet | Implements the isotope wavelet function |
 IsotopeWaveletTransform< PeakType > | A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the FeatureFinderAlgorithmIsotopeWavelet class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform |
 IsotopicDist | |
 ISpectraReader | The interface of read-access to a list of spectra |
 ISpectraWriter | |
 ISpectrumAccess | The interface of a mass spectrometry experiment |
  SpectrumAccessOpenMS | An implementation of the OpenSWATH Spectrum Access interface using OpenMS |
  SpectrumAccessOpenMSCached | An implementation of the Spectrum Access interface using on-disk caching |
 iterator | |
  HashGrid< Cluster >::ConstIterator | Constant element iterator for the hash grid |
  HashGrid< Cluster >::Iterator | Element iterator for the hash grid |
  AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > | Forward iterator for an area of peaks in an experiment |
  IntensityIteratorWrapper< IteratorT > | An iterator wrapper to access peak intensities instead of the peak itself |
 AASequence::Iterator | Iterator class for AASequence |
 ITransitionGroup | |
  TransitionGroupOpenMS< SpectrumT, TransitionT > | An implementation of the OpenSWATH Transition Group Access interface using OpenMS |
  MockTransitionGroup | Mock object implementing ITransitionGroup |
 ItraqConstants | Some constants used throughout iTRAQ classes |
  ItraqChannelExtractor | [experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map |
  ItraqQuantifier | Does post-processing on raw iTRAQ channel quantitation |
 ItraqQuantifier::ItraqQuantifierStats | Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion) |
 JavaInfo | Detect Java and retrieve information |
 KroenikFile | File adapter for Kroenik (HardKloer sibling) files |
 LayerData | Class that stores the data for one layer |
 LayerStatisticsDialogTemplate | |
  LayerStatisticsDialog | Dialog showing statistics about the data of the current layer |
 LCElutionPeak | |
 LCMS | |
 LCMSCData | |
 LibSVMEncoder | Serves for encoding sequences into feature vectors |
 LightModification | |
 LightPeptide | |
 LightProtein | |
 LightTargetedExperiment | |
 LightTransition | |
 LinearInterpolation< Key, Value > | Provides access to linearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero |
 LinearInterpolation< double > | |
 LinearRegression | This class offers functions to perform least-squares fits to a straight line model, |
 list< T > | STL class |
  Annotations1DContainer | Container for annotations to content of Spectrum1DCanvas |
 ListUtils | Collection of utility functions for management of vectors |
 LocalLinearMap::LLMParam | Define parameters needed by the Local Linear Map (LLM) model |
 LocalLinearMap | Trained Local Linear Map (LLM) model for peak intensity prediction |
 LogStreamBuf::LogCacheStruct | Holds a counter of occurrences and an index for the occurrence sequence of the corresponding log message |
 LogConfigHandler | The LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream |
 LogStreamNotifier | |
 LPWrapper | |
 map< K, T > | STL class |
  Map< char, const OpenMS::Residue * > | |
  Map< char, double > | |
  Map< const OpenMS::Residue *, char > | |
  Map< double, std::vector< OpenMS::MassDecomposition > > | |
  Map< double, std::vector< OpenMS::RichPeak1D > > | |
  Map< OpenMS::EnzymaticDigestion::BindingSite, OpenMS::EnzymaticDigestion::CleavageModel > | |
  Map< OpenMS::HMMState *, double > | |
  Map< OpenMS::HMMState *, OpenMS::Map< OpenMS::HMMState *, double > > | |
  Map< OpenMS::HMMState *, OpenMS::Map< OpenMS::HMMState *, size_t > > | |
  Map< OpenMS::HMMState *, OpenMS::Map< OpenMS::HMMState *, std::pair< OpenMS::HMMState *, OpenMS::HMMState * > > > | |
  Map< OpenMS::HMMState *, OpenMS::Map< OpenMS::HMMState *, std::vector< double > > > | |
  Map< OpenMS::HMMState *, std::set< OpenMS::HMMState * > > | |
  Map< OpenMS::Size, std::set< PeptideProteinMatchInformation > > | |
  Map< OpenMS::String, const OpenMS::Element * > | |
  Map< OpenMS::String, IntList > | |
  Map< OpenMS::String, OpenMS::AASequence > | |
  Map< OpenMS::String, OpenMS::ControlledVocabulary::CVTerm > | |
  Map< OpenMS::String, OpenMS::HMMState * > | |
  Map< OpenMS::String, OpenMS::Instrument > | |
  Map< OpenMS::String, OpenMS::Map< OpenMS::String, OpenMS::Map< OpenMS::String, unsigned int > > > | |
  Map< OpenMS::String, OpenMS::Map< OpenMS::String, OpenMS::Residue * > > | |
  Map< OpenMS::String, OpenMS::Map< OpenMS::String, std::pair< OpenMS::String, OpenMS::String > > > | |
  Map< OpenMS::String, OpenMS::PILISCrossValidation::Option > | |
  Map< OpenMS::String, OpenMS::ProteinHit > | |
  Map< OpenMS::String, OpenMS::Sample > | |
  Map< OpenMS::String, OpenMS::Software > | |
  Map< OpenMS::String, OpenMS::SourceFile > | |
  Map< OpenMS::String, OpenMS::String > | |
  Map< OpenMS::String, size_t > | |
  Map< OpenMS::String, std::set< const OpenMS::Residue * > > | |
  Map< OpenMS::String, std::set< const OpenMS::ResidueModification * > > | |
  Map< OpenMS::String, std::set< OpenMS::String > > | |
  Map< OpenMS::String, std::vector< OpenMS::CVMappingRule > > | |
  Map< OpenMS::String, std::vector< OpenMS::CVTerm > > | |
  Map< OpenMS::String, std::vector< OpenMS::DataProcessing > > | |
  Map< OpenMS::String, std::vector< OpenMS::Internal::SemanticValidator::OpenMS::CVTerm > > | |
  Map< OpenMS::String, unsigned int > | |
  Map< PointType::CoordinateType, DBoundingBox< 1 > > | |
  Map< QString, QList< OpenMS::TOPPASResource > > | |
  Map< QString, QString > | |
  Map< size_t, OpenMS::Map< size_t, std::set< OpenMS::String > > > | |
  Map< size_t, OpenMS::String > | |
  Map< size_t, size_t > | |
  Map< size_t, std::vector< double > > | |
  Map< String, vector< pair< double, double > > > | |
  Map< unsigned int, const OpenMS::Element * > | |
  Map< unsigned int, std::vector< OpenMS::PeptideHit > > | |
  Map< unsigned int, std::vector< OpenMS::ResidueModification > > | |
  Map< unsigned int, unsigned int > | |
  Map< Key, T > | Map class based on the STL map (containing several convenience functions) |
 MapAlignmentEvaluationAlgorithm | Base class for all Caap evaluation algorithms |
  MapAlignmentEvaluationAlgorithmPrecision | Caap evaluation algorithm to obtain a precision value |
  MapAlignmentEvaluationAlgorithmRecall | Caap evaluation algorithm to obtain a recall value |
 MapAlignmentTransformer | The MapAlignmentTransformer class |
 MapConversion | |
 AccurateMassSearchEngine::MappingEntry_ | |
 MappingParam | Filename mappings for all input/output files |
 MarkerIonExtractor | |
 MassDecomposer< ValueType, DecompositionValueType > | An interface to handle decomposing of integer values/masses over a set of integer weights (alphabet) |
  IntegerMassDecomposer< ValueType, DecompositionValueType > | Implements MassDecomposer interface using algorithm and data structures described in paper "Efficient Mass Decomposition" S. Böcker, Z. Lipták, ACM SAC-BIO, 2004 doi:10.1145/1066677.1066715 |
 MassDecomposition | Class represents a decomposition of a mass into amino acids |
 MassExplainer | Computes empirical formulas for given mass differences using a set of allowed elements |
 IMSAlphabet::MassSortingCriteria_ | Private class-functor to sort out elements in mass ascending order |
 MassTrace | A container type that gathers peaks similar in m/z and moving along retention time |
 FeatureFinderAlgorithmPickedHelperStructs::MassTrace | Helper struct for mass traces used in FeatureFinderAlgorithmPicked |
 mean_and_stddev | Functor to compute the mean and stddev of sequence using the std::foreach algorithm |
 MetaInfo | A Type-Name-Value tuple class |
 MetaInfoInterface | Interface for classes that can store arbitrary meta information (Type-Name-Value tuples) |
  Acquisition | Information about one raw data spectrum that was combined with several other raw data spectra |
  AcquisitionInfo | Description of the combination of raw data to a single spectrum |
  ChromatogramSettings | Representation of chromatogram settings, e.g. SRM/MRM chromatograms |
   MSChromatogram< ChromatogramPeakType > | |
   MSChromatogram< PeakT > | The representation of a chromatogram |
  ConsensusMap | A container for consensus elements |
  ConsensusMap::FileDescription | Source file description for input files |
  ContactPerson | Contact person information |
  CVTermList | Representation of controlled vocabulary term list |
   IncludeExcludeTarget | This class stores a SRM/MRM transition |
   Precursor | Precursor meta information |
   Product | Product meta information |
   ReactionMonitoringTransition | This class stores a SRM/MRM transition |
   Software | Description of the software used for processing |
   SourceFile | Description of a file location, used to store the origin of (meta) data |
   Compound | |
   Configuration | |
   Contact | |
   Instrument | |
   Peptide | |
   Peptide::Modification | |
   Prediction | |
   Protein | |
   Publication | |
   RetentionTime | |
   TraMLProduct | |
  DataProcessing | Description of the applied preprocessing steps |
  ExperimentalSettings | Description of the experimental settings |
  Identification | Represents a object which can store the information of an analysisXML instance |
  IdentificationHit | Represents a object which can store the information of an analysisXML instance |
  Instrument | Description of a MS instrument |
  InstrumentSettings | Description of the settings a MS Instrument was run with |
  IonDetector | Description of a ion detector (part of a MS Instrument) |
  IonSource | Description of an ion source (part of a MS Instrument) |
  MassAnalyzer | Description of a mass analyzer (part of a MS Instrument) |
  MetaInfoDescription | Description of the meta data arrays of MSSpectrum |
   MSChromatogram< PeakT >::FloatDataArray | Float data array class |
   MSChromatogram< PeakT >::IntegerDataArray | Float data array class |
   MSChromatogram< PeakT >::StringDataArray | String data array class |
   MSSpectrum< PeakT >::FloatDataArray | Float data array class |
   MSSpectrum< PeakT >::IntegerDataArray | Integer data array class |
   MSSpectrum< PeakT >::StringDataArray | String data array class |
  PeptideHit | Representation of a peptide hit |
  PeptideIdentification | Represents the peptide hits for a spectrum |
  ProteinHit | Representation of a protein hit |
  ProteinIdentification | Representation of a protein identification run |
  ProteinIdentification::SearchParameters | Search parameters of the DB search |
  RichPeak1D | A 1-dimensional raw data point or peak with meta information |
  RichPeak2D | A 2-dimensional raw data point or peak with meta information |
   BaseFeature | A basic LC-MS feature |
    ConsensusFeature | A 2-dimensional consensus feature |
    Feature | An LC-MS feature |
     MRMFeature | A multi-chromatogram MRM feature |
  Sample | Meta information about the sample |
  SampleTreatment | Base class for sample treatments (Digestion, Modification, Tagging, ...) |
   Digestion | Meta information about digestion of a sample |
   Modification | Meta information about chemical modification of a sample |
    Tagging | Meta information about tagging of a sample e.g. ICAT labeling |
  ScanWindow | Scan window description |
  SpectrumIdentification | Represents a object which can store the information of an analysisXML instance |
  SpectrumSettings | Representation of 1D spectrum settings |
   MSSpectrum< OpenMS::Peak2D > | |
   MSSpectrum< Peak1D > | |
   MSSpectrum< PeakType > | |
   MSSpectrum< RichPeak1D > | |
   MSSpectrum< PeakT > | The representation of a 1D spectrum |
 MetaInfoRegistry | Registry which assigns unique integer indices to strings |
 LayerStatisticsDialog::MetaStatsValue_ | Struct representing the statistics about one meta information |
 MinimumDistance | Basic data structure for distances between clusters |
 TraceFitter::ModelData | |
 ModelDescription< D > | Stores the name and parameters of a model |
 ModificationDefinition | Representation of modification definition |
 ModificationDefinitionsSet | Representation of a set of modification definitions |
 MzIdentMLDOMHandler::ModificationParam | |
 ModificationsDB | Database which holds all residue modifications from UniMod |
 ModifiedPeptideGenerator | |
 ModifierRep | Implements modification for suffix arrays |
 MRMRTNormalizer | The MRMRTNormalizer will find retention time peptides in data |
 MRMScoring | This class implements different scores for peaks found in SRM/MRM |
 MRMTransitionGroup< SpectrumType, TransitionType > | The representation of a transition group that has information about the individual chromatograms as well as the transitions it refers to |
 MRMTransitionGroup< SpectrumT, TransitionT > | |
 MS1FeatureMerger | |
 MS1Signal | |
 MS2ConsensusSpectrum | |
  ClusteredMS2ConsensusSpectrum | |
   MS2Feature | |
 MS2Fragment | |
 MS2Info | |
 ProteinResolver::MSDGroup | Representation of an msd group. Contains peptides, proteins and a pointer to its ISD group |
 MsInspectFile | File adapter for MsInspect files |
 MSNumpressCoder | Class to encode and decode data encoded with MSNumpress |
 MSPeak | |
 MultiGradient | A gradient of multiple colors and arbitrary distances between colors |
 MultiplexClustering::MultiplexDistance | Scaled Euclidean distance for clustering |
 MultiplexFilterResult | Data structure storing all peaks (and optionally their raw data points) corresponding to one specific peak pattern |
 MultiplexFilterResultPeak | Data structure storing a single peak that passed all filters |
 MultiplexFilterResultRaw | Data structure storing a single raw data point that passed all filters |
 MultiplexPeakPattern | Data structure for pattern of isotopic peaks |
 MzIdentMLDOMHandler | XML DOM handler for MzIdentMLFile |
 MzMLHandlerHelper | |
 MzMLSpectrumDecoder | A class to decode input strings that contain an mzML chromatogram or spectrum tag |
 MzTab | Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/ |
 MzTabAssayMetaData | |
 MzTabContactMetaData | |
 MzTabCVMetaData | |
 MzTabFile | File adapter for MzTab files |
 MzTabInstrumentMetaData | |
 MzTabMetaData | |
 MzTabModificationMetaData | |
 MzTabMSRunMetaData | |
 MzTabNullAbleInterface | |
  MzTabModification | |
  MzTabNullAbleBase | |
   MzTabBoolean | |
   MzTabDoubleList | |
   MzTabIntegerList | |
   MzTabModificationList | |
  MzTabNullNaNAndInfAbleInterface | |
   MzTabNullNaNAndInfAbleBase | |
    MzTabDouble | |
    MzTabInteger | |
  MzTabParameter | |
  MzTabParameterList | |
  MzTabSpectraRef | |
  MzTabString | |
  MzTabStringList | |
 MzTabPeptideSectionRow | |
 MzTabProteinSectionRow | |
 MzTabPSMSectionRow | |
 MzTabSampleMetaData | |
 MzTabSmallMoleculeSectionRow | |
 MzTabSoftwareMetaData | |
 MzTabStudyVariableMetaData | |
 SplineSpectrum::Navigator | Iterator class for access of spline packages |
 SignalToNoiseEstimatorMedianRapid::NoiseEstimator | Class to compute the noise value at a given position |
 noncopyable | |
  TransformationModel | Base class for transformation models |
   TransformationModelBSpline | B-spline (non-linear) model for transformations |
   TransformationModelInterpolated | Interpolation model for transformations |
   TransformationModelLinear | Linear model for transformations |
 NonNegativeLeastSquaresSolver | Wrapper for a non-negative least squares (NNLS) solver |
 MSNumpressCoder::NumpressConfig | Configuration class for MSNumpress |
 OMSSACSVFile | File adapter for OMSSACSV files |
 OnDiscMSExperiment< PeakT, ChromatogramPeakT > | Representation of a mass spectrometry experiment on disk |
 OpenMSOSInfo | |
 OpenSwath_Scores | A structure to hold the different scores computed by OpenSWATH |
 OpenSwath_Scores_Usage | A structure to store which scores should be used by the Algorithm |
 OpenSwathDataAccessHelper | Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces |
 OpenSwathHelper | A helper class that is used by several OpenSWATH tools |
 OpenSwathScoring | A class that calls the scoring routines |
 OpenSwathTSVWriter | Class to write out an OpenSwath TSV output (mProphet input) |
 MS1FeatureMerger::OPERATOR_FEATURE_TR | |
 LCMS::OPERATOR_FeatureCompare | |
 LCMS::OPERATOR_MZ | |
 OptimizePick | This class provides the non-linear optimization of the peak parameters |
 PILISCrossValidation::Option | This struct represents a cross validation option |
 OptimizePick::OptPeakFunctor | |
 OSBinaryDataArray | The datastructures used by the OpenSwath interfaces |
 OSChromatogram | A single chromatogram |
 OSChromatogramMeta | Identifying information for a chromatogram |
 OSSpectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
 OSSpectrumMeta | Identifying information for a spectrum |
 Param | Management and storage of parameters / INI files |
 ParamEditorTemplate | |
  ParamEditor | A GUI for editing or viewing a Param object |
 Param::ParamEntry | Parameter entry used to store the actual information inside of a Param entry |
 ParameterInformation | Struct that captures all information of a command line parameter |
 Param::ParamIterator | Forward const iterator for the Param class |
 Param::ParamNode | Node inside a Param object which is used to build the internal tree |
 IMSIsotopeDistribution::Peak | Structure that represents an isotope peak - pair of mass and abundance |
 Peak1D | A 1-dimensional raw data point or peak |
  Precursor | Precursor meta information |
  RichPeak1D | A 1-dimensional raw data point or peak with meta information |
 Peak2D | A 2-dimensional raw data point or peak |
  FeatureHandle | Representation of a Peak2D, RichPeak2D or Feature |
   FeatureHandle::FeatureHandleMutable_ | Helper class returned by FeatureHandle::asMutable(), which see |
  RichPeak2D | A 2-dimensional raw data point or peak with meta information |
 PeakPickerCWT::PeakArea_ | Class for the internal peak representation |
 PeakPickerHiRes::PeakBoundary | Structure for peak boundaries |
 PeakCandidate | A small structure to hold peak candidates |
 PeakPickerMaxima::PeakCandidate | The PeakCandidate describes the output of the peak picker |
 PeakFileOptions | Options for loading files containing peak data |
 PeakIndex | Index of a peak or feature |
 PeakIntensityPredictor | Predict peak heights of peptides based on Local Linear Map model |
 PeakPickerMaxima | This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width |
 MultiplexFiltering::PeakReference | Structure for peak position in neighbouring spectra |
 PeakShape | Internal representation of a peak shape (used by the PeakPickerCWT) |
 PeakTypeEstimator | Estimates if the data of a spectrum is raw data or peak data |
 PeakWidthEstimator | Rough estimation of the peak width at m/z |
 PenaltyFactors | Class for the penalty factors used during the optimization |
  PenaltyFactorsIntensity | Class for the penalty factors used during the optimization |
 PepIterator | Abstract base class for different peptide iterators |
  EdwardsLippertIterator | Finds all Peptide Candidates with given masses and given fasta file |
   EdwardsLippertIteratorTryptic | EdwardsLippertIterator that only retrieves tryptic sequences |
  FastaIterator | Iterator over FASTA file |
  FastaIteratorIntern | Iterator for a FASTA file |
  TrypticIterator | Finds all tryptic Peptides with every missed cleavage |
 PepNovoInfile | PepNovo input file adapter |
 PepNovoOutfile | Representation of a PepNovo output file |
 PILISCrossValidation::Peptide | This struct represents a peptide spectrum pair |
 Peptide | |
 PeptideAndProteinQuant::PeptideData | Quantitative and associated data for a peptide |
 ProteinResolver::PeptideEntry | Peptide. First in silico. If experimental is set to true it is MS/MS derived |
 MzIdentMLDOMHandler::PeptideEvidence | |
 PeptideEvidence | Representation of a peptide evidence |
 PeptideProteinMatchInformation | |
 CompNovoIdentificationBase::Permut | Simple class to store permutations and a score |
 PeakShape::PositionLess | Comparison of mz_positions |
 PrecisionWrapper< FloatingPointType > | Wrapper class to implement output with appropriate precision. See precisionWrapper() |
 PrecursorMassComparator | |
 FuzzyStringComparator::PrefixInfo_ | Wrapper for the prefix information computed for the failure report |
 ProbablePhosphoSites | |
 ProcessData | |
 ProductModel< D > | Class for product models i.e. models with D independent dimensions |
 ProgressLogger | Base class for all classes that want to report their progress |
  AccurateMassSearchEngine | An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB) |
  AverageLinkage | AverageLinkage ClusterMethod |
  BaseGroupFinder | The base class of all element group finding algorithms |
  BaseSuperimposer | The base class of all superimposer algorithms |
  CachedmzML | An class that uses on-disk caching to read and write spectra and chromatograms |
   MSDataCachedConsumer | Transforming and cached writing consumer of MS data |
  ChromatogramExtractor | The ChromatogramExtractor extracts chromatograms from a spectra file |
  ChromatogramExtractorAlgorithm | The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data |
  CompleteLinkage | CompleteLinkage ClusterMethod |
  ConfidenceScoring | |
  ConsensusXMLFile | This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation |
  DTA2DFile | DTA2D File adapter |
  ElutionPeakDetection | Extracts chromatographic peaks from a mass trace |
  FeatureFinder | The main feature finder class |
  FeatureFindingMetabo | |
  FeatureXMLFile | This class provides Input/Output functionality for feature maps |
  GaussFilter | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data |
  GridBasedClustering< Metric > | 2D hierarchical clustering implementation optimized for large data sets containing many small clusters i.e. dimensions of clusters << dimension of entire dataset |
  InternalCalibration | A simple calibration method using linear interpolation of given reference masses |
  IonizationSimulation | Simulates Protein ionization |
  LinearResampler | Linear Resampling of raw data |
  MapAlignmentAlgorithm | Base class for all map-alignment algorithms |
  MascotGenericFile | Mascot input file adapter |
  MascotInfile | Mascot input file adapter |
  MassTraceDetection | A mass trace extraction method that gathers peaks similar in m/z and moving along retention time |
  MetaboliteSpectralMatching | |
  MorphologicalFilter | This class implements baseline filtering operations using methods from mathematical morphology |
  MRMDecoy | This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object |
  MRMFeatureFinderScoring | The MRMFeatureFinder finds and scores peaks of transitions that co-elute |
  MS2File | MS2 input file adapter |
  MSSim | Central class for simulation of mass spectrometry experiments |
  MultiplexClustering | Clusters results from multiplex filtering |
  MultiplexFiltering | Base class for filtering centroided and profile data for peak patterns |
   MultiplexFilteringCentroided | Filters centroided data for peak patterns |
   MultiplexFilteringProfile | Filters centroided and profile data for peak patterns |
  MzDataFile | File adapter for MzData files |
  MzIdentMLFile | File adapter for MzIdentML files |
  MzMLFile | File adapter for MzML files |
  MzQuantMLFile | File adapter for MzQuantML files |
  MzXMLFile | File adapter for MzXML 2.1 files |
  OpenSwathWorkflow | Class to execute an OpenSwath Workflow |
  PeakPickerCWT | This class implements a peak picking algorithm using wavelet techniques |
  PeakPickerHiRes | This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width |
  PeakPickerIterative | This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data) |
  PeakPickerSH | |
  QcMLFile | File adapter for QcML files |
  RawMSSignalSimulation | Simulates MS signals for a given set of peptides |
  SavitzkyGolayFilter | Computes the Savitzky-Golay filter coefficients using QR decomposition |
  SignalToNoiseEstimator< Container > | This class represents the abstract base class of a signal to noise estimator |
  SingleLinkage | SingleLinkage ClusterMethod |
  SVMWrapper | Serves as a wrapper for the libsvm |
  SwathFile | File adapter for Swath files |
  TOFCalibration | This class implements an external calibration for TOF data using external calibrant spectra |
  ToolDescriptionFile | File adapter for ToolDescriptor files |
  TraMLFile | File adapter for HUPO PSI TraML files |
  TransitionTSVReader | This class can convert TraML and TSV files into each other |
  XMassFile | File adapter for 'XMass Analysis (fid)' files |
  SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > > | |
 ProgressLogger::ProgressLoggerImpl | This class represents an actual implementation of a logger |
  GUIProgressLoggerImpl | Implements a GUI version of the ProgressLoggerImpl |
 Protein | |
 PeptideAndProteinQuant::ProteinData | Quantitative and associated data for a protein |
 ProteinResolver::ProteinEntry | Protein from FASTA file |
 ProteinIdentification::ProteinGroup | Bundles multiple (e.g. indistinguishable) proteins in a group |
 ProteinInference | [experimental class] given a peptide quantitation, infer corresponding protein quantities |
 PSProteinInference | This class implements protein inference for the precursor ion selection strategies |
 IsobaricChannelExtractor::PuritySate_ | Small struct to capture the current state of the purity computation |
 QApplication | |
  QApplicationTOPP | Extension to the QApplication for running TOPPs GUI tools |
 QDate | |
  Date | Date Class |
 QDateTime | |
  DateTime | DateTime Class |
 QDialog | |
  DataFilterDialog | Dialog for creating and changing a DataFilter |
  FeatureEditDialog | Dialog for editing a feature |
  HistogramDialog | Dialog that show a HistogramWidget |
  Spectrum1DPrefDialog | Preferences dialog for Spectrum1DWidget |
  Spectrum2DPrefDialog | Preferences dialog for Spectrum2DWidget |
  Spectrum3DPrefDialog | Preferences dialog for Spectrum3DWidget |
  TOPPViewPrefDialog | Preferences dialog for TOPPView |
  LayerStatisticsDialog | Dialog showing statistics about the data of the current layer |
  ListEditor | Editor for editing int, double and string lists (including output and input file lists) |
  MetaDataBrowser | A meta data visualization widget |
  SaveImageDialog | Dialog for saving an image |
  Spectrum1DGoToDialog | Simple goto/set visible area dialog for exact placement of the viewing window |
  Spectrum2DGoToDialog | GoTo dialog used to zoom to a m/z and retention time range or to a feature |
  SpectrumAlignmentDialog | Lets the user select two spectra and set the parameters for the spectrum alignment |
  TheoreticalSpectrumGenerationDialog | Dialog which allows to enter an AA sequence and generates a theoretical spectrum for it |
  ToolsDialog | TOPP tool selection dialog |
  TOPPASInputFileDialog | Dialog which allows to specify an input file |
  TOPPASInputFilesDialog | Dialog which allows to specify a list of input files |
  TOPPASIOMappingDialog | Dialog which allows to configure the input/output parameter mapping of an edge |
  TOPPASOutputFilesDialog | Dialog which allows to specify the directory for the output files |
  TOPPASToolConfigDialog | TOPP tool configuration dialog |
  TOPPASVertexNameDialog | Dialog which allows to change the name of an input vertex |
  TOPPViewOpenDialog | Dataset opening options for TOPPView |
 QFileSystemWatcher | |
  FileWatcher | Watcher that monitors file changes |
 QGLWidget | |
  Spectrum3DOpenGLCanvas | OpenGL Canvas for 3D-visualization of map data |
 QGraphicsItem | |
  TOPPASEdge | An edge representing a data flow in TOPPAS |
  TOPPASVertex | The base class of the different vertex classes |
   TOPPASInputFileListVertex | A vertex representing an input file list |
   TOPPASMergerVertex | A special vertex that allows to merge several inputs |
   TOPPASOutputFileListVertex | A vertex representing an output file list |
   TOPPASToolVertex | A vertex representing a TOPP tool |
 QGraphicsScene | |
  TOPPASScene | A container for all visual items of a TOPPAS workflow |
 QGraphicsView | |
  TOPPASWidget | Widget visualizing and allowing to edit TOPP pipelines |
 QItemDelegate | |
  ListEditorDelegate | Internal delegate class |
  ParamEditorDelegate | Internal delegate class for QTreeWidget |
 QLineEdit | |
  OpenMSLineEdit | Custom QLineEdit which emits a signal when losing focus (such that we can commit its data) |
 QListWidget | |
  ListTable | |
 QMainWindow | |
  IDEvaluationBase | Main window of the IDEvaluation tool |
  INIFileEditorWindow | Shows the ParamEditor widget in a QMainWindow with a toolbar |
  TOPPASBase | Main window of the TOPPAS tool |
  TOPPViewBase | Main window of TOPPView tool |
 QObject | |
  MascotRemoteQuery | Class which handles the communication between OpenMS and the Mascot server |
  TOPPASEdge | An edge representing a data flow in TOPPAS |
  TOPPASResource | Represents a data resource for TOPPAS workflows |
  TOPPASResources | A dictionary mapping string keys to lists of TOPPASResource objects |
  TOPPASVertex | The base class of the different vertex classes |
  TOPPViewBehaviorInterface | Interface class to model different behaviors of TOPPView |
   TOPPViewIdentificationViewBehavior | Behavior of TOPPView in identification mode |
   TOPPViewSpectraViewBehavior | Behavior of TOPPView in spectra view mode |
 QProcess | |
  FakeProcess | A FakeProcess class |
 QTabBar | |
  EnhancedTabBar | Convenience tab bar implementation |
  TOPPASTabBar | Convenience tab bar implementation |
 QTCluster | A representation of a QT cluster used for feature grouping |
 QTextEdit | |
  TOPPASLogWindow | QTextEdit implementation with a "clear" button in the context menu |
 QTreeWidget | |
  ParamTree | QTreeWidget that emits a signal whenever a new row is selected |
  TOPPASTreeView | Tree view implementation for the list of TOPP tools |
 QuadraticRegression | |
 QcMLFile::QualityParameter | Representation of a quality parameter |
 QWidget | |
  AxisWidget | Widget that represents an axis of a graph |
  BaseVisualizerGUI | A base class for all visualizer classes |
   AcquisitionInfoVisualizer | Class that displays all meta information for AcquisitionInfo objects |
   AcquisitionVisualizer | Class that displays all meta information for Acquisition objects |
   ContactPersonVisualizer | Class that displays all meta information for ContactPerson objects |
   DataProcessingVisualizer | Class that displays all meta information for DataProcessing objects |
   DigestionVisualizer | Class that displays all meta information of digestion objects |
   DocumentIdentifierVisualizer | Class that displays all meta information for DocumentIdentifier objects |
   ExperimentalSettingsVisualizer | Class that displays all meta information for ExperimentalSettings objects |
   GradientVisualizer | GradientVisualizer is a visualizer class for objects of type gradient |
   HPLCVisualizer | Class that displays all meta information for HPLC objects |
   InstrumentSettingsVisualizer | Class that displays all meta information for InstrumentSettings objects |
   InstrumentVisualizer | Class that displays all meta information for an MS instrument |
   IonDetectorVisualizer | Class that displays all meta information for IonDetector objects |
   IonSourceVisualizer | Class that displays all meta information for IonSource objects |
   MassAnalyzerVisualizer | Class that displays all meta information for MassAnalyzer objects |
   MetaInfoDescriptionVisualizer | Class that displays all meta information for MetaInfoDescription objects |
   MetaInfoVisualizer | MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member |
   ModificationVisualizer | Class that displays all meta information of modification objects |
   PeptideHitVisualizer | Class that displays all meta information for PeptideHit objects |
   PeptideIdentificationVisualizer | Class that displays all meta information for PeptideIdentification objects |
   PrecursorVisualizer | Class that displays all meta information for Precursor objects |
   ProductVisualizer | Class that displays all meta information for Product objects |
   ProteinHitVisualizer | Class that displays all meta information for ProteinHit objects |
   ProteinIdentificationVisualizer | Class that displays all meta information for ProteinIdentification objects |
   SampleVisualizer | Class that displays all meta information of sample objects |
   ScanWindowVisualizer | Class that displays all meta information for ScanWindow objects |
   SoftwareVisualizer | Class that displays all meta information for Software objects |
   SourceFileVisualizer | Class that displays all meta information for SourceFile objects |
   SpectrumSettingsVisualizer | Class that displays all meta information for SpectrumSettings objects |
   TaggingVisualizer | Class that displays all meta information of tagging objects |
  ColorSelector | A widget for selecting a color |
  HistogramWidget | Widget which can visualize a histogram |
  MultiGradientSelector | A widget witch allows constructing gradients of multiple colors |
  ParamEditor | A GUI for editing or viewing a Param object |
  SpectraIdentificationViewWidget | Tabular visualization / selection of identified spectra |
  SpectraViewWidget | Hierarchical visualization and selection of spectra |
  SpectrumCanvas | Base class for visualization canvas classes |
  SpectrumWidget | Base class for spectrum widgets |
 QWorkspace | |
  EnhancedWorkspace | |
 RangeManager< D > | Handles the management of a position and intensity range |
 RangeManager< 1 > | |
  MSChromatogram< ChromatogramPeakType > | |
  MSSpectrum< OpenMS::Peak2D > | |
  MSSpectrum< Peak1D > | |
  MSSpectrum< PeakType > | |
  MSSpectrum< RichPeak1D > | |
  MSChromatogram< PeakT > | The representation of a chromatogram |
  MSSpectrum< PeakT > | The representation of a 1D spectrum |
 RangeManager< 2 > | |
  MSExperiment< OpenMS::Peak1D > | |
  MSExperiment< Peak1D > | |
  MSExperiment< SimPointType > | |
  MSExperiment<> | |
  ConsensusMap | A container for consensus elements |
  FeatureMap | A container for features |
  MSExperiment< PeakT, ChromatogramPeakT > | In-Memory representation of a mass spectrometry experiment |
 ConsensusFeature::Ratio | Slim struct to feed the need for systematically storing of ratios ( |
 RawData | |
 RealMassDecomposer | Handles decomposing of non-integer values/masses over a set of non-integer weights with an error allowed |
 Base64::Reinterpreter32_ | Internal class needed for type-punning |
 Base64::Reinterpreter64_ | Internal class needed for type-punning |
 Residue | Representation of a residue |
 ResidueDB | Residue data base which holds residues |
 ResidueModification | Representation of a modification |
 ProteinResolver::ResolverResult | |
 RNPxlModificationMassesResult | |
 RNPxlModificationsGenerator | |
 RNPxlReportRow | |
 RNPxlReportRowHeader | |
 ROCCurve | ROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cutoff values |
 SAValue< Index< StringSet< Peptide >, IndexWotd<> > > | |
 PeptideHit::ScoreLess | Lesser predicate for scores of hits |
 ProteinHit::ScoreLess | Lesser predicate for scores of hits |
 ProteinHit::ScoreMore | Greater predicate for scores of hits |
 PeptideHit::ScoreMore | Greater predicate for scores of hits |
 FeatureFinderAlgorithmPickedHelperStructs::Seed | Helper structure for seeds used in FeatureFinderAlgorithmPicked |
 SeedListGenerator | Generate seed lists for feature detection |
 SequestInfile | Sequest input file adapter |
 SequestOutfile | Representation of a Sequest output file |
 set< K > | STL class |
  IsotopeCluster::ChargedIndexSet | Index set with associated charge estimate |
 SHFeature | |
 SignalToNoiseEstimatorMedianRapid | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based) |
 SimpleOpenMSSpectraFactory | A factory method that returns two ISpectrumAccess implementations |
 SimProtein | Plain data object holding sequence and abundance information on a single protein |
 SimRandomNumberGenerator | Wrapper class for random number generators used by the simulation classes |
 ROCCurve::simsortdec | Predicate for sort() |
 SingletonRegistry | Holds pointers to unique instance of a singleton factory |
 LPWrapper::SolverParam | Struct that holds the parameters of the LP solver |
 SparseVector< Value > | SparseVector implementation. The container will not actually store a specified type of element - the sparse element, e.g. zero (by default) |
 SparseVector< float > | |
 SparseVector< Value >::SparseVectorConstIterator | Const_iterator for SparseVector |
 SparseVector< Value >::SparseVectorConstReverseIterator | Const_reverse_iterator for SparseVector |
 SparseVector< Value >::SparseVectorIterator | Random access iterator for SparseVector including the hop() function to jump to the next non-sparse element |
 SparseVector< Value >::SparseVectorReverseIterator | Random access reverse iterator for SparseVector including the hop() function to jump to the next non-sparse element |
 SpecArrayFile | File adapter for SpecArray (.pepList) files |
 SpectralMatch | |
 SpectralMatchScoreComparator | |
 Spectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
 Spectrum1DGoToDialogTemplate | |
  Spectrum1DGoToDialog | Simple goto/set visible area dialog for exact placement of the viewing window |
 Spectrum1DPrefDialogTemplate | |
  Spectrum1DPrefDialog | Preferences dialog for Spectrum1DWidget |
 Spectrum2DGoToDialogTemplate | |
  Spectrum2DGoToDialog | GoTo dialog used to zoom to a m/z and retention time range or to a feature |
 Spectrum2DPrefDialogTemplate | |
  Spectrum2DPrefDialog | Preferences dialog for Spectrum2DWidget |
 Spectrum3DPrefDialogTemplate | |
  Spectrum3DPrefDialog | Preferences dialog for Spectrum3DWidget |
 SpectrumAddition | The SpectrumAddition is used to add up individual spectra |
 SpectrumAlignmentDialogTemplate | |
  SpectrumAlignmentDialog | Lets the user select two spectra and set the parameters for the spectrum alignment |
 MzMLHandler< MapType >::SpectrumData | Data necessary to generate a single spectrum |
 MzXMLHandler< MapType >::SpectrumData | Data necessary to generate a single spectrum |
 MzIdentMLDOMHandler::SpectrumIdentification | |
 MzIdentMLDOMHandler::SpectrumIdentificationProtocol | |
 SpectrumMeta | Identifying information for a spectrum |
 Spline2d< ValType > | Wrapper for Spline interpolation |
 SplinePackage | Fundamental data structure for SplineSpectrum |
 SplineSpectrum | Data structure for spline interpolation of MS1 spectra |
 PeptideAndProteinQuant::Statistics | Statistics for processing summary |
 StopWatch | StopWatch Class |
 streambuf | |
  LogStreamBuf | Stream buffer used by LogStream |
 FuzzyStringComparator::StreamElement_ | Stores information about characters, numbers, and white spaces loaded from the InputStream |
 StreamHandler | Provides a central class to register globally used output streams. Currently supported streams are |
 LogStreamBuf::StreamStruct | Holds a stream that is connected to the LogStream. It also includes the minimum and maximum level at which the LogStream redirects messages to this stream |
 StringListUtils | Utilities operating on lists of Strings |
 StringManager | Helper class for XML parsing that handles the memory management for conversions of Xerces strings |
 StringUtils | |
 SuffixArray | Abstract class for suffix array |
  SuffixArraySeqan | Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum |
   SuffixArrayTrypticSeqan | Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum |
  SuffixArrayTrypticCompressed | Class that implements a suffix array for a String. It can be used to find peptide Candidates for a MS spectrum |
 Summary | Summary of fitting results |
 SuperHirnParameters | SuperHirn parameters singleton class containing all static configuration variables |
 SuperHirnUtil | |
 SVMData | Data structure used in SVMWrapper |
 SvmTheoreticalSpectrumGenerator::SvmModelParameterSet | Simple container storing the model parameters required for simulation |
 SvmTheoreticalSpectrumGeneratorSet | Loads SvmTheoreticalSpectrumGenerator instances for different charges |
 SwathMap | Data structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2 |
 SwathWindowLoader | Class to read a file describing the Swath Windows |
 SysInfo | Some static functions to get system information |
 TargetedExperiment | This class stores an prediction of an SRM/MRM transition |
 TargetedExperiment | |
 TextFile | This class provides some basic file handling methods for text files |
  CsvFile | This class handles csv files. Currently only loading is implemented |
 FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern | Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked |
 TheoreticalSpectrumGenerationDialogTemplate | |
  TheoreticalSpectrumGenerationDialog | Dialog which allows to enter an AA sequence and generates a theoretical spectrum for it |
 ToolDescriptionInternal | ToolDescription Class |
  ToolDescription | |
 ToolExternalDetails | |
 ToolHandler | |
 TOPPASInputFileDialogTemplate | |
  TOPPASInputFileDialog | Dialog which allows to specify an input file |
 TOPPASInputFilesDialogTemplate | |
  TOPPASInputFilesDialog | Dialog which allows to specify a list of input files |
 TOPPASIOMappingDialogTemplate | |
  TOPPASIOMappingDialog | Dialog which allows to configure the input/output parameter mapping of an edge |
 TOPPASOutputFilesDialogTemplate | |
  TOPPASOutputFilesDialog | Dialog which allows to specify the directory for the output files |
 TOPPASVertexNameDialogTemplate | |
  TOPPASVertexNameDialog | Dialog which allows to change the name of an input vertex |
 TOPPBase | Base class for TOPP applications |
  SimpleSearchEngine | |
  TOPPRNPxl | |
 TOPPASScene::TOPPProcess | Stores the information for a TOPP process |
 TOPPViewOpenDialogTemplate | |
  TOPPViewOpenDialog | Dataset opening options for TOPPView |
 TOPPViewPrefDialogTemplate | |
  TOPPViewPrefDialog | Preferences dialog for TOPPView |
 Param::ParamIterator::TraceInfo | Struct that captures information on entered / left nodes for ParamIterator |
 IDDecoyProbability::Transformation_ | Struct to be used to store a transformation (used for fitting) |
 TransformationDescription | Generic description of a coordinate transformation |
 TransitionHelper | |
 IsotopeWaveletTransform< PeakType >::TransSpectrum | Internally (only by GPUs) used data structure . It allows efficient data exchange between CPU and GPU and avoids unnecessary memory moves. The class is tailored on the isotope wavelet transform and is in general not applicable on similar - but different - situations |
 TransitionTSVReader::TSVTransition | Internal structure to represent a transition |
 TwoDOptimization::TwoDOptFunctor | |
 unary_function | |
  HasActivationMethod< SpectrumType > | Predicate that determines if a spectrum was generated using any activation method given in the constructor list |
  HasMetaValue< MetaContainer > | Predicate that determines if a class has a certain metavalue |
  HasPrecursorCharge< SpectrumType > | Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list |
  HasScanMode< SpectrumType > | Predicate that determines if a spectrum has a certain scan mode |
  HasScanPolarity< SpectrumType > | Predicate that determines if a spectrum has a certain scan polarity |
  InIntensityRange< PeakType > | Predicate that determines if a peak lies inside/outside a specific intensity range |
  InMSLevelRange< SpectrumType > | Predicate that determines if a spectrum lies inside/outside a specific MS level set |
  InMzRange< PeakType > | Predicate that determines if a peak lies inside/outside a specific m/z range |
  InPrecursorMZRange< SpectrumType > | Predicate that determines if a spectrum's precursor is within a certain m/z range |
  InRTRange< SpectrumType > | Predicate that determines if a spectrum lies inside/outside a specific retention time range |
  IsEmptySpectrum< SpectrumType > | Predicate that determines if a spectrum is empty |
  IsInCollisionEnergyRange< SpectrumType > | Predicate that determines if an MSn spectrum was generated with a collision energy in the given range |
  IsInIsolationWindowSizeRange< SpectrumType > | Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range |
  IsZoomSpectrum< SpectrumType > | Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum |
  UnaryComposeFunctionAdapter< OP1, OP2 > | Represents the function object unary adapter |
  mySqrt | |
 UniqueIdGenerator | A generator for unique ids |
 UniqueIdIndexer< RandomAccessContainer > | A base class for random access containers for classes derived from UniqueIdInterface that adds functionality to convert a unique id into an index into the container |
 UniqueIdIndexer< ConsensusMap > | |
  ConsensusMap | A container for consensus elements |
 UniqueIdIndexer< FeatureMap > | |
  FeatureMap | A container for features |
 UniqueIdInterface | A base class defining a common interface for all classes having a unique id |
  ConsensusMap | A container for consensus elements |
  FeatureHandle | Representation of a Peak2D, RichPeak2D or Feature |
  FeatureMap | A container for features |
  RichPeak2D | A 2-dimensional raw data point or peak with meta information |
 CVTerm::Unit | |
 SparseVector< Value >::ValueProxy | Class ValueProxy allows the SparseVector to differentiate between writing and reading, so zeros can be ignored See "more effective c++" section 30 |
 vector< T > | STL class |
  Matrix< double > | |
  Matrix< unsigned int > | |
  MSChromatogram< ChromatogramPeakType > | |
  MSSpectrum< OpenMS::Peak2D > | |
  MSSpectrum< Peak1D > | |
  MSSpectrum< PeakType > | |
  MSSpectrum< RichPeak1D > | |
  AcquisitionInfo | Description of the combination of raw data to a single spectrum |
  ConsensusMap | A container for consensus elements |
  FeatureFinderAlgorithmPickedHelperStructs::MassTraces | Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked |
  FeatureMap | A container for features |
  Matrix< Value > | A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access |
  MSChromatogram< PeakT > | The representation of a chromatogram |
  MSChromatogram< PeakT >::FloatDataArray | Float data array class |
  MSChromatogram< PeakT >::IntegerDataArray | Float data array class |
  MSChromatogram< PeakT >::StringDataArray | String data array class |
  MSSpectrum< PeakT > | The representation of a 1D spectrum |
  MSSpectrum< PeakT >::FloatDataArray | Float data array class |
  MSSpectrum< PeakT >::IntegerDataArray | Integer data array class |
  MSSpectrum< PeakT >::StringDataArray | String data array class |
 VersionInfo::VersionDetails | |
 VersionInfo | Version information class |
 TOPPASVertex::VertexRoundPackage | Info for one edge and round, to be passed to next node |
 Weights | Represents a set of weights (double values and scaled with a certain precision their integer counterparts) with a quick access |
 WeightWrapper | Encapsulated weight queries to simplify mono vs average weight computation |
  SuffixArrayPeptideFinder | Wrapper for easy use of sufArray |
  SuffixArraySeqan | Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum |
  SuffixArrayTrypticCompressed | Class that implements a suffix array for a String. It can be used to find peptide Candidates for a MS spectrum |
 InclusionExclusionList::WindowDistance_ | Determine distance between two spectra |
 XMLFile | Base class for loading/storing XML files that have a handler derived from XMLHandler |
  ConsensusXMLFile | This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation |
  CVMappingFile | Used to load CvMapping files |
  FeatureXMLFile | This class provides Input/Output functionality for feature maps |
  IdXMLFile | Used to load and store idXML files |
  SemanticValidator | Semantically validates XML files using CVMappings and a ControlledVocabulary |
  MascotXMLFile | Used to load MascotXML files |
  MzDataFile | File adapter for MzData files |
  MzIdentMLFile | File adapter for MzIdentML files |
  MzMLFile | File adapter for MzML files |
  MzQuantMLFile | File adapter for MzQuantML files |
  MzXMLFile | File adapter for MzXML 2.1 files |
  OMSSAXMLFile | Used to load OMSSAXML files |
  ParamXMLFile | The file pendant of the Param class used to load and store the param datastructure as paramXML |
  PepXMLFile | Used to load and store PepXML files |
  PepXMLFileMascot | Used to load Mascot PepXML files |
  ProtXMLFile | Used to load (storing not supported, yet) ProtXML files |
  PTMXMLFile | Used to load and store PTMXML files |
  QcMLFile | File adapter for QcML files |
  ToolDescriptionFile | File adapter for ToolDescriptor files |
  TraMLFile | File adapter for HUPO PSI TraML files |
  TransformationXMLFile | Used to load and store TransformationXML files |
  UnimodXMLFile | Used to load XML files from unimod.org files |
  XTandemInfile | XTandem input file |
  XTandemXMLFile | Used to load XTandemXML files |
 XTandemInfileNote | Note representation of bioml structure used by XTandem |
 bool | |
 ChromatogramPeakType | |
 double | |
 float | |
 FloatDataArray | |
 Int | |
 IntegerDataArray | |
 pair< std::string, long > | |
 PeakT | |
 size_t | |
 StringDataArray | |
 UInt | |
 unsigned int | |