Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 123456]
 C_Alloc_base< _Tp, _Alloc >
 C_Alloc_base< _Val, std::allocator< _Node< _Val > > >
 C_Bracket_accessor< _Val >
 C_Node_compare< _Val, _Acc, _Cmp >
 C_Region< __K, _Val, _SubVal, _Acc, _Cmp >
 CAAIndexRepresentation of selected AAIndex properties
 CAASequenceRepresentation of a peptide/protein sequence
 COPXLDataStructs::AASeqWithMassThe AASeqWithMass struct represents a normal peptide with its precomputed mass
 COPXLDataStructs::AASeqWithMassComparatorThe AASeqWithMassComparator is a comparator for AASeqWithMass objects
 CFuzzyStringComparator::AbortComparisonInternal exception class
 CAbsoluteQuantitationMethodAbsoluteQuantitationMethod is a class to hold information about the quantitation method and for applying and/or generating the quantitation method
 CAbsoluteQuantitationStandardsAbsoluteQuantitationStandards is a class to handle the relationship between runs, components, and their actual concentrations
 CAbsoluteQuantitationStandardsFileLoad files containing runConcentration data
 CSiriusMSFile::AccessionInfo< class to store information about accessions
 CAcqusHandlerRead-only acqus File handler for XMass Analysis
 CACSpawnSpin-off search path through the trie, which can deal with ambiguous AAs and mismatches
 CACTrieAn Aho Corasick trie (a set of nodes with suffix links mainly)
 CAdductCompareComparator for adducts
 Calways_true< _Tp >
 CMzIdentMLDOMHandler::AnalysisSoftwareStruct to hold the used analysis software for that file
 CSimpleSearchEngineAlgorithm::AnnotatedHit_Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space
 CAnnotation1DItemAn abstract class acting as an interface for the different 1D annotation items
 CArea< N_DIM >
 CArea< 2 >
 CAreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >Forward iterator for an area of peaks in an experiment
 CArgsCustom arguments to allow for looping calls
 CQcMLFile::AttachmentRepresentation of an attachment
 CAveragePosition< D >Maintain an average position by summing up positions with weights
 CAxisPainterDraws a coordinate axis. It has only static methods, that's why the constructor is private
 CAxisTickCalculatorCalculates ticks for a given value range
 CBase64Class to encode and decode Base64
 CBaseVisualizer< ObjectType >A base class for all visualizer classes
 CBaseVisualizer< Acquisition >
 CBaseVisualizer< AcquisitionInfo >
 CBaseVisualizer< ContactPerson >
 CBaseVisualizer< DataProcessing >
 CBaseVisualizer< Digestion >
 CBaseVisualizer< DocumentIdentifier >
 CBaseVisualizer< ExperimentalSettings >
 CBaseVisualizer< Gradient >
 CBaseVisualizer< HPLC >
 CBaseVisualizer< Instrument >
 CBaseVisualizer< InstrumentSettings >
 CBaseVisualizer< IonDetector >
 CBaseVisualizer< IonSource >
 CBaseVisualizer< MassAnalyzer >
 CBaseVisualizer< MetaInfoDescription >
 CBaseVisualizer< MetaInfoInterface >
 CBaseVisualizer< Modification >
 CBaseVisualizer< PeptideHit >
 CBaseVisualizer< PeptideIdentification >
 CBaseVisualizer< Precursor >
 CBaseVisualizer< Product >
 CBaseVisualizer< ProteinHit >
 CBaseVisualizer< ProteinIdentification >
 CBaseVisualizer< Sample >
 CBaseVisualizer< ScanWindow >
 CBaseVisualizer< Software >
 CBaseVisualizer< SourceFile >
 CBaseVisualizer< SpectrumSettings >
 CBaseVisualizer< Tagging >
 Cbasic_string< Char >STL class
 CBasicStatistics< RealT >Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation
 CBasicStatistics< CoordinateType >
 CBasicStatistics< double >
 CBilinearInterpolation< 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
 CMzMLHandlerHelper::BinaryDataRepresentation for binary data in mzML
 CBinaryDataArrayThe datastructures used by the OpenSwath interfaces
 CBinaryTreeNodeElements of a binary tree used to represent a hierarchical clustering process
 CBinnedSpectrumThis is a binned representation of a PeakSpectrum
 CFeatureFinderAlgorithmIsotopeWavelet::BoxElementInternally used data structure for the sweep line algorithm
 CIsotopeWaveletTransform< PeakType >::BoxElementInternally used data structure
 CBSpline< T >
 CBSpline2dB spline interpolation
 CBSpline< double >
 CQTCluster::BulkDataClass to store the bulk internal data (neighbors, annotations, etc.)
 CBzip2IfstreamDecompresses files which are compressed in the bzip2 format (*.bz2)
 CCachedmzMLAn class that uses on-disk caching to read and write spectra and chromatograms
 CInternalCalibration::CalibrantStats_Statistics when adding peptide calibrants
 CCalibrationDataA helper class, holding all calibration points
 CItraqConstants::ChannelInfoStores information on an iTRAQ channel
 CChargePairRepresentation of a (putative) link between two Features, which stem from the same compound but have different charge (including different adduct ions (H+, Na+, ..)
 CTheoreticalSpectrumGenerationDialog::CheckBoxStruct for all information about a check box of an ion
 CChromatogramA single chromatogram
 CMzMLHandler::ChromatogramDataData necessary to generate a single chromatogram
 CChromatogramMetaIdentifying information for a chromatogram
 CChromatogramPeakA 1-dimensional raw data point or peak for chromatograms
 CChromatogramToolsConversion class to convert chromatograms
 CChromeleonFileLoad Chromeleon HPLC text file and save it into a `MSExperiment`
 CChromExtractParamsChromatogramExtractor parameters
 CMSSpectrum::ChunkUsed to remember what subsets in a spectrum are sorted already to allow faster sorting of the spectrum
 CCitationStores Citations for individual TOPP tools
 COPXLDataStructs::CLSMScoreComparatorComparator to sort CrossLinkSpectrumMatches by the main score
 CClusterAnalyzerBundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's)
 CClusterFunctorBase class for cluster functors
 CClusterHierarchicalHierarchical clustering with generic clustering functions
 CClusteringGridData structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering
 CClusterProxyKDProxy for a (potential) cluster
 CColorizerColor and style the fonts shown on cout/cerr (or other streams)
 CMapAlignmentAlgorithmSpectrumAlignment::CompareInner class necessary for using the sort algorithm
 CCompareMzTabMMatchRefData model of MzTabM files. Please see the official MzTabM specification at
 CCompomerHolds information on an edge connecting two features from a (putative) charge ladder
 CMRMFeatureQC::ComponentGroupPairQCsQuality Controls (QCs) for multiple components (between or within component_groups)
 CMRMFeaturePicker::ComponentGroupParamsStructure to contain information about a component group with its parameters
 CMRMFeatureQC::ComponentGroupQCsQuality Controls (QCs) within a component group
 CMRMFeaturePicker::ComponentParamsStructure to contain information about a single component with its parameters
 CMRMFeatureQC::ComponentQCsQuality Controls (QCs) for individual components
 CMetaboTargetedAssay::CompoundSpectrumPairCompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum
 CMetaboTargetedAssay::CompoundTargetDecoyPairCompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum (target, decoy)
 CConsensusMapNormalizerAlgorithmMedianAlgorithms of ConsensusMapNormalizer
 CConsensusMapNormalizerAlgorithmQuantileAlgorithms of ConsensusMapNormalizer
 CConsensusMapNormalizerAlgorithmThresholdAlgorithms of ConsensusMapNormalizer
 CAASequence::ConstIteratorConstIterator for AASequence
 CHashGrid< Cluster >::ConstIteratorConstant element iterator for the hash grid
 CNASequence::ConstIteratorConstIterator of NASequence class
 CConstRefVector< ContainerT >This vector holds pointer to the elements of another container
 CConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >ConstIterator for the ConstRefVector
 CMSExperiment::ContainerAdd_< ContainerValueType, addMassTraces >Helper class to add either general data points in set2DData or use mass traces from meta values
 CMSExperiment::ContainerAdd_< ContainerValueType, false >
 CMSExperiment::ContainerAdd_< ContainerValueType, true >
 CContaminants::ContaminantsSummaryStructure for storing results
 CContinuousWaveletTransformThis class is the base class of the continuous wavelet transformation
 CControlledVocabularyRepresentation of a controlled vocabulary
 CConvexHull2DA 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling
 COPXLDataStructs::CrossLinkSpectrumMatchThe CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum in OpenPepXL
 CCsiFingerIdMzTabWriter::CsiAdapterHitInternal structure used in SiriusAdapter that is used for the conversion of the Csi:FingerID output to an mzTab
 CCubicSpline2dCubic spline interpolation as described in R.L. Burden, J.D. Faires, Numerical Analysis, 4th ed. PWS-Kent, 1989, ISBN 0-53491-585-X, pp. 126-131
 CCVMappingRuleRepresentation of a CV Mapping rule used by CVMappings
 CCVMappingsRepresentation of controlled vocabulary mapping rules (for PSI formats)
 CCVMappingTermRepresentation of controlled vocabulary term
 CCVReferenceControlled Vocabulary Reference
 CControlledVocabulary::CVTermRepresentation of a CV term
 CCVTermRepresentation of controlled vocabulary term
 CSemanticValidator::CVTermRepresentation of a parsed CV term
 CEmgFitter1D::DataHelper struct (contains the size of an area and a raw data container)
 COptimizePeakDeconvolution::DataClass containing the data needed for optimization
 CTwoDOptimization::DataHelper struct (contains the size of an area and a raw data container)
 CMzIdentMLDOMHandler::DatabaseInputStruct to hold the information from the DatabaseInput xml tag
 CDataFilters::DataFilterRepresentation of a peak/feature filter combining FilterType, FilterOperation and a value (either double or String)
 CDataFiltersDataFilter array providing some convenience functions
 CTransformationModel::DataPointCoordinate pair (with optional annotation)
 CDataTabBaseAll tabs need to implement this interface
 CDataValueClass to hold strings, numeric values, lists of strings and lists of numeric values
 CDateTimeDateTime Class
 CMzIdentMLDOMHandler::DBSequenceStruct to hold the information from the DBSequence xml tag
 CDeconvolvedSpectrumA class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroups representing masses. For MSn n>1, a PeakGroup representing the precursor mass is also added in this class. Properly assigning a precursor mass from the original precursor peak and its deconvolution result is very important in top down proteomics. This assignment is performed here for conventional datasets. But for FLASHIda acquired datasets, the assignment is already done by FLASHIda. So this class simply use the results from FLASHIda log file for assignment. The parsing of FLASHIda log file is done in FLASHDeconv tool class
 CDecoyGeneratorMethods to generate isobaric decoy sequences for DDA target-decoy searches
 CDecoyHelperHelper class for calculations on decoy proteins
 CDecoyHelper::DecoyStatisticsStruct for intermediate results needed for calculations on decoy proteins
 CFalseDiscoveryRate::DecoyStringHelperFinds decoy strings in ProteinIdentification runs
 CDefaultParamHandlerA base class for all classes handling default parameters
 CMultiplexDeltaMasses::DeltaMassMass shift with corresponding label set
 CACNode::DepthHitsInternal struct to steal one bit from depth to use as hit indicator
 CDigestionEnzymeBase class for digestion enzymes
 CDigestionEnzymeDB< DigestionEnzymeType, InstanceType >Digestion enzyme database (base class)
 CDigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
 CDigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
 CIDFilter::DigestionFilterIs peptide evidence digestion product of some protein
 CDimBaseA base class for a dimension which represents a certain unit (e.g. RT or m/z). Derived classes implement virtual functions, which receive a well-defined data type, e.g. a Feature, and return the appropriate value for their dimension (the DimRT class would return the RT of the feature). This makes it possible to extract dimensions using a runtime configuration of DimBase instances. Very useful when mapping units (RT, m/z) to axis when plotting etc
 CDimMapper< N_DIM >Allows dynamical switching (at runtime) between a dimension (RT, m/z, int, IM, etc) and X,Y,Z coordinates. You can set either of them, and query the other. The Mapping is stored internally. The unit to which the X,Y,Z coordinates currently mapped onto can also be queried (useful for axis labels etc)
 CDimMapper< 2 >
 CDIntervalBase< D >A base class for D-dimensional interval
 CDistanceMatrix< Value >A two-dimensional distance matrix, similar to OpenMS::Matrix
 CFeatureDistance::DistanceParams_Structure for storing distance parameters
 CDocumentIdentifierManage source document information
 CListUtils::DoubleTolerancePredicate_Predicate to check double equality with a given tolerance
 CDPeak< dimensions >Metafunction to choose among Peak1D respectively Peak2D through a template argument
 CDPosition< D, TCoordinateType >Representation of a coordinate in D-dimensional space
 CDPosition< 1 >
 CDPosition< 2 >
 CDPosition< 2, Int64 >
 CDPosition< 2U >
 CDPosition< DIMENSION >
 CDTAFileFile adapter for DTA files
 CEDTAFileFile adapter for Enhanced DTA files
 CElementRepresentation of an element
 CElementDBSingleton that stores elements and isotopes
 CEmgScoringScoring of an elution peak using an exponentially modified gaussian distribution model
 CEmpiricalFormulaRepresentation of an empirical formula
 CEnhancedTabBarWidgetInterfaceWidgets that are placed into an EnhancedTabBar must implement this interface
 CEnzymaticDigestionClass for the enzymatic digestion of sequences
 CEuclideanSimilarityCompareFunctor for 2Dpoints
 CexceptionSTL class
 CExperimentalDesignRepresentation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class
 CExperimentalDesignFileLoad an experimental design from a TSV file. (see ExperimentalDesign for details on the supported format)
 CExposedVector< VectorElement >Makes a vector<VectorElement> available in the derived class and exposed commonly used vector member functions at class level
 CExposedVector< ConsensusFeature >
 CExposedVector< Feature >
 CExternalProcessMBoxA wrapper around ExternalProcess to conveniently show a MessageBox when an error occurs
 CFactoryBaseBase class for Factory<T>
 CFAIMSHelperHelper functions for FAIMS data
 CFASTAContainer< TBackend >Template parameter for vector-based FASTA access
 CFASTAContainer< TFI_File >FASTAContainer<TFI_File> will make FASTA entries available chunk-wise from start to end by loading it from a FASTA file. This avoids having to load the full file into memory. While loading, the container will memorize the file offsets of each entry, allowing to read an arbitrary i'th entry again from disk. If possible, only entries from the currently cached chunk should be queried, otherwise access will be slow
 CFASTAContainer< TFI_Vector >FASTAContainer<TFI_Vector> simply takes an existing vector of FASTAEntries and provides the same interface with a potentially huge speed benefit over FASTAContainer<TFI_File> since it does not need disk access, but at the cost of memory
 CFASTAFile::FASTAEntryFASTA entry type (identifier, description and sequence) The first String corresponds to the identifier that is written after the > in the FASTA file. The part after the first whitespace is stored in description and the text from the next line until the next > (exclusive) is stored in sequence
 CFeatureFinderAlgorithmMetaboIdent::FeatureCompareComparison functor for features
 CFeatureFinderIdentificationAlgorithm::FeatureCompareComparison functor for features
 CAbsoluteQuantitationStandards::featureConcentrationStructure to hold a single component and its corresponding known concentration
 CFeatureFileOptionsOptions for loading files containing features
 CFeatureFinderIdentificationAlgorithm::FeatureFilterPeptidesPredicate for filtering features by assigned peptides:
 CFeatureFinderAlgorithmMetaboIdent::FeatureFilterQualityPredicate for filtering features by overall quality
 CFeatureFinderIdentificationAlgorithm::FeatureFilterQualityPredicate for filtering features by overall quality:
 CFeatureFinderAlgorithmPickedHelperStructsWrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes
 CFeatureFinderDefsThe purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes
 CFeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompoundCompound in the assay library
 CFeatureHypothesisInternal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis)
 CFeatureMapping::FeatureMappingInfoStores information required for preprocessing
 CFeatureMapping::FeatureToMs2IndicesStores preprocessed feature mapping information
 CIsotopeWavelet::fi_Internal union for fast computation of the power function
 CFileBasic file handling operations
 CFileHandlerFacilitates file handling by file type recognition
 CFileMappingMaps input/output files to filenames for the external program
 CFileTypeListHolds a vector of known file types, e.g. as a way to specify supported input formats
 CFileTypesCentralizes the file types recognized by FileHandler
 CFileTypeList::FilterElements_Hold filter items (for Qt dialogs) along with their OpenMS type
 CFlagSet< ENUM >Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64
 CFlagSet< LayerDataBase::DataType >
 CFlagSet< TV_STATUS >
 CFLASHDeconvFeatureFileFLASHDeconv feature level output *.tsv, *.ms1ft (for Promex), *.feature (for TopPIC) file formats
 CFLASHDeconvHelperStructsWrapper struct for all the structs needed by the FLASHDeconv Three structures are defined: PrecalculatedAveragine, TopPicItem, and LogMzPeak i) PrecalculatedAveragine - to match observed isotopic envelope against theoretical one, theoretical envelope from averagine model should be quickly calculated. To do so, precalculate averagines for different masses at the beginning of FLASHDeconv runs ii) TopPicItem - represent TopPic identification. Currently used for Qscore training. TopPic is the top-down proteomics identification tool ( iii) LogMzPeak - Log transformed peak from original peak. Contains information such as charge, isotope index, and uncharged mass
 CFLASHDeconvSpectrumFileFLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats
 CRNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_Single fragment annotation
 CFuzzyStringComparatorFuzzy comparison of strings, tolerates numeric differences
 CGammaDistributionFitter::GammaDistributionFitResultStruct to represent the parameters of a gamma distribution
 CGammaDistributionFitterImplements a fitter for the Gamma distribution
 CGaussFilterAlgorithmThis class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data
 CGaussFitter::GaussFitResultStruct of parameters of a Gaussian distribution
 CGaussFitterImplements a fitter for Gaussian functions
 CSignalToNoiseEstimator< Container >::GaussianEstimateProtected struct to store parameters my, sigma for a Gaussian distribution
 CIDFilter::GetMatchingItems< HitType, Entry >Builds a map index of data that have a String index to find matches and return the objects
 CIDFilter::GetMatchingItems< OpenMS::PeptideEvidence, OpenMS::FASTAFile::FASTAEntry >
 CConfidenceScoring::GLM_Binomial GLM
 CGlobalExceptionHandlerOpenMS global exception handler
 CGradientRepresentation of a HPLC gradient
 CGravitatorManipulates X or Y component of points in the X-Y plane, by assuming one axis (either X or Y axis) has gravity acting upon it
 CGridBasedClusterBasic data structure for clustering
 CGridFeatureRepresentation of a feature in a hash grid
 CGridSearch< TupleTypes >
 CGUILockRAII class to disable the GUI and set a busy cursor and go back to the original state when this class is destroyed
 CGumbelDistributionFitter::GumbelDistributionFitResultStruct to represent the parameters of a gumbel distribution
 CGumbelMaxLikelihoodFitter::GumbelDistributionFitResultStruct to represent the parameters of a gumbel distribution
 CGumbelDistributionFitterImplements a fitter for the Gumbel distribution
 CGumbelMaxLikelihoodFitterImplements a fitter for the Gumbel distribution
 CGzipIfstreamDecompresses files which are compressed in the gzip format (*.gzip)
 CHasActivationMethod< SpectrumType >Predicate that determines if a spectrum was generated using any activation method given in the constructor list
 CIDFilter::HasDecoyAnnotation< HitType >Is this a decoy hit?
 CIDFilter::HasGoodScore< HitType >Is the score of this hit at least as good as the given value?
 Chash< OpenMS::Index >
 Chash< OpenMS::String >
 CHashGrid< Cluster >Container for (2-dimensional coordinate, value) pairs
 CIDFilter::HasMatchingAccession< HitType >Given a list of protein accessions, do any occur in the annotation(s) of this hit?
 CIDFilter::HasMatchingAccessionUnordered< HitType >Given a list of protein accessions, do any occur in the annotation(s) of this hit?
 CIDFilter::HasMaxMetaValue< HitType >Does a meta value of this hit have at most the given value?
 CIDFilter::HasMaxRank< HitType >Is the rank of this hit below or at the given cut-off?
 CHasMetaValue< MetaContainer >Predicate that determines if a class has a certain metavalue
 CIDFilter::HasMetaValue< HitType >Is a meta value with given key and value set on this hit?
 CIDFilter::HasNoHits< IdentificationType >Is the list of hits of this peptide/protein ID empty?
 CHasPrecursorCharge< SpectrumType >Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list
 CHasScanMode< SpectrumType >Predicate that determines if a spectrum has a certain scan mode
 CHasScanPolarity< SpectrumType >Predicate that determines if a spectrum has a certain scan polarity
 CHDF5ConnectorFile adapter for HDF5 files
 CHiddenMarkovModelHidden Markov Model implementation of PILIS
 CHistogram< ValueType, BinSizeType >Representation of a histogram
 CHMMStateHidden Markov Model State class for the Hidden Markov Model
 CHPLCRepresentation of a HPLC experiment
 CHyperScoreAn implementation of the X!Tandem HyperScore PSM scoring function
 CIBSpectraFileImplements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results
 CIChromatogramsReaderThe interface of read-access to a list of chromatograms
 CIDBoostGraphCreates and maintains a boost graph based on the OpenMS ID datastructures
 CIDConflictResolverAlgorithmResolves ambiguous annotations of features with peptide identifications
 CMs2IdentificationRate::IdentificationRateDataStructure for storing results
 CIDRipper::IdentificationRunsRepresents a set of IdentificationRuns
 CIDFilterCollection of functions for filtering peptide and protein identifications
 CIDScoreGetterSetterA class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps
 CIMDataConverterThis class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models
 CMobilityPeak2D::IMLessComparator by IM position
 CMSSpectrum::IMLessComparator for the ion mobility
 CIMSAlphabetHolds an indexed list of bio-chemical elements
 CIMSAlphabetParser< AlphabetElementType, Container, InputSource >An abstract templatized parser to load the data that is used to initialize Alphabet objects
 CIMSDataConsumerThe interface of a consumer of spectra and chromatograms
 CIMSElementRepresents a chemical atom with name and isotope distribution
 CIMSIsotopeDistributionRepresents a distribution of isotopes restricted to the first K elements
 CIndentedStreamClass for writing data which spans multiple lines with an indentation for each line (all except the first)
 CIndexedMzMLDecoderA class to analyze indexedmzML files and extract the offsets of individual tags
 CIndexedMzMLFileLoaderA class to load an indexedmzML file
 CIndexedMzMLHandlerA low-level class to read an indexedmzML file
 CFeatureHandle::IndexLessComparator by map and unique id
 CInIntensityRange< PeakType >Predicate that determines if a peak lies inside/outside a specific intensity range
 CInMSLevelRange< SpectrumType >Predicate that determines if a spectrum lies inside/outside a specific MS level set
 CInMzRange< PeakType >Predicate that determines if a peak lies inside/outside a specific m/z range
 CInPrecursorMZRange< SpectrumType >Predicate that determines if a spectrum's precursor is within a certain m/z range
 CInputFileInformation about input files that were processed
 CFuzzyStringComparator::InputLineStores information about the current input line (i.e., stream for the line and the current position in the stream)
 CInRTRange< SpectrumType >Predicate that determines if a spectrum lies inside/outside a specific retention time range
 CInspectInfileInspect input file adapter
 CInspectOutfileRepresentation of an Inspect outfile
 CIntensityIteratorWrapper< IteratorT >An iterator wrapper to access peak intensities instead of the peak itself
 CChromatogramPeak::IntensityLessComparator by intensity
 CTransformationModelInterpolated::InterpolatorThe class defines a generic interpolation technique used in the TransformationModelInterpolated
 CTOPPASToolVertex::IOInfoStores the information for input/output files/lists
 CIonMobilityScoringA class that calls the ion mobility scoring routines
 Cios_baseSTL class
 CIPeptideIdsAbstract base class which defines an interface for PeptideIdentifications
 CIsEmptySpectrum< SpectrumType >Predicate that determines if a spectrum is empty
 CIDScoreGetterSetter::IsHitType< T >
 CIDScoreGetterSetter::IsIDType< T >
 CIsInCollisionEnergyRange< SpectrumType >Predicate that determines if an MSn spectrum was generated with a collision energy in the given range
 CIsInIsolationWindow< SpectrumType >Predicate that determines if the isolation window covers ANY of the given m/z values
 CIsInIsolationWindowSizeRange< SpectrumType >Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range
 CIsobaricQuantitationMethod::IsobaricChannelInformationSummary of an isobaric quantitation channel
 CIsobaricIsotopeCorrectorPerforms isotope impurity correction on the intensities extracted from an isobaric labeling experiment
 CIsobaricNormalizerPerforms median normalization on the extracted ratios of isobaric labeling experiment
 CIsobaricQuantifierStatisticsStatistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion)
 CIsoSpecGeneratorWrapperInterface for the IsoSpec algorithm - a generator of infinitely-resolved theoretical spectra
 CIsoSpecWrapperA convenience class for the IsoSpec algorithm - easier to use than the IsoSpecGeneratorWrapper classes
 CIsotopeClusterStores information about an isotopic cluster (i.e. potential peptide charge variants)
 CIsotopeDistributionCachePre-calculate isotope distributions for interesting mass ranges
 CFeatureFinderAlgorithmPickedHelperStructs::IsotopePatternHelper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked
 CIsotopePatternGeneratorProvides an interface for different isotope pattern generator methods
 CIsotopeWaveletImplements the isotope wavelet function
 CIsotopeWaveletTransform< 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
 CISpectraReaderThe interface of read-access to a list of spectra
 CISpectrumAccessThe interface of a mass spectrometry experiment
 CIsZoomSpectrum< SpectrumType >Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum
 CAASequence::IteratorIterator class for AASequence
 CHashGrid< Cluster >::IteratorElement iterator for the hash grid
 CNASequence::IteratorIterator of NASequence class
 Cset< K >::iteratorSTL iterator class
 CItraqConstantsSome constants used throughout iTRAQ classes
 CJavaInfoDetect Java and retrieve information
 CKDTreeFeatureNodeA node of the kD-tree with pointer to corresponding data and index
 CKroenikFileFile adapter for Kroenik (HardKloer sibling) files
 CMultiplexDeltaMassesGenerator::LabelComplete label information
 CLayerStatisticsCompute summary statistics (count/min/max/avg) about a container, e.g. intensity, charge, meta values, ..
 CLayerStoreDataBase class to store either the currently visible or all data of a canvas
 CLinearInterpolation< 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
 CLinearInterpolation< KeyType >
 CLinearRegressionThis class offers functions to perform least-squares fits to a straight line model, \( Y(c,x) = c_0 + c_1 x \)
 CLinearRegressionWithoutInterceptThis class offers functions to perform least-squares fits to a straight line model, \( Y(c,x) = c_0 + c_1 x \)
 Clist< T >STL class
 CListUtilsCollection of utility functions for management of vectors
 CInternalCalibration::LockMassHelper class, describing a lock mass
 CLogStreamBuf::LogCacheStructHolds a counter of occurrences and an index for the occurrence sequence of the corresponding log message
 CLogConfigHandlerThe LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream
 CFLASHDeconvHelperStructs::LogMzPeakLog transformed peak. After deconvolution, all necessary information from deconvolution such as charge and isotope index is stored
 CPercolatorFeatureSetHelper::lq_PeptideEvidenceFor accession dependent sorting of PeptideEvidences
 CPercolatorFeatureSetHelper::lq_ProteinHitFor accession dependent sorting of ProteinHits
 CMapAlignmentAlgorithmKDAn efficient reference-free feature map alignment algorithm for unlabeled data
 CMapAlignmentEvaluationAlgorithmBase class for all Caap evaluation algorithms
 CMapAlignmentTransformerThis class collects functions for applying retention time transformations to data structures
 CProteinIdentification::MappingTwo way mapping from ms-run-path to protID|pepID-identifier
 CMappingParamFilename mappings for all input/output files
 CConsensusFeature::MapsLessCompare by the sets of consensus elements (lexicographically)
 CMapUtilities< MapType >Utilities for Feature and ConsensusMap
 CMapUtilities< ConsensusMap >
 CMapUtilities< FeatureMap >
 CMassDecomposer< ValueType, DecompositionValueType >An interface to handle decomposing of integer values/masses over a set of integer weights (alphabet)
 CMassDecomposer< long unsigned int, unsigned int >
 CMassDecompositionClass represents a decomposition of a mass into amino acids
 CMassExplainerComputes empirical formulas for given mass differences using a set of allowed elements
 CFLASHDeconvHelperStructs::MassFeatureMass feature (Deconvolved masses in spectra are traced by Mass tracing to generate mass features - like LC-MS features)
 CIMSAlphabet::MassSortingCriteria_Private class-functor to sort out elements in mass ascending order
 CFeatureFinderAlgorithmPickedHelperStructs::MassTraceHelper struct for mass traces used in FeatureFinderAlgorithmPicked
 CMassTraceA container type that gathers peaks similar in m/z and moving along retention time
 CFeatureFinderAlgorithmMetaboIdent::MassTraceBoundsBoundaries for a mass trace in a feature
 CMatchedIterator< CONT_T, TRAIT, CONST_T >For each element in the reference container the closest peak in the target will be searched. If no match is found within the tolerance window, the peak will be skipped over
 CMatrix< _Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols >
 Cmean_and_stddevFunctor to compute the mean and stddev of sequence using the std::foreach algorithm
 CSysInfo::MemUsageA convenience class to report either absolute or delta (between two timepoints) RAM usage
 CMessagePasserFactory< Label >
 CMetaboTargetedTargetDecoy::MetaboTargetDecoyMassMappingMetaboTargetDecoyMassMapping introduces a mapping of target and decoy masses and their respective compound reference using an identifier
 CMetaboTargetedAssayThis class provides methods for the extraction of targeted assays for metabolomics
 CMetaboTargetedTargetDecoyResolve overlapping fragments and missing decoys for experimental specific decoy generation in targeted/pseudo targeted metabolomics
 CMetaInfoA Type-Name-Value tuple class
 CMetaInfoInterfaceInterface for classes that can store arbitrary meta information (Type-Name-Value tuples)
 CMetaInfoInterfaceUtilsUtilities operating on containers inheriting from MetaInfoInterface
 CMetaInfoRegistryRegistry which assigns unique integer indices to strings
 CMetaKeyGetter< T >
 CMinimumDistanceBasic data structure for distances between clusters
 CMobilityPeak1D::MobilityLessComparator by mobility position
 CMobilityPeak1DA 1-dimensional raw data mobility point or peak. The unit (ms, 1/K_0, etc) is implicit
 CMobilityPeak2DA 2-dimensional raw data point or peak
 CModelDescription< D >Stores the name and parameters of a model
 CModificationDefinitionRepresentation of modification definition
 CModificationDefinitionsSetRepresentation of a set of modification definitions
 CMzIdentMLDOMHandler::ModificationParamStruct to hold the information from the ModificationParam xml tag
 CModificationsDBReturns a pointer to a modified residue given a residue and a pointer to a modification from the
 CModificationsDBDatabase which holds all residue modifications from UniMod
 CIdentificationData::ModifyMultiIndexAddProcessingStep< ElementType >Helper functor for adding processing steps to elements in a boost::multi_index_container structure
 CIdentificationData::ModifyMultiIndexAddScore< ElementType >Helper functor for adding scores to elements in a boost::multi_index_container structure
 CIdentificationData::ModifyMultiIndexRemoveParentMatches< ElementType >Helper functor for removing invalid parent matches from elements in a boost::multi_index_container structure
 CMorpheusScoreAn implementation of the Morpheus PSM scoring function Inspired by a C# implementation by C. Wenger released under MIT license
 CMQEvidenceBuilds a MaxQuant Evidence.txt
 CMQExporterHelperHelper class for common functions and NON trivial values needed for exporting MaxQuant outputs
 CMQMsmsBuilds a MaxQuant msms.txt
 CMRMFeaturePicker_MRMFeaturePicker_ defines the structures containing parameters to be used in [MRMTransitionGroupPicker](MRMTransitionGroupPicker) for components and components groups
 CMRMFeatureQCThe MRMFeatureQC is a class to handle the parameters and options for MRMFeatureFilter
 CMRMIonSeriesGenerate theoretical fragment ion series for use in MRMAssay and MRMDecoy
 CMRMRTNormalizerThe MRMRTNormalizer will find retention time peptides in data
 CMRMScoringThis class implements different scores for peaks found in SRM/MRM
 CMRMTransitionGroup< ChromatogramType, TransitionType >The representation of a group of transitions in a targeted proteomics experiment
 CMRMTransitionGroup< SpectrumT, TransitionT >
 CProteinResolver::MSDGroupRepresentation of an msd group. Contains peptides, proteins and a pointer to its ISD group
 CMsInspectFileFile adapter for MsInspect files
 CMSNumpressCoderClass to encode and decode data encoded with MSNumpress
 CMSstatsFileFile adapter for MSstats files
 CMultiGradientA gradient of multiple colors and arbitrary distances between colors
 CMultiplexDeltaMassesData structure for mass shift pattern
 CMultiplexClustering::MultiplexDistanceScaled Euclidean distance for clustering
 CMultiplexFilteredMSExperimentData structure storing all peaks (and optionally their raw data points) of an experiment corresponding to one specific peak pattern
 CMultiplexFilteredPeakData structure storing a single peak that passed all filters
 CMultiplexIsotopicPeakPatternData structure for pattern of isotopic peaks
 CMultiplexSatelliteCentroidedData structure storing a single satellite peak
 CMultiplexSatelliteProfileData structure storing a single satellite data point
 CMzIdentMLDOMHandlerXML DOM handler for MzIdentMLFile
 CMobilityPeak2D::MZLessComparator by m/z position
 CMSChromatogram::MZLessComparator for the retention time
 CPeak1D::MZLessComparator by m/z position
 CPeak2D::MZLessComparator by m/z position
 CMzMLHandlerHelperHelper for mzML file format
 CMzMLSpectrumDecoderA class to decode input strings that contain an mzML chromatogram or spectrum tag
 CMzMLSqliteHandlerSqlite handler for storing spectra and chromatograms in sqMass format
 CMzMLSqliteSwathHandlerSqlite handler for SWATH data sets
 CMzQCFileFile adapter for mzQC files used to load and store mzQC files
 CMzTabFileFile adapter for MzTab files
 CMzTabMAssayMetaDataMztabM Assay Metadata
 CMzTabMDatabaseMetaDataMztabM Database Metadata
 CMzTabMetaDataAll meta data of a mzTab file. Please refer to specification for documentation
 CMzTabMFileFile adapter for MzTab-M files
 CMzTabMMetaDataMztabM Metadata
 CMzTabMMSRunMetaDataMztabM MSRun Metadata
 CMzTabModificationData model of MzTab files
 CMzTabMSmallMoleculeEvidenceSectionRowSME Small molecule evidence section (mztab-m)
 CMzTabMSmallMoleculeFeatureSectionRowSMF Small molecule feature section (mztab-m)
 CMzTabMSmallMoleculeSectionRowSML Small molecule section (mztab-m)
 CMzTabMStudyVariableMetaDataMztabM StudyVariable Metadata
 CMzTabNucleicAcidSectionRowNUC - Nucleic acid section (table-based)
 CMzTabOligonucleotideSectionRowOLI - Oligonucleotide section (table-based)
 CMzTabOSMSectionRowOSM - OSM (oligonucleotide-spectrum match) section (table-based)
 CMzTabPeptideSectionRowPEP - Peptide section (Table based)
 CMzTabProteinSectionRowPRT - Protein section (Table based)
 CMzTabPSMSectionRowPSM - PSM section (Table based)
 CMzTabSmallMoleculeSectionRowSML Small molecule section (table based)
 CMZTrafoModelCreate and apply models of a mass recalibration function
 CReactionMonitoringTransition::NameLessComparator by name
 CNASequenceRepresentation of a nucleic acid sequence
 CSplineInterpolatedPeaks::NavigatorIterator class for access of spline packages
 CNeedlemanWunschThis class contains functions that are used to calculate the global alignment score of two amino acid sequences. This class uses the Needleman-Wunsch algorithm. For match and mismatch it uses a similarity scoring matrix
 CSignalToNoiseEstimatorMedianRapid::NoiseEstimatorClass to compute the noise value at a given position
 C_Alloc_base< _Tp, _Alloc >::NoLeakAlloc
 CNonNegativeLeastSquaresSolverWrapper for a non-negative least squares (NNLS) solver
 CMSNumpressCoder::NumpressConfigConfiguration class for MSNumpress
 COMSSACSVFileFile adapter for OMSSACSV files
 COnDiscMSExperimentRepresentation of a mass spectrometry experiment on disk
 COpenMSBuildInfoStruct with some static methods to get informations on the build configuration
 COpenSwath_ScoresA structure to hold the different scores computed by OpenSWATH
 COpenSwath_Scores_UsageA structure to store which scores should be used by the OpenSWATH Algorithm
 COpenSwathDataAccessHelperSeveral helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces
 COpenSwathHelperA helper class that is used by several OpenSWATH tools
 COpenSwathOSWWriterClass to write out an OpenSwath OSW SQLite output (PyProphet input)
 COpenSwathScoringA class that calls the scoring routines
 COpenSwathTSVWriterClass to write out an OpenSwath TSV output (mProphet input)
 COptimizePickThis class provides the non-linear optimization of the peak parameters
 COPXLHelperFunctions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code
 COSBinaryDataArrayThe datastructures used by the OpenSwath interfaces
 COSChromatogramA single chromatogram
 COSChromatogramMetaIdentifying information for a chromatogram
 COSSpectrumThe structure that captures the generation of a peak list (including the underlying acquisitions)
 COSSpectrumMetaIdentifying information for a spectrum
 COSWDataHolds all or partial information from an OSW file
 COSWFileThis class serves for reading in and writing OpenSWATH OSW files
 COSWHierarchyHierarchy levels of the OSWData tree
 COSWPeptidePrecursorA peptide with a charge state
 COSWProteinA Protein is the highest entity and contains one or more peptides which were found/traced
 COSWTransitionHigh-level meta data of a transition
 COverlapDetectorA heuristic: Given a set of levels (rows), try to add items at to topmost row which does not overlap an already placed item in this row (according to its x-coordinate)
 CPainterBaseAn empty base class with some static convenience functions
 Cpair_hashSimple hash function for Scoring::pos2D
 COfflinePrecursorIonSelection::PairComparatorSecondElement< PairType >
 CAreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::Param
 CParamManagement and storage of parameters / INI files
 CParamCTDFileSerializes a Param class in paramCTD file format. Note: only storing is currently possible
 CParamCWLFileLoad from JSON (in a Common Workflow Language (CWL) compatible way) into the Param class
 CParam::ParamEntryParameter entry used to store the actual information inside of a Param entry
 CParameterInformationStruct that captures all information of a command line parameter
 CParam::ParamIteratorForward const iterator for the Param class
 CParam::ParamNodeNode inside a Param object which is used to build the internal tree
 CParamValueClass to hold strings, numeric values, vectors of strings and vectors of numeric values using the stl types
 CParentGroup: Group of ambiguously identified parent sequences (e.g. protein group)
 CParseErrorThrows filename and message if test is false
 CIMSIsotopeDistribution::PeakStructure that represents an isotope peak - pair of mass and abundance
 CPeak1DA 1-dimensional raw data point or peak
 CPeak2DA 2-dimensional raw data point or peak
 CPeptideHit::PeakAnnotationContains annotations of a peak
 CPeakPickerCWT::PeakArea_Class for the internal peak representation
 CPeakPickerHiRes::PeakBoundaryStructure for peak boundaries
 CPeakCandidateA small structure to hold peak candidates
 CPeakPickerMaxima::PeakCandidateThe PeakCandidate describes the output of the peak picker
 CPeakFileOptionsOptions for loading files containing peak data
 CPeakGroupClass describing a deconvolved mass. A mass contains multiple (LogMz) peaks of different charges and isotope indices. PeakGroup is the set of such peaks representing a single monoisotopic mass. PeakGroup also contains features that define the quality of it. It is used by Qscore calculation. DeconvolvedSpectrum consists of PeakGroups
 CPeakIndexIndex of a peak or feature
 CPeakPickerMaximaThis 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
 CPeakShapeInternal representation of a peak shape (used by the PeakPickerCWT)
 CPeakTypeEstimatorEstimates if the data of a spectrum is raw data or peak data
 CPeakWidthEstimatorRough estimation of the peak width at m/z
 CPenaltyFactorsClass for the penalty factors used during the optimization
 CIdentificationDataConverter::PepIDCompareFunctor for ordering peptide IDs by RT and m/z (if available)
 CPepNovoInfilePepNovo input file adapter
 CPepNovoOutfileRepresentation of a PepNovo output file
 CFeatureFinderIdentificationAlgorithm::PeptideCompareComparison functor for (unassigned) peptide IDs
 CPeptideAndProteinQuant::PeptideDataQuantitative and associated data for a peptide
 CIDFilter::PeptideDigestionFilterFilter Peptide Hit by its digestion product
 CProteinResolver::PeptideEntryPeptide. First in silico. If experimental is set to true it is MS/MS derived
 CMzIdentMLDOMHandler::PeptideEvidenceStruct to hold the PeptideEvidence information
 CPeptideEvidenceRepresentation of a peptide evidence
 COPXLHelper::PeptideIDScoreComparatorA comparator for PeptideIdentifications that compares the scores in the first PeptideHit
 CPeptideProteinResolutionResolves shared peptides based on protein scores
 CPeptideHit::PepXMLAnalysisResultAnalysis Result (containing search engine / prophet results)
 CPercolatorFeatureSetHelperPercolator feature set and integration helper
 CPercolatorInfileClass for storing Percolator tab-delimited input files
 CPercolatorOutfileClass for reading Percolator tab-delimited output files
 CChromatogramPeak::PositionLessComparator by position. As this class has dimension 1, this is basically an alias for RTLess
 CMobilityPeak1D::PositionLessComparator by position. As this class has dimension 1, this is basically an alias for MobilityLess
 CMobilityPeak2D::PositionLessComparator by position. Lexicographical comparison (first IM then m/z) is done
 CPeak1D::PositionLessComparator by position. As this class has dimension 1, this is basically an alias for MZLess
 CPeak2D::PositionLessComparator by position. Lexicographical comparison (first RT then m/z) is done
 CPeakShape::PositionLessComparison of mz_positions
 CFLASHDeconvHelperStructs::PrecalculatedAveragineAveragine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine calculation
 CPrecisionWrapper< FloatingPointType >Wrapper class to implement output with appropriate precision. See precisionWrapper()
 CPrecursorCorrectionThis class provides methods for precursor correction
 CPrecursorPurityPrecursor purity or noise estimation
 CSimpleSVM::PredictionSVM/SVR prediction result
 CFuzzyStringComparator::PrefixInfo_Wrapper for the prefix information computed for the failure report
 COPXLDataStructs::PreprocessedPairSpectraThe PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spectra to each other
 CProductModel< D >Class for product models i.e. models with D independent dimensions
 CReactionMonitoringTransition::ProductMZLessComparator by Product ion MZ
 CProgressLoggerBase class for all classes that want to report their progress
 CProgressLogger::ProgressLoggerImplThis class represents an actual implementation of a logger
 CLayerDataDefs::ProjectionDataResult of computing a projection on X and Y axis in a 2D Canvas; see LayerDataBase::getProjection()
 CPeptideAndProteinQuant::ProteinDataQuantitative and associated data for a protein
 CProteinResolver::ProteinEntryProtein from FASTA file
 CIDBoostGraph::ProteinGroupIndistinguishable protein groups (size, nr targets, score)
 CProteinIdentification::ProteinGroupBundles multiple (e.g. indistinguishable) proteins in a group
 CProteinHit::ProteinHitAccessionHashHash of a ProteinHit based on its accession only!
 CProteinInference[experimental class] given a peptide quantitation, infer corresponding protein quantities
 COPXLDataStructs::ProteinProteinCrossLinkThe ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL
 CPScoreImplementation of the PScore PSM scoring algorithm
 CHyperScore::PSMDetailCompute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match
 CPSProteinInferenceThis class implements protein inference for the precursor ion selection strategies
 CIsobaricChannelExtractor::PuritySate_Small struct to capture the current state of the purity computation
 CPythonInfoDetect Python and retrieve information
 CQCBaseThis class serves as an abstract base class for all QC classes
 CQscoreQscore : quality score for PeakGroup. This class is being updated. For now, simply it calculate the Qscore using a fixed weight vector. The weight vector has been determined by logistic regression. But afterwards, the training part for the Qscore should be added in here. Or other technique such as deep learning would be used. This class also contains tsv output function. The tsv file contains features of PeakGroups which are used for training
 CQTClusterA representation of a QT cluster used for feature grouping
 CBaseFeature::QualityLessCompare by quality
 CQcMLFile::QualityParameterRepresentation of a quality parameter
 CQvalueQvalue : contains functions to calculate Qvalues from deconvolution quality score
 CRAIICleanupException-safe way of executing arbitrary code at the end of a scope
 CRangeInternal structure to store a lower and upper bound of an m/z range
 CRangeBaseBase class for a simple range with minimum and maximum
 CRangeStats< VALUE_TYPE >Struct representing the statistics about a set of values
 CRangeStatsTypeOrigin and name of a statistic
 CPeptideHit::RankLessLesser predicate for scores of hits
 CRANSAC< TModelType >This class provides a generic implementation of the RANSAC outlier detection algorithm. Is implemented and tested after the SciPy reference:
 CRansacModel< ModelT >Generic plug-in template base class using 'Curiously recurring template pattern' (CRTP) to allow for arbitrary RANSAC models (e.g. linear or quadratic fits)
 CRansacModel< RansacModelLinear >
 CRansacModel< RansacModelQuadratic >
 CRANSACParamA simple struct to carry all the parameters required for a RANSAC run
 CConsensusFeature::RatioSlim struct to feed the need for systematically storing of ratios (
 CRealMassDecomposerHandles decomposing of non-integer values/masses over a set of non-integer weights with an error allowed
 CIdentificationData::RefTranslatorStructure that maps references of corresponding objects after copying
 CBase64::Reinterpreter32_Internal class needed for type-punning
 CBase64::Reinterpreter64_Internal class needed for type-punning
 CResidueRepresentation of an amino acid residue
 CResidueDBOpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called
 CResidueDBModifies the residue at index in the sequence and potentially in the
 CResidueModificationRepresentation of a modification on an amino acid residue
 CResidueModificationSets the modification of AA at index by providing a pointer to a in the
 CFalseDiscoveryRate::DecoyStringHelper::ResultFinds the most common decoy string in the accessions of proteins. Checks for suffix and prefix and some common decoy strings. Only successful if more than 30% had a common string
 CMorpheusScore::ResultScore and subscores
 CRibonucleotideRepresentation of a ribonucleotide (modified or unmodified)
 CRibonucleotideDBDatabase of ribonucleotides (modified and unmodified)
 CIDRipper::RipFileContentRepresents the content of an IDRipper output file
 CIDRipper::RipFileIdentifierIdentifies an IDRipper output file
 CIDRipper::RipFileIdentifierIdxComparatorProvides a 'less' operation for RipFileIdentifiers that ignores the out_basename and origin_fullname members
 CRNPxlFragmentAnnotationHelperConvenience functions to construct appealing fragment annotation strings and store them as PeptideHit::PeakAnnotation
 CRNPxlReportCreate report
 CRNPxlReportRowStruct to hold a single report line
 CRNPxlReportRowHeaderCreate header line
 CROCCurveROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cutoff values
 CMzTabNucleicAcidSectionRow::RowCompareComparison operator for sorting rows
 CMzTabOligonucleotideSectionRow::RowCompareComparison operator for sorting rows
 CMzTabOSMSectionRow::RowCompareComparison operator for sorting rows
 CMzTabPeptideSectionRow::RowCompareComparison operator for sorting rows
 CMzTabProteinSectionRow::RowCompareComparison operator for sorting rows
 CMzTabPSMSectionRow::RowCompareComparison operator for sorting rows
 CChromatogramPeak::RTLessComparator by RT position
 CMobilogram::RTLessComparator for the RT of the mobilogram
 CMSSpectrum::RTLessComparator for the retention time
 CMZTrafoModel::RTLessComparator by position. As this class has dimension 1, this is basically an alias for MZLess
 CPeak2D::RTLessComparator by RT position
 COSSpectrumMeta::RTLessComparator for the retention time
 CConfidenceScoring::RTNorm_Helper for RT normalization (range 0-100)
 CFeatureFinderIdentificationAlgorithm::RTRegionRegion in RT in which a peptide elutes:
 CAbsoluteQuantitationStandards::runConcentrationStructure to map runs to components to known concentrations
 CRWrapperR-Wrapper Class
 CPeptideHit::ScoreLessLesser predicate for scores of hits
 CProteinHit::ScoreLessLesser predicate for scores of hits
 CPeptideHit::ScoreMoreGreater predicate for scores of hits
 CProteinHit::ScoreMoreGreater predicate for scores of hits
 CFeatureFinderAlgorithmPickedHelperStructs::SeedHelper structure for seeds used in FeatureFinderAlgorithmPicked
 CSeedListGeneratorGenerate seed lists for feature detection
 CPeptideHit::SequenceLessComparatorLesser predicate for (modified) sequence of hits
 CSequestInfileSequest input file adapter
 CSequestOutfileRepresentation of a Sequest output file
 Cset< K >STL class
 Cshared_xerces_ptr< T >
 CSignalToNoiseEstimatorMedianRapidEstimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based)
 CSimpleOpenMSSpectraFactoryA factory method that returns two ISpectrumAccess implementations
 CSimpleTSGXLMS::SimplePeakA simple struct to represent peaks with mz and charge and sort them easily
 CSimpleTSGXLMS::SimplePeakComparatorComparator to sort SimplePeaks by mz
 CROCCurve::simsortdecPredicate for sort()
 CSingletonRegistryHolds pointers to unique instance of a singleton factory
 CSiriusMzTabWriter::SiriusAdapterHitInternal structure used in SiriusAdapter that is used for the conversion of the sirius output to an mzTab
 CSiriusFragmentAnnotation::SiriusTargetDecoySpectraSiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from SIRIUS)
 CSiriusAdapterAlgorithm::SiriusTemporaryFileSystemObjectsStruct for temporary folder structure
 CConsensusFeature::SizeLessCompare by size(), the number of consensus elements
 CLPWrapper::SolverParamStruct that holds the parameters of the LP solver
 CSparseVector< _Scalar, _Flags, _StorageIndex >
 CSpecArrayFileFile adapter for SpecArray (.pepList) files
 CIDMapper::SpectraIdentificationStateResult of a partitioning by identification state with mapPrecursorsToIdentifications()
 CQCBase::SpectraMapMap to find a spectrum via its NativeID
 CSpectrumThe structure that captures the generation of a peak list (including the underlying acquisitions)
 CSpectrumAdditionThe SpectrumAddition is used to add up individual spectra
 CMzMLHandler::SpectrumDataData necessary to generate a single spectrum
 CMzXMLHandler::SpectrumDataData necessary to generate a single spectrum
 CMzIdentMLDOMHandler::SpectrumIdentificationStruct to hold the information from the SpectrumIdentification xml tag
 CMzIdentMLDOMHandler::SpectrumIdentificationProtocolStruct to hold the information from the SpectrumIdentificationProtocol xml tag
 CSpectrumLookupHelper class for looking up spectra based on different attributes
 CSpectrumMetaIdentifying information for a spectrum
 CSpectrumMetaDataLookup::SpectrumMetaDataMeta data of a spectrum
 CSplineInterpolatedPeaksData structure for spline interpolation of MS1 spectra and chromatograms
 CSplinePackageFundamental data structure for SplineInterpolatedPeaks
 CSqliteConnectorFile adapter for Sqlite files
 CSqMassFile::SqMassConfigConfiguration class for SqMassFile
 CSqMassFileAn class that uses on-disk SQLite database to read and write spectra and chromatograms
 Csquared_difference< _Tp, _Dist >
 Csquared_difference< typename _Acc::result_type, typename _Acc::result_type >
 Csquared_difference_counted< _Tp, _Dist >
 CFragmentMassError::StatisticsStructure for storing results: average and variance of all FragmentMassErrors in ppm
 CPeptideAndProteinQuant::StatisticsStatistics for processing summary
 CPSMExplainedIonCurrent::StatisticsStructure for storing results: average and variance over all PSMs
 CStatsCounterSimple counting struct, for non-numerical occurrences of meta-values
 CIdentificationDataConverter::StepOptCompareFunctor for ordering StepOpt (by date of the steps, if available):
 CStopWatchThis class is used to determine the current process' CPU (user and/or kernel) and wall time
 CFuzzyStringComparator::StreamElement_Stores information about characters, numbers, and white spaces loaded from the InputStream
 CStreamHandlerProvides a central class to register globally used output streams. Currently supported streams are
 CLogStreamBuf::StreamStructHolds 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
 CStringListUtilsUtilities operating on lists of Strings
 CStringViewStringView provides a non-owning view on an existing string
 CDBSuitability::SuitabilityDataStruct to store results
 CSummarySummary of fitting results
 CSummaryStatistics< T >Helper class to gather (and dump) some statistics from a e.g. vector<double>
 CSwathMapData structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2
 CSwathQCQuality Control function for OpenSwath
 CSwathWindowLoaderClass to read a file describing the Swath Windows
 CSysInfoSome functions to get system information
 CTaggerCalculate sequence tags from m/z values
 CMetaboTargetedAssay::TargetDecoyGroupTargetDecoyGroup stores the mz, rt and file number in correspondence to the index of a MetaboTargetedAssay vector
 CTargetedExperimentA description of a targeted experiment containing precursor and production ions
 CFile::TempDirClass representing a temporary directory
 CFile::TemporaryFiles_Internal helper class, which holds temporary filenames and deletes these files at program exit
 CTextFileThis class provides some basic file handling methods for text files
 CFeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePatternHelper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked
 CToolDescriptionInternalToolDescription Class
 CToolInfoA struct to pass information about the tool as one parameter
 CTOPPBaseBase class for TOPP applications
 CTOPPASScene::TOPPProcessStores the information for a TOPP process
 CParam::ParamIterator::TraceInfoStruct that captures information on entered / left nodes for ParamIterator
 CIDDecoyProbability::Transformation_Struct to be used to store a transformation (used for fitting)
 CTransformationDescriptionGeneric description of a coordinate transformation
 CTransformationModelBase class for transformation models
 CTransformationDescription::TransformationStatisticsSummary statistics before/after applying the transformation. For deviations before/after transformation, the percentiles 100, 99, 95, 90, 75, 50, 25 are returned
 CIsotopeWaveletTransform< PeakType >::TransSpectrumInternally (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
 CTriqlerFileFile adapter for Triqler files
 CTransitionTSVFile::TSVTransitionInternal structure to represent a transition
 CTVToolDiscoveryScans for tools and generates a param for each asynchronously
 Cunique_xerces_ptr< T >
 CUniqueIdGeneratorA generator for unique ids
 CUniqueIdIndexer< T >A base class for containers with elements derived from UniqueIdInterface. This adds functionality to convert a unique id into an index into the container
 CUniqueIdIndexer< ConsensusMap >
 CUniqueIdIndexer< FeatureMap >
 CUniqueIdInterfaceA base class defining a common interface for all classes having a unique id
 CUpdateCheckHelper Functions to perform an update query to the OpenMS REST server
 CValueTraitTrait for MatchedIterator to find pairs with a certain distance, which is computed directly on the value_type of the container
 CVecLowPrecision< T >
 Cvector< T >STL class
 CVersionInfoVersion information class
 CTOPPASVertex::VertexRoundPackageInfo for one edge and round, to be passed to next node
 CWeightsRepresents a set of weights (double values and scaled with a certain precision their integer counterparts) with a quick access
 CWeightWrapperEncapsulated weight queries to simplify mono vs average weight computation
 CWizardGUILock< TWidgetClass >RAII class to switch to certain TabWidget, disable the GUI and go back to the orignal Tab when this class is destroyed
 COPXLDataStructs::XLPrecursorThe XLPrecursor struct represents a cross-link candidate in the process of filtering candidates by precursor masses in OpenPepXL
 COPXLDataStructs::XLPrecursorComparatorThe XLPrecursorComparator is a comparator for XLPrecursors, that allows direct comparison of the XLPrecursor precursor mass with double numbers
 CXMLFileBase class for loading/storing XML files that have a handler derived from XMLHandler
 CXQuestScoresAn implementation of the scores for cross-link identification from the xQuest algorithm (O. Rinner et al., 2008, "Identification of cross-linked peptides from large sequence databases")
 CZlibCompressionCompresses and uncompresses data using zlib