OpenMS  2.8.0
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_Base_iterator
 C_Bracket_accessor< _Val >
 ►C_Node_base
 C_Node_compare< _Val, _Acc, _Cmp >
 C_Region< __K, _Val, _SubVal, _Acc, _Cmp >
 CAA
 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
 CAccurateMassSearchResult
 CACNode
 CAcqusHandlerRead-only acqus File handler for XMass Analysis
 CACSpawnSpin-off search path through the trie, which can deal with ambiguous AAs and mismatches
 CTOPPViewMenu::ActionRequirement_
 CACTrieAn Aho Corasick trie (a set of nodes with suffix links mainly)
 CACTrieState
 CAdduct
 CAdductCompareComparator for adducts
 CAdductInfo
 CMSstatsFile::AggregatedConsensusInfo
 CTriqlerFile::AggregatedConsensusInfo
 Calways_true< _Tp >
 CPepXMLFile::AminoAcidModification
 CMzIdentMLDOMHandler::AnalysisSoftwareStruct to hold the used analysis software for that file
 CMSQuantifications::AnalysisSummary
 CNucleicAcidSearchEngine::AnnotatedHit
 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
 CAnnotationStatistics
 CMassTraceDetection::Apex
 CAppliedProcessingStep
 CMSQuantifications::Assay
 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 >
 CBayesianProteinInferenceAlgorithm
 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
 CEnzymaticDigestionLogModel::BindingSite_
 ►CBinInputStream
 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+, ..)
 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
 CMSSpectrum::Chunks
 CCitationStores Citations for individual TOPP tools
 CEnzymaticDigestionLogModel::CleavageModel_
 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
 CMzTab::CMMzTabStream
 CCmpHypothesesByScore
 CCmpMassTraceByMZ
 CColorBrewer
 ►CTargetedSpectraExtractor::Comparator
 CMapAlignmentAlgorithmSpectrumAlignment::CompareInner class necessary for using the sort algorithm
 CAccurateMassSearchEngine::CompareEntryAndMass_
 CCompareMzTabMMatchRefData model of MzTabM files. Please see the official MzTabM specification at https://github.com/HUPO-PSI/mzTab/tree/master/specification_document-releases/2_0-Metabolomics-Release
 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
 CSiriusMSFile::CompoundInfo
 CMetaboTargetedAssay::CompoundTargetDecoyPairCompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum (target, decoy)
 CConnectedComponent
 CConsensusMapNormalizerAlgorithmMedianAlgorithms of ConsensusMapNormalizer
 CConsensusMapNormalizerAlgorithmQuantileAlgorithms of ConsensusMapNormalizer
 CConsensusMapNormalizerAlgorithmThresholdAlgorithms of ConsensusMapNormalizer
 CConsoleUtils
 CAASequence::ConstIteratorConstIterator for AASequence
 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 >
 CRawMSSignalSimulation::ContaminantInfo
 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
 CCsiFingerIdMzTabWriter::CsiAdapterIdentification
 CCsiFingerIdMzTabWriter::CsiAdapterRun
 CCsiFingerIdMzTabWriter
 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
 CCV
 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
 CEGHFitter1D::DataHelper struct (contains the size of an area and a raw data container)
 CEmgFitter1D::DataHelper struct (contains the size of an area and a raw data container)
 COptimizePeakDeconvolution::DataClass containing the data needed for optimization
 COptimizePick::Data
 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
 CDaTrait
 CMzIdentMLDOMHandler::DBSequenceStruct to hold the information from the DBSequence xml tag
 CDBSuitability_friend
 CDecoyGeneratorMethods to generate isobaric decoy sequences for DDA target-decoy searches
 CDecoyHelperHelper class for calculations on decoy proteins
 CFalseDiscoveryRate::DecoyStringHelperFinds decoy strings in ProteinIdentification runs
 ►Cdefault_dfs_visitor
 ►CDefaultHandler
 ►CDefaultParamHandlerA base class for all classes handling default parameters
 CDeisotoper
 CMultiplexDeltaMasses::DeltaMassMass shift with corresponding label set
 CACNode::DepthHitsInternal struct to steal one bit from depth to use as hit indicator
 CSvmTheoreticalSpectrumGenerator::DescriptorSetA set of descriptors for a single training row
 ►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
 ►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
 CColorBrewer::Distinct
 ►CDocumentIdentifierManage source document information
 CDocumentIDTaggerTags OpenMS file containers with a DocumentID
 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< DIMENSION >
 CDTAFileFile adapter for DTA files
 CEDTAFileFile adapter for Enhanced DTA files
 CElementRepresentation of an element
 CQTCluster::Element
 CElementDBSingleton that stores elements
 CEmgGradientDescent_friend
 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
 CEnzymaticDigestionLogModelClass for the Log L model of enzymatic digestion of proteins
 ►CErrorHandler
 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)
 CExternalProcessMBoxA wrapper around ExternalProcess to conveniently show a MessageBox when an error occurs
 CChromatogramExtractorAlgorithm::ExtractionCoordinates
 ►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
 CFeatureMapping::FeatureMappingInfoStores information required for preprocessing
 CFeatureMapping::FeatureToMs2IndicesStores preprocessed feature mapping information
 CIsotopeWavelet::fi_Internal union for fast computation of the power function
 CFIAMSScheduler
 CFileBasic file handling operations
 CFileHandlerFacilitates file handling by file type recognition
 CFileMappingMaps input/output files to filenames for the external program
 CFileTypes::FileTypeListHolds a vector of known file types, e.g. as a way to specify supported input formats
 CFileTypesCentralizes the file types recognized by FileHandler
 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 >
 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
 ►CLevMarqFitter1D::GenericFunctor
 ►CTraceFitter::GenericFunctor
 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
 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 orignal 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
 CNucleicAcidSearchEngine::HasInvalidLength
 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
 CHit
 CConsensusIDAlgorithm::HitInfo
 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
 CIChromatogramsWriter
 ►CIDataFrameWriter
 CIDBoostGraphCreates and maintains a boost graph based on the OpenMS ID datastructures
 CIDConflictResolverAlgorithmResolves ambiguous annotations of features with peptide identifications
 CIdentificationDataConverter
 CMs2IdentificationRate::IdentificationRateDataStructure for storing results
 CIDRipper::IdentificationRunsRepresents a set of IdentificationRuns
 CIDFilterCollection of functions for filtering peptide and protein identifications
 CMzTab::IDMzTabStream
 CIDScoreGetterSetterA class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps
 CInclusionExclusionList::IEWindow
 ►CIFeature
 CILPDCWrapper
 CIMDataConverterThis class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models
 ►CIMRMFeature
 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
 CIMTypes
 CIndex
 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
 CPSLPFormulation::IndexLess
 CPSLPFormulation::IndexTripleStruct that holds the indices of the precursors in the feature map and the ilp formulation
 CInIntensityRange< PeakType >Predicate that determines if a peak lies inside/outside a specific intensity range
 CINIUpdater
 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)
 ►CInputSource
 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
 CChromatogramPeak::IntensityLessComparator by intensity
 CPeak1D::IntensityLess
 CPeak2D::IntensityLess
 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
 CCompNovoIonScoringBase::IonScore
 CDeNovoIonScoring::IonScoreIonScore
 CSvmTheoreticalSpectrumGenerator::IonTypeNested class
 ►Cios_baseSTL class
 ►CIPeptideIdsAbstract base class which defines an interface for obtained PeptideIdentifications
 CProteinResolver::ISDGroup
 CIsEmptySpectrum< SpectrumType >Predicate that determines if a spectrum is empty
 CIDScoreGetterSetter::IsHitType< T >
 CIDScoreGetterSetter::IsIDType< T >
 ►CISignalToNoise
 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)
 CIsotopeDistribution
 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
 CISpectraWriter
 ►CISpectrumAccessThe interface of a mass spectrometry experiment
 CIsZoomSpectrum< SpectrumType >Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum
 ►Citerator
 ►CIterator
 ►Citerator
 CAASequence::IteratorIterator class for AASequence
 CNASequence::IteratorIterator of NASequence class
 ►Citerator
 ►Cset< K >::iteratorSTL iterator class
 ►CITransitionGroup
 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
 ►CLayerAnnotatorBase
 ►CLayerDataBaseClass that stores the data for one layer
 CLayerStack
 ►CLayerStatisticsCompute summary statistics (count/min/max/avg) about a container, e.g. intensity, charge, meta values, ..
 CLibSVMEncoderServes for encoding sequences into feature vectors
 CLightCompound
 CLightModification
 CLightProtein
 CLightTargetedExperiment
 CLightTransition
 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< double >
 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
 CLocalLinearMap::LLMParamDefine parameters needed by the Local Linear Map (LLM) model
 CLocalLinearMapTrained Local Linear Map (LLM) model for peak intensity prediction
 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
 CLogStreamNotifier
 CSimpleTSGXLMS::LossIndex
 CTheoreticalSpectrumGeneratorXLMS::LossIndex
 CLPWrapper
 CPercolatorFeatureSetHelper::lq_PeptideEvidenceFor accession dependent sorting of PeptideEvidences
 CPercolatorFeatureSetHelper::lq_ProteinHitFor accession dependent sorting of ProteinHits
 ►Cmap< K, T >STL class
 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
 CMapConversion
 CProteinIdentification::MappingTwo way mapping from ms-run-path to protID|pepID-identifier
 CAccurateMassSearchEngine::MappingEntry_
 CMappingParamFilename mappings for all input/output files
 CConsensusFeature::MapsLessCompare by the sets of consensus elements (lexicographically)
 CModifiedPeptideGenerator::MapToResidueType
 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
 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
 CTargetedSpectraExtractor::Match
 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
 CTraceFitter::ModelData
 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
 CModifiedNASequenceGenerator
 CModifiedPeptideGenerator
 CIdentificationData::ModifyMultiIndexAddProcessingStep< ElementType >Helper functor for adding processing steps to elements in a @t 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
 CMRMBatchFeatureSelector
 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
 ►CMRMFeatureSelector
 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
 CExperimentalDesign::MSFileSectionEntry
 CMsInspectFileFile adapter for MsInspect files
 CMSNumpressCoderClass to encode and decode data encoded with MSNumpress
 CMSPGenericFile_friend
 CMSstatsFileFile adapter for MSstats files
 CMSstatsFile::MSstatsLine_
 CMSstatsFile::MSstatsTMTLine_
 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
 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
 CMzTabAssayMetaData
 ►CMzTabBase
 CMzTabBoolean
 CMzTabContactMetaData
 CMzTabCVMetaData
 CMzTabDouble
 CMzTabDoubleList
 CMzTabFileFile adapter for MzTab files
 CMzTabInstrumentMetaData
 CMzTabInteger
 CMzTabIntegerList
 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
 CMzTabModificationList
 CMzTabModificationMetaData
 CMzTabMSmallMoleculeEvidenceSectionRowSME Small molecule evidence section (mztab-m)
 CMzTabMSmallMoleculeFeatureSectionRowSMF Small molecule feature section (mztab-m)
 CMzTabMSmallMoleculeSectionRowSML Small molecule section (mztab-m)
 CMzTabMSRunMetaData
 CMzTabMStudyVariableMetaDataMztabM StudyVariable Metadata
 CMzTabNucleicAcidSectionRowNUC - Nucleic acid section (table-based)
 CMzTabOligonucleotideSectionRowOLI - Oligonucleotide section (table-based)
 CMzTabOSMSectionRowOSM - OSM (oligonucleotide-spectrum match) section (table-based)
 CMzTabParameter
 CMzTabParameterList
 CMzTabPeptideSectionRowPEP - Peptide section (Table based)
 CMzTabProteinSectionRowPRT - Protein section (Table based)
 CMzTabPSMSectionRowPSM - PSM section (Table based)
 CMzTabSampleMetaData
 CMzTabSmallMoleculeSectionRowSML Small molecule section (table based)
 CMzTabSoftwareMetaData
 CMzTabSpectraRef
 CMzTabString
 CMzTabStringList
 CMzTabStudyVariableMetaData
 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 serves for the calculation of the global alignment score of two amino acid sequences by using the Needleman-Wunsch-Algorithm. For match and mismatch it uses a similarity scoring matrix
 CQTCluster::Neighbor
 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
 COpenMSOSInfo
 COpenSwath_Ind_Scores
 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
 COptimizePick::OptPeakFunctor
 COPXLDataStructs
 COPXLHelperFunctions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code
 COPXLSpectrumProcessingAlgorithms
 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
 COSWIndexTrace
 COSWPeakGroup
 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
 COverlapDetectorGiven 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)
 ►CPainter1DBaseA base class for painting all items from a data layer (as supported by class derived from here) onto a 1D Canvas
 COfflinePrecursorIonSelection::PairComparatorSecondElement< PairType >
 CParamManagement and storage of parameters / INI files
 CParam@TODO loop over all runs
 CParamCTDFileSerializes a Param class in paramCTD file format. Note: only storing is currently possible
 CParam::ParamEntryParameter entry used to store the actual information inside of a Param entry
 CParameterInformationStruct that captures all information of a command line parameter
 CSiriusAdapterAlgorithm::ParameterModifier
 ►CSiriusAdapterAlgorithm::ParameterSection
 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)
 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
 CPeakIntegrator::PeakArea
 CPeakPickerCWT::PeakArea_Class for the internal peak representation
 CPeakIntegrator::PeakBackground
 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
 CPeakIndexIndex of a peak or feature
 CPeakIntensityPredictorPredict peak heights of peptides based on Local Linear Map model
 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)
 CPeakIntegrator::PeakShapeMetrics
 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
 CPeptide
 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)
 COSWFile::PercolatorFeature
 CPercolatorFeatureSetHelperPercolator feature set and integration helper
 CPercolatorInfileClass for storing Percolator tab-delimited input files
 CPercolatorOutfileClass for reading Percolator tab-delimited output files
 CCompNovoIdentificationBase::PermutSimple class to store permutations and a score
 CChromatogramPeak::PositionLessComparator by position. As this class has dimension 1, this is basically an alias for RTLess
 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
 CPpmTrait
 CPrecisionWrapper< FloatingPointType >Wrapper class to implement output with appropriate precision. See precisionWrapper()
 CPrecursorCorrectionThis class provides methods for precursor correction
 CNucleicAcidSearchEngine::PrecursorInfo
 CPrecursorMassComparator
 CPrecursorPurityPrecursor purity or noise estimation
 CSimpleSVM::PredictionSVM 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
 CProbablePhosphoSites
 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
 CProtein
 CPeptideAndProteinQuant::ProteinDataQuantitative and associated data for a protein
 CProteinResolver::ProteinEntryProtein from FASTA file
 CIDBoostGraph::ProteinGroupPlaceholder for peptides with the same parent proteins or protein groups
 CProteinIdentification::ProteinGroupBundles multiple (e.g. indistinguishable) proteins in a group
 CProteinHit::ProteinHitAccessionHashHash of a ProteinHit based on its accession only!
 CProteinHit::ProteinHitPtrAccessionHash
 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
 CPrecursorPurity::PurityScores
 CPythonInfoDetect Python and retrieve information
 ►CQApplication
 ►CQCBaseThis class serves as an abstract base class for all QC classes
 ►CQDate
 ►CQDialog
 ►CQFileSystemWatcher
 ►CQGraphicsItem
 ►CQGraphicsScene
 ►CQGraphicsView
 ►CQItemDelegate
 ►CQLineEdit
 ►CQListWidget
 ►CQMainWindow
 ►CQMdiArea
 ►CQObject
 ►CQOpenGLFunctions_2_0
 ►CQOpenGLWidget
 ►CQProcess
 ►CQTabBar
 ►CQTableWidget
 ►CQTabWidget
 CQTClusterA representation of a QT cluster used for feature grouping
 ►CQTextEdit
 ►CQTreeWidget
 CQuadraticRegression
 CBaseFeature::QualityLessCompare by quality
 CQcMLFile::QualityParameterRepresentation of a quality parameter
 ►CQWidget
 CRAIICleanupException-safe way of executing arbitrary code at the end of a scope
 CRandomShuffler
 CRangeInternal structure to store a lower and upper bound of an m/z range
 ►CRangeBaseBase class for a simple range with minimum and maximum
 ►CRangeBases
 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: http://wiki.scipy.org/Cookbook/RANSAC
 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 (
 ►Creal_policies
 ►Creal_policies
 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
 ►CRefVariant
 CBase64::Reinterpreter32_Internal class needed for type-punning
 CBase64::Reinterpreter64_Internal class needed for type-punning
 CResidueRepresentation of a 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
 CResidueModificationSets the modification of AA at index by providing a pointer to a in the
 CProteinResolver::ResolverResult
 CDecoyHelper::Result
 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
 CFeatureSummary::Result
 CIdentificationSummary::Result
 CMorpheusScore::ResultScore and subscores
 CTIC::Result
 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
 CRNPxlMarkerIonExtractor
 CRNPxlModificationMassesResult
 CRNPxlModificationsGenerator
 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
 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
 CExperimentalDesign::SampleSection
 CMs2SpectrumStats::ScanEvent
 CPSLPFormulation::ScanLess
 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
 CMRMFeatureSelector::SelectorParameters
 CPrecursorIonSelection::SeqTotalScoreMoreCompare by score
 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
 CSimProteinPlain data object holding sequence and abundance information on a single protein
 CSimRandomNumberGeneratorWrapper class for random number generators used by the simulation classes
 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
 CSiriusMzTabWriter::SiriusAdapterIdentification
 CSiriusMzTabWriter::SiriusAdapterRun
 CSiriusFragmentAnnotation
 CSiriusMSFile
 CSiriusMzTabWriter
 CSiriusMzTabWriter::SiriusSpectrumMSInfo
 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
 CMzMLFile::SpecInfo
 CIDMapper::SpectraIdentificationStateResult of a partitioning by identification state with mapPrecursorsToIdentifications()
 CSpectralMatch
 CSpectralMatchScoreComparator
 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 >
 ►Cstatic_visitor
 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
 ►Cstreambuf
 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
 CStringManager
 CStringUtilsHelper
 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>
 CTargetedExperiment::SummaryStatistics
 CSVMDataData structure used in SVMWrapper
 CSvmTheoreticalSpectrumGenerator::SvmModelParameterSetSimple container storing the model parameters required for simulation
 CSvmTheoreticalSpectrumGeneratorSetLoads SvmTheoreticalSpectrumGenerator instances for different charges
 CSwathGUILockRAII class to switch to certain TabWidget, disable the GUI and go back to the orignal Tab when this class is destroyed
 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
 CTargetedExperiment
 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
 CStopWatch::TimeDiff_
 ►CToolDescriptionInternalToolDescription Class
 CToolExternalDetails
 CToolHandler
 CToolInfoA struct to pass information about the tool as one parameter
 CTOPPASVertex::TOPPASFilenames
 ►CTOPPBaseBase class for TOPP applications
 CTOPPASScene::TOPPProcessStores the information for a TOPP process
 CPrecursorIonSelection::TotalScoreMoreCompare by score
 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
 CTransitionHelper
 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
 CTriqlerFile::TriqlerLine_
 CTransitionTSVFile::TSVTransitionInternal structure to represent a transition
 CTVToolDiscoveryScans for tools/utils and generates a param for each asynchronously
 CTwoDOptimization::TwoDOptFunctor
 Cunique_xerces_ptr< T >
 CIdentificationSummary::UniqueID
 CUniqueIdGeneratorA generator for unique ids
 CUniqueIdIndexer< 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
 ►CUniqueIdIndexer< ConsensusMap >
 ►CUniqueIdIndexer< FeatureMap >
 ►CUniqueIdInterfaceA base class defining a common interface for all classes having a unique id
 CCVTerm::Unit
 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
 CPSLPFormulation::VariableIndexLess
 CVecLowPrecision< T >
 ►Cvector< T >STL class
 CVector2< Real >
 CVersionInfo::VersionDetails
 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
 CInclusionExclusionList::WindowDistance_Determine distance between two spectra
 CXCorrArrayType
 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
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