|   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 |  | 
|   PepXMLFile::AminoAcidModification |  | 
|   MSQuantifications::AnalysisSummary |  | 
|   Annotation1DItem | An abstract class acting as an interface for the different 1D annotation items | 
|    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^2 spectrum it is tried to identify the most probable phosphorylation-site(s). For each phosphorylation site a score is calculated, which is an indicator for the probability that this site is phosphorylated. 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 | 
|   AveragePosition< 2 > |  | 
|   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 | 
|   BasicStatistics< CoordinateType > |  | 
|   BasicStatistics< Real > |  | 
|    AsymmetricStatistics< Real > | Internal class for asymmetric distributions | 
|   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 | 
|    IntensityLess< FeaFiModuleType > | Comparator that allows to compare the indices of two peaks by their intensity | 
|    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 | 
|   MzMLHandler< MapType >::BinaryData | Spectrum representation | 
|   BinaryDataArray | The datastructures used by the OpenSwath interfaces | 
|   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 | 
|   SILACFiltering::BlacklistEntry | Structure for blacklist | 
|   FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::BoxElement | Internally used data structure for the sweep line algorithm | 
|   IsotopeWaveletTransform< PeakType >::BoxElement | Internally used data structure | 
|   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 | 
|   Chromatogram | A single chromatogram | 
|   ChromatogramMeta | Identifying information for a chromatogram | 
|   ChromatogramMeta | Identifying information for a chromatogram | 
|   ChromatogramPeak | A 1-dimensional raw data point or peak for chromatograms | 
|   ChromatogramTools | Conversion class to interconvert chromatograms | 
|   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 | 
|   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 | 
|   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 | 
|   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 | 
|   cudaHelp | An internally used class, subsuming several variables | 
|   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 | 
|   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) | 
|   LmaGaussFitter1D::Data | Helper struct (contains the size of an area and a raw data container) | 
|   LmaIsotopeFitter1D::Data | Helper struct (contains the size of an area, a raw data container, the relative abundance of i-th isotopic peak and the distance between consecutive isotopic peaks) | 
|   OptimizePeakDeconvolution::Data | Class containing the data needed for optimization | 
|   OptimizePick::Data |  | 
|   TwoDOptimization::Data | Helper struct (contains the size of an area and a raw data container) | 
|   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 | 
|   DBAdapter | A class for accessing and storing data in a SQL database | 
|   DBConnection | A class for connecting to a SQL database | 
|   DefaultHandler |  | 
|    XMLHandler | Base class for XML handlers | 
|     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 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 | 
|      LmaGaussModel | Normal distribution model for elution profiles | 
|      LmaIsotopeModel | 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 |  | 
|    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, FeatureType > | Implements a module of the FeatureFinder algorithm | 
|     ModelFitter< PeakType, FeatureType > | Tests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model | 
|     SimpleExtender< PeakType, FeatureType > | Simple feature extension algorithm | 
|     SimpleSeeder< PeakType, FeatureType > | Simple seeding class that uses the strongest peak as next seed | 
|    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< PeakType, FeatureType > | Abstract base class for FeatureFinder algorithms | 
|     FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType > |  | 
|     FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType > | Implements the isotope wavelet feature finder | 
|     FeatureFinderAlgorithmMRM< PeakType, FeatureType > | FeatureFinderAlgorithm for MRM experiments | 
|     FeatureFinderAlgorithmPicked< PeakType, FeatureType > | FeatureFinderAlgorithm for picked peaks | 
|     FeatureFinderAlgorithmSH< PeakType, FeatureType > | The Superhirn FeatureFinderAlgorithm | 
|     FeatureFinderAlgorithmSimple< PeakType, FeatureType > | FeatureFinderAlgorithm implementation using the Simple* modules | 
|     FeatureFinderAlgorithmSimplest< PeakType, FeatureType > | FeatureFinderAlgorithm implementation using the Simple* modules | 
|    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 (GSL implementation) for parameter optimization | 
|      EmgFitter1D | Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization | 
|      LmaGaussFitter1D | Gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization | 
|      LmaIsotopeFitter1D | Isotope distribution fitter (1-dim.) approximated using Levenberg-Marquardt algorithm (GSL 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 functionalty 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 | 
|    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 | 
|    MorphologicalFilter | This class implements baseline filtering operations using methods from mathematical morphology | 
|    MRMFeatureFinderScoring | The MRMFeatureFinder finds and scores peaks of transitions that coelute | 
|    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 | 
|    PeakPickerSH |  | 
|    PeakSpectrumCompareFunctor | Base class for compare functors of spectra, that return a similiarity value for two spectra | 
|     CompareFouriertransform | Compare Discrete Cosines value from a Fourier transformation, also known as Discrete Cosines Transformation | 
|     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 valdidation 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 signales 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 specra | 
|    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< PeakType > | Abstract fitter for RT profile fitting | 
|     EGHTraceFitter< PeakType > | A RT Profile fitter using an Exponential Gaussian Hybrid background model | 
|     GaussTraceFitter< PeakType > | Fitter for RT profiles using a gaussian background model | 
|    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< 1 > |  | 
|    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 | 
|    FeatureMap< OpenMS::Feature > |  | 
|    FeatureMap<> |  | 
|    ConsensusMap | A container for consensus elements | 
|    ExperimentalSettings | Description of the experimental settings | 
|     MSExperiment< OpenMS::Peak1D > |  | 
|     MSExperiment< Peak1D > |  | 
|     MSExperiment< SimPointType > |  | 
|     MSExperiment< PeakT, ChromatogramPeakT > | Representation of a mass spectrometry experiment | 
|     MSQuantifications |  | 
|    FeatureMap< FeatureT > | A container for features | 
|   DocumentIDTagger | Tags OpenMS file containers with a DocumentID | 
|   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 | 
|     DBConnection::InvalidQuery | Exception in case of an invalid Query | 
|     DBConnection::NotConnected | Exception in case of trying to execute a query without having established a database connection | 
|     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 | 
|   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 |  | 
|   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< PeakType, FeatureType > | FeatureFinderAlgorithm for MRM experiments | 
|    FeatureFinderAlgorithmPicked< PeakType, FeatureType > | FeatureFinderAlgorithm for picked peaks | 
|    FeatureFinderAlgorithmSH< PeakType, FeatureType > | The Superhirn FeatureFinderAlgorithm | 
|    FeatureFinderAlgorithmSimple< PeakType, FeatureType > | FeatureFinderAlgorithm implementation using the Simple* modules | 
|    FeatureFinderAlgorithmSimplest< PeakType, FeatureType > | FeatureFinderAlgorithm implementation using the Simple* modules | 
|    Fitter1D | Abstract base class for all 1D-dimensional model fitter | 
|    ModelFitter< PeakType, FeatureType > | Tests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model | 
|    SimpleExtender< PeakType, FeatureType > | Simple feature extension algorithm | 
|    SimpleSeeder< PeakType, FeatureType > | Simple seeding class that uses the strongest peak as next seed | 
|   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 | 
|   GlobalExceptionHandler | OpenMS global exception handler | 
|   glp_prob |  | 
|   Gradient | Representation of a HPLC gradient | 
|   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 | 
|   HiddenMarkovModel | Hidden Markov Model implementation of PILIS | 
|   HierarchicalClustering< PointRef > | Generic 2-dimensional hierarchical clustering with geometric hashing | 
|   HierarchicalClustering< SILACPattern * > |  | 
|    SILACClustering | Clustering implementation for SILAC stuff | 
|   Histogram< ValueType, BinSizeType > | Representation of a histogram | 
|   HMMState | Hidden Markov Model State class for the Hidden Markov Model | 
|   HPLC | Representation of a HPLC experiment | 
|   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 Alphabetobjects | 
|   IMSAlphabetParser<> |  | 
|    IMSAlphabetTextParser | Implements abstract AlphabetParserto read data from the plain text format | 
|   IMSElement | Represents a chemical atom with name and isotope distribution | 
|   IMSIsotopeDistribution | Represents a distribution of isotopes restricted to the first K elements | 
|   PSLPFormulation::IndexTriple | Struct that holds the indices of the precursors in the feature map and the ilp formulation | 
|   SimpleExtender< PeakType, FeatureType >::IndexWithPriority | A helper structure to sort indizes by their priority | 
|   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 | 
|   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 | Prealculate isotope distributions for interesting mass ranges | 
|   FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern | Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked | 
|   IsotopeWavelet | Implements the isotope wavelet function | 
|   IsotopeWaveletParallelFor< PeakType, FeatureType > | A class for distributing the data over several GPUs using Intel Threading Building Blocks | 
|   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 | 
|   IsotopeWaveletTransform< OpenMS::Peak2D > |  | 
|   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 OpenSWATH Spectrum Access interface using Disk caching | 
|   AASequence::Iterator | Iterator class for AASequence | 
|   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 | 
|   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) | 
|   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< DoubleReal > |  | 
|   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 | 
|   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 occurences and an index for the occurence 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< char, Size > |  | 
|    Map< const OpenMS::Element *, SignedSize > |  | 
|    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 > > |  | 
|    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 *, Size > |  | 
|    Map< OpenMS::HMMState *, std::pair< OpenMS::HMMState *, OpenMS::HMMState * > > |  | 
|    Map< OpenMS::HMMState *, std::set< OpenMS::HMMState * > > |  | 
|    Map< OpenMS::HMMState *, std::vector< double > > |  | 
|    Map< OpenMS::Size, std::set< OpenMS::Size > > |  | 
|    Map< OpenMS::String, const OpenMS::Element * > |  | 
|    Map< OpenMS::String, OpenMS::AASequence > |  | 
|    Map< OpenMS::String, OpenMS::ControlledVocabulary::CVTerm > |  | 
|    Map< OpenMS::String, OpenMS::CVReference > |  | 
|    Map< OpenMS::String, OpenMS::HMMState * > |  | 
|    Map< OpenMS::String, OpenMS::Instrument > |  | 
|    Map< OpenMS::String, OpenMS::IntList > |  | 
|    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::Map< OpenMS::String, unsigned int > > |  | 
|    Map< OpenMS::String, OpenMS::PILISCrossValidation::Option > |  | 
|    Map< OpenMS::String, OpenMS::ProteinHit > |  | 
|    Map< OpenMS::String, OpenMS::Residue * > |  | 
|    Map< OpenMS::String, OpenMS::Sample > |  | 
|    Map< OpenMS::String, OpenMS::Software > |  | 
|    Map< OpenMS::String, OpenMS::SourceFile > |  | 
|    Map< OpenMS::String, OpenMS::String > |  | 
|    Map< OpenMS::String, Size > |  | 
|    Map< OpenMS::String, std::pair< OpenMS::String, OpenMS::String > > |  | 
|    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, std::vector< OpenMS::String > > |  | 
|    Map< OpenMS::String, unsigned int > |  | 
|    Map< PointType::CoordinateType, DBoundingBox< 1 > > |  | 
|    Map< QString, QList< OpenMS::TOPPASResource > > |  | 
|    Map< QString, QString > |  | 
|    Map< Size, OpenMS::Map< Size, std::set< OpenMS::String > > > |  | 
|    Map< Size, OpenMS::String > |  | 
|    Map< Size, Size > |  | 
|    Map< Size, std::set< OpenMS::String > > |  | 
|    Map< Size, std::vector< double > > |  | 
|    Map< Size, String > |  | 
|    Map< String, DoubleReal > |  | 
|    Map< String, set< String > > |  | 
|    Map< String, vector< pair< DoubleReal, DoubleReal > > > |  | 
|    Map< UInt64, FileDescription > |  | 
|    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 serveral 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 | 
|   MappingParam | Filename mappings for all input/output files | 
|   MarkerIonExtractor |  | 
|   MassDecomposer< ValueType, DecompositionValueType > | An inteface to handle decomposing of integer values/masses over a set of integer weights (alphabet) | 
|    IntegerMassDecomposer< ValueType, DecompositionValueType > | Implements MassDecomposerinterface using algorithm and data structures described in paper "Efficient Mass Decomposition" S. Bcker, Zs. Liptk, ACM SAC-BIO, 2004 | 
|   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< PeakType > | 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 | Descripton 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 a ion source (part of a MS Instrument) | 
|    MassAnalyzer | Descripton 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 | 
|    PeptideEvidence | Representation of a MzIdentML PeptideEvidence | 
|    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 mith 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<> |  | 
|      BinnedSpectrum | This is a binned representation of a PeakSpectrum | 
|     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 | 
|   ModelDescription< D > | Stores the name and parameters of a model | 
|   ModelDescription< 2 > |  | 
|   ModificationDefinition | Representation of modification definition | 
|   ModificationDefinitionsSet | Representation of a set of modification definitions | 
|   ModificationMassesResult |  | 
|   ModificationsDB | Database which holds all residue modifications from UniMod | 
|   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 |  | 
|   MsInspectFile | File adapter for MsInspect files | 
|   MSPeak |  | 
|   MultiGradient | A gradient of multiple colors and arbitrary distances between colors | 
|   MzTab | Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/ | 
|   MzTabFile | File adapter for MzTab files | 
|   MzTabNullAbleInterface |  | 
|    MzTabModification |  | 
|    MzTabNullAbleBase |  | 
|     MzTabBoolean |  | 
|     MzTabDoubleList |  | 
|     MzTabModificationList |  | 
|    MzTabNullNaNAndInfAbleInterface |  | 
|     MzTabNullNaNAndInfAbleBase |  | 
|      MzTabDouble |  | 
|      MzTabInteger |  | 
|    MzTabParameter |  | 
|    MzTabParameterList |  | 
|    MzTabSpectraRef |  | 
|    MzTabString |  | 
|    MzTabStringList |  | 
|   MzTabPeptideSectionRow |  | 
|   MzTabProteinSectionRow |  | 
|   MzTabSmallMoleculeSectionRow |  | 
|   MzTabSubIdMetaData |  | 
|   MzTabUnitIdMetaData |  | 
|   NonNegativeLeastSquaresSolver | Wrapper for a non-negative least squares (NNLS) solver | 
|   OMSSACSVFile | File adapter for OMSSACSV files | 
|   OpenMSOSInfo |  | 
|   OpenSwath_Scores | A structure to hold the different scores computed by the FeatureFinder | 
|   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 | 
|   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 | 
|   pair |  | 
|    HierarchicalClustering< PointRef >::BoundingBox | Bounding box of cluster | 
|   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 mith 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 | 
|   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 | 
|   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 | This class implements a peak width estimation algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). Peaks are detected and a spline is fitted to the raw data in a window around the peak. Then a search for to the half-maximum is performed on the spline to the left and right of the peak maximum. The Full Width at the Half Maximum is collected. Finally a linear regression is performed to determine FWHM(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 seqences | 
|    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 |  | 
|   CompNovoIdentificationBase::Permut | Simple class to store permutations and a score | 
|   PersistentObject | Base class for all persistent objects | 
|    MSChromatogram< ChromatogramPeakType > |  | 
|    MSExperiment< OpenMS::Peak1D > |  | 
|    MSExperiment< Peak1D > |  | 
|    MSExperiment< SimPointType > |  | 
|    MSSpectrum< OpenMS::Peak2D > |  | 
|    MSSpectrum< Peak1D > |  | 
|    MSSpectrum< PeakType > |  | 
|    MSSpectrum< RichPeak1D > |  | 
|    MSSpectrum<> |  | 
|    MSChromatogram< PeakT > | The representation of a chromatogram | 
|    MSExperiment< PeakT, ChromatogramPeakT > | Representation of a mass spectrometry experiment | 
|    MSSpectrum< PeakT > | The representation of a 1D spectrum | 
|   PeakShape::PositionLess | Comparison of mz_positions | 
|   PrecisionWrapper< FloatingPointType > | Wrapper class to implement output with appropriate precision. See precisionWrapper() | 
|   FuzzyStringComparator::PrefixInfo_ | Wrapper for the prefix information computed for the failure report | 
|   SimpleExtender< PeakType, FeatureType >::IndexWithPriority::PriorityLess | Compares two indizes by priority | 
|   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 progess | 
|    AccurateMassSearchEngine |  | 
|    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 | 
|    ChromatogramExtractor | The ChromatogramExtractor extracts chromatograms from a mzML file | 
|    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 | 
|    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 | 
|    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 coelute | 
|    MS2File | MS2 input file adapter | 
|    MSSim | Central class for simulation of mass spectrometry experiments | 
|    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 | 
|    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 | 
|    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 | 
|    SILACAnalyzer | Algorithm to use for SILACAnalysis | 
|    SILACFiltering | Filtering for SILAC data | 
|    SingleLinkage | SingleLinkage ClusterMethod | 
|    SVMWrapper | Serves as a wrapper for the libsvm | 
|    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 > > |  | 
|   Protein |  | 
|   PeptideAndProteinQuant::ProteinData | Quantitative and associated data for a protein | 
|   ProteinResolver::ProteinEntry |  | 
|   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 | 
|   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 | 
|    DBOpenDialog | Dialog that allow selecting a spectrum from a DB | 
|    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 | 
|   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 specra | 
|    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 managment of a position and intensity range | 
|   RangeManager< 1 > |  | 
|    MSChromatogram< ChromatogramPeakType > |  | 
|    MSSpectrum< OpenMS::Peak2D > |  | 
|    MSSpectrum< Peak1D > |  | 
|    MSSpectrum< PeakType > |  | 
|    MSSpectrum< RichPeak1D > |  | 
|    MSSpectrum<> |  | 
|    MSChromatogram< PeakT > | The representation of a chromatogram | 
|    MSSpectrum< PeakT > | The representation of a 1D spectrum | 
|   RangeManager< 2 > |  | 
|    FeatureMap< OpenMS::Feature > |  | 
|    FeatureMap<> |  | 
|    MSExperiment< OpenMS::Peak1D > |  | 
|    MSExperiment< Peak1D > |  | 
|    MSExperiment< SimPointType > |  | 
|    ConsensusMap | A container for consensus elements | 
|    FeatureMap< FeatureT > | A container for features | 
|    MSExperiment< PeakT, ChromatogramPeakT > | 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 |  | 
|   PeakWidthEstimator::Result |  | 
|   RNPxlReportRow |  | 
|   RNPxlReportRowHeader |  | 
|   ROCCurve | ROCCurves show the tradeoff in sensitivity and specitivity 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 |  | 
|   SILACFilter | Filter to use for SILACFiltering | 
|   SILACPoint | A single SILAC point | 
|    SILACPattern | A single SILAC pattern containing multiple found points | 
|   SimpleOpenMSSpectraFactory | A factory method that returns two ISpectrumAccess implementations | 
|   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< Real > |  | 
|   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 | 
|   Spectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) | 
|   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 adds together a list of spectra | 
|   SpectrumAlignmentDialogTemplate |  | 
|    SpectrumAlignmentDialog | Lets the user select two spectra and set the parameters for the spectrum alignment | 
|   SILACFiltering::SpectrumInterpolation | Wrapper class for spectrum interpolation | 
|   SpectrumMeta | Identifying information for a spectrum | 
|   SpectrumMeta | Identifying information for a spectrum | 
|   PeptideAndProteinQuant::Statistics | Statistics for processing summary | 
|   StopWatch | StopWatch Class | 
|   streambuf |  | 
|    LogStreamBuf | Stream buffer used by LogStream | 
|   FuzzyStringComparator::StreamElement_ | Stores information about characters, numbers, and whitesspaces 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 | 
|   StringManager | Helper class for XML parsing that handles the memory management for conversions of Xerces strings | 
|   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 | 
|   TargetedExperiment |  | 
|   TargetedExperiment | This class stores an prediction of an SRM/MRM transition | 
|   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 | 
|    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 | 
|   TransformationModel | Base class for transformation models | 
|    TransformationModelBSpline | B-spline model for transformations | 
|    TransformationModelInterpolated | Interpolation model for transformations | 
|    TransformationModelLinear | Linear model for transformations | 
|   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 | 
|   HierarchicalClustering< PointRef >::TreeDistance | Wrapper class for two trees and the corresponding distance | 
|   HierarchicalClustering< PointRef >::TreeNode | Tree node used for clustering | 
|   TransitionTSVReader::TSVTransition |  | 
|   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 | 
|    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< Feature > > |  | 
|    FeatureMap<> |  | 
|   UniqueIdIndexer< FeatureMap< FeatureT > > |  | 
|    FeatureMap< FeatureT > | A container for features | 
|   UniqueIdIndexer< FeatureMap< OpenMS::Feature > > |  | 
|    FeatureMap< OpenMS::Feature > |  | 
|   UniqueIdInterface | A base class defining a common interface for all classes having a unique id | 
|    FeatureMap< OpenMS::Feature > |  | 
|    FeatureMap<> |  | 
|    ConsensusMap | A container for consensus elements | 
|    FeatureHandle | Representation of a Peak2D, RichPeak2D or Feature | 
|    FeatureMap< FeatureT > | A container for features | 
|    RichPeak2D | A 2-dimensional raw data point or peak with meta information | 
|   CVTerm::Unit |  | 
|   unordered_multimap |  | 
|    HierarchicalClustering< PointRef >::Cluster | Set of points. Describes a cluster on the grid. A point consists of a PointCoordinate and a PointRef | 
|   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 | 
|    FeatureMap< OpenMS::Feature > |  | 
|    FeatureMap<> |  | 
|    Matrix< double > |  | 
|    Matrix< unsigned int > |  | 
|    MSChromatogram< ChromatogramPeakType > |  | 
|    MSSpectrum< OpenMS::Peak2D > |  | 
|    MSSpectrum< Peak1D > |  | 
|    MSSpectrum< PeakType > |  | 
|    MSSpectrum< RichPeak1D > |  | 
|    MSSpectrum<> |  | 
|    AcquisitionInfo | Description of the combination of raw data to a single spectrum | 
|    ConsensusMap | A container for consensus elements | 
|    DoubleList | DoubleReal list | 
|    FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType > | Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked | 
|    FeatureMap< FeatureT > | A container for features | 
|    IntList | Int list | 
|    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 | 
|    SampleChannels | Container for multiple channels of SampleProteins | 
|    SampleProteins | Container for FASTAEntry & abundance information | 
|    StringList | String list | 
|     TextFile | This class provides some basic file handling methods for text files | 
|      CsvFile | This class handles csv files. Currently only loading is implemented | 
|   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 | 
|   XMLFormatTarget |  | 
|    OpenMSXMLFormatTarget |  | 
|   XTandemInfileNote | Note representation of bioml structure used by XTandem | 
|   double |  | 
|   FeatureT |  | 
|   FloatDataArray |  | 
|   Int |  | 
|   IntegerDataArray |  | 
|   MassTrace< PeakType > |  | 
|   pair< FASTAFile::FASTAEntry, MetaInfoInterface > |  | 
|   PeakT |  | 
|   Real |  | 
|   StringDataArray |  | 
|   unsigned int |  |