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 >
CKDTree< 2, KDTreeFeatureNode >
►C_Alloc_base< _Val, std::allocator< _Node< _Val > > >
CKDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
►C_Base_iterator
C_Iterator< _Val, _Ref, _Ptr >
C_Bracket_accessor< _Val >
►C_Node_base
C_Node< _Val >
C_Node_compare< _Val, _Acc, _Cmp >
C_Region< __K, _Val, _SubVal, _Acc, _Cmp >
CAAcid_
CAAIndex	Representation of selected AAIndex properties
CAASequence	Representation of a peptide/protein sequence
COPXLDataStructs::AASeqWithMass	The AASeqWithMass struct represents a normal peptide with its precomputed mass
COPXLDataStructs::AASeqWithMassComparator	The AASeqWithMassComparator is a comparator for AASeqWithMass objects
CFuzzyStringComparator::AbortComparison	Internal exception class
CAbsoluteQuantitationMethod	AbsoluteQuantitationMethod is a class to hold information about the quantitation method and for applying and/or generating the quantitation method
CAbsoluteQuantitationStandards	AbsoluteQuantitationStandards is a class to handle the relationship between runs, components, and their actual concentrations
CAbsoluteQuantitationStandardsFile	Load files containing runConcentration data
CSiriusMSFile::AccessionInfo	< class to store information about accessions
CAccurateMassSearchResult
CAcqusHandler	Read-only acqus File handler for XMass Analysis
CTOPPViewMenu::ActionRequirement_
CAdduct
CAdductInfo
CMSstatsFile::AggregatedConsensusInfo
CTriqlerFile::AggregatedConsensusInfo
CAhoCorasickAmbiguous	Extended Aho-Corasick algorithm capable of matching ambiguous amino acids in the pattern (i.e. proteins)
Calways_true< _Tp >
CPepXMLFile::AminoAcidModification
CMzIdentMLDOMHandler::AnalysisSoftware	Struct 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
►CAnnotation1DItem	An abstract class acting as an interface for the different 1D annotation items
CAnnotation1DCaret	An annotation item which paints a set of carets on the canvas
CAnnotation1DDistanceItem	An annotation item which represents a measured distance between two peaks
CAnnotation1DPeakItem	A peak annotation item
CAnnotation1DTextItem	An annotation item which represents an arbitrary text on the canvas
CAnnotation1DVerticalLineItem	An annotation item which represents a vertical line and text label on top
CAnnotationStatistics
CMassTraceDetection::Apex
CAppliedProcessingStep	A processing step that was applied to a data item, possibly with associated scores
CMSQuantifications::Assay
CQcMLFile::Attachment	Representation of an attachment
CAveragePosition< D >	Maintain an average position by summing up positions with weights
CAxisPainter	Draws a coordinate axis. It has only static methods, that's why the constructor is private
CAxisTickCalculator	Calculates ticks for a given value range
CBase64	Class to encode and decode Base64
CBaseVisualizer< ObjectType >	A base class for all visualizer classes
►CBaseVisualizer< Acquisition >
CAcquisitionVisualizer	Class that displays all meta information for Acquisition objects
►CBaseVisualizer< AcquisitionInfo >
CAcquisitionInfoVisualizer	Class that displays all meta information for AcquisitionInfo objects
►CBaseVisualizer< ContactPerson >
CContactPersonVisualizer	Class that displays all meta information for ContactPerson objects
►CBaseVisualizer< DataProcessing >
CDataProcessingVisualizer	Class that displays all meta information for DataProcessing objects
►CBaseVisualizer< Digestion >
CDigestionVisualizer	Class that displays all meta information of digestion objects
►CBaseVisualizer< DocumentIdentifier >
CDocumentIdentifierVisualizer	Class that displays all meta information for DocumentIdentifier objects
►CBaseVisualizer< ExperimentalSettings >
CExperimentalSettingsVisualizer	Class that displays all meta information for ExperimentalSettings objects
►CBaseVisualizer< Gradient >
CGradientVisualizer	GradientVisualizer is a visualizer class for objects of type gradient
►CBaseVisualizer< HPLC >
CHPLCVisualizer	Class that displays all meta information for HPLC objects
►CBaseVisualizer< Instrument >
CInstrumentVisualizer	Class that displays all meta information for an MS instrument
►CBaseVisualizer< InstrumentSettings >
CInstrumentSettingsVisualizer	Class that displays all meta information for InstrumentSettings objects
►CBaseVisualizer< IonDetector >
CIonDetectorVisualizer	Class that displays all meta information for IonDetector objects
►CBaseVisualizer< IonSource >
CIonSourceVisualizer	Class that displays all meta information for IonSource objects
►CBaseVisualizer< MassAnalyzer >
CMassAnalyzerVisualizer	Class that displays all meta information for MassAnalyzer objects
►CBaseVisualizer< MetaInfoDescription >
CMetaInfoDescriptionVisualizer	Class that displays all meta information for MetaInfoDescription objects
►CBaseVisualizer< MetaInfoInterface >
CMetaInfoVisualizer	MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member
►CBaseVisualizer< Modification >
CModificationVisualizer	Class that displays all meta information of modification objects
►CBaseVisualizer< PeptideHit >
CPeptideHitVisualizer	Class that displays all meta information for PeptideHit objects
►CBaseVisualizer< PeptideIdentification >
CPeptideIdentificationVisualizer	Class that displays all meta information for PeptideIdentification objects
►CBaseVisualizer< Precursor >
CPrecursorVisualizer	Class that displays all meta information for Precursor objects
►CBaseVisualizer< Product >
CProductVisualizer	Class that displays all meta information for Product objects
►CBaseVisualizer< ProteinHit >
CProteinHitVisualizer	Class that displays all meta information for ProteinHit objects
►CBaseVisualizer< ProteinIdentification >
CProteinIdentificationVisualizer	Class that displays all meta information for ProteinIdentification objects
►CBaseVisualizer< Sample >
CSampleVisualizer	Class that displays all meta information of sample objects
►CBaseVisualizer< ScanWindow >
CScanWindowVisualizer	Class that displays all meta information for ScanWindow objects
►CBaseVisualizer< Software >
CSoftwareVisualizer	Class that displays all meta information for Software objects
►CBaseVisualizer< SourceFile >
CSourceFileVisualizer	Class that displays all meta information for SourceFile objects
►CBaseVisualizer< SpectrumSettings >
CSpectrumSettingsVisualizer	Class that displays all meta information for SpectrumSettings objects
►CBaseVisualizer< Tagging >
CTaggingVisualizer	Class that displays all meta information of tagging objects
►Cbasic_string< Char >	STL class
►Cstring	STL class
CString	A more convenient string class
CBasicStatistics< RealT >	Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation
CBasicStatistics< CoordinateType >
►CBasicStatistics< double >
CAsymmetricStatistics< RealT >	Internal class for asymmetric distributions
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::BinaryData	Representation for binary data in mzML
CBinaryDataArray	The datastructures used by the OpenSwath interfaces
CBinaryTreeNode	Elements of a binary tree used to represent a hierarchical clustering process
CEnzymaticDigestionLogModel::BindingSite_
►CBinInputStream
CBzip2InputStream	Implements the BinInputStream class of the xerces-c library in order to read bzip2 compressed XML files
CGzipInputStream	Implements the BinInputStream class of the xerces-c library in order to read gzip compressed XML files
CBinnedSpectrum	This is a binned representation of a PeakSpectrum
CBitsPerValue< AAcid >
CFeatureFinderAlgorithmIsotopeWavelet::BoxElement	Internally used data structure for the sweep line algorithm
CIsotopeWaveletTransform< PeakType >::BoxElement	Internally used data structure
CBSpline< T >
CBSpline2d	B spline interpolation
CBSpline< double >
CQTCluster::BulkData	Class to store the bulk internal data (neighbors, annotations, etc.)
CBzip2Ifstream	Decompresses files which are compressed in the bzip2 format (*.bz2)
►CCachedmzML	An class that uses on-disk caching to read and write spectra and chromatograms
CSpectrumAccessOpenMSCached	An implementation of the Spectrum Access interface using on-disk caching
CInternalCalibration::CalibrantStats_	Statistics when adding peptide calibrants
CCalibrationData	A helper class, holding all calibration points
CItraqConstants::ChannelInfo	Stores information on an iTRAQ channel
CChargePair	Representation of a (putative) link between two Features, which stem from the same compound but have different charge (including different adduct ions (H+, Na+, ..)
CChromatogram	A single chromatogram
CMzMLHandler::ChromatogramData	Data necessary to generate a single chromatogram
CChromatogramMeta	Identifying information for a chromatogram
CChromatogramPeak	A 1-dimensional raw data point or peak for chromatograms
CChromatogramTools	Conversion class to convert chromatograms
CChromeleonFile	Load Chromeleon HPLC text file and save it into a `MSExperiment`
CChromExtractParams	ChromatogramExtractor parameters
CMSSpectrum::Chunk	Used to remember what subsets in a spectrum are sorted already to allow faster sorting of the spectrum
CMSSpectrum::Chunks
CCitation	Stores Citations for individual TOPP tools
CEnzymaticDigestionLogModel::CleavageModel_
COPXLDataStructs::CLSMScoreComparator	Comparator to sort CrossLinkSpectrumMatches by the main score
CClusterAnalyzer	Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's)
►CClusterFunctor	Base class for cluster functors
CAverageLinkage	AverageLinkage ClusterMethod
CCompleteLinkage	CompleteLinkage ClusterMethod
CSingleLinkage	SingleLinkage ClusterMethod
CClusterHierarchical	Hierarchical clustering with generic clustering functions
CClusteringGrid	Data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering
CClusterProxyKD	Proxy for a (potential) cluster
CMzTab::CMMzTabStream
CCmpHypothesesByScore
CCmpMassTraceByMZ
CColorBrewer
►CTargetedSpectraExtractor::Comparator
CTargetedSpectraExtractor::BinnedSpectrumComparator
CMapAlignmentAlgorithmSpectrumAlignment::Compare	Inner class necessary for using the sort algorithm
CAccurateMassSearchEngine::CompareEntryAndMass_
CCompareTypeImpl< AAcid, char >
CCompareTypeImpl< AAcid, uint8_t >
CCompomer	Holds information on an edge connecting two features from a (putative) charge ladder
CMRMFeatureQC::ComponentGroupPairQCs	Quality Controls (QCs) for multiple components (between or within component_groups)
CMRMFeaturePicker::ComponentGroupParams	Structure to contain information about a component group with its parameters
CMRMFeatureQC::ComponentGroupQCs	Quality Controls (QCs) within a component group
CMRMFeaturePicker::ComponentParams	Structure to contain information about a single component with its parameters
CMRMFeatureQC::ComponentQCs	Quality Controls (QCs) for individual components
CSiriusMSFile::CompoundInfo
CMetaboTargetedAssay::CompoundTargetDecoyPair	CompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum (target, decoy)
CConnectedComponent
CConsensusMapNormalizerAlgorithmMedian	Algorithms of ConsensusMapNormalizer
CConsensusMapNormalizerAlgorithmQuantile	Algorithms of ConsensusMapNormalizer
CConsensusMapNormalizerAlgorithmThreshold	Algorithms of ConsensusMapNormalizer
CConsoleUtils
CAASequence::ConstIterator	ConstIterator for AASequence
CNASequence::ConstIterator	ConstIterator of NASequence class
CConstRefVector< ContainerT >	This vector holds pointer to the elements of another container
►CConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >	ConstIterator for the ConstRefVector
CConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >	Mutable iterator 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::ContaminantsSummary	Structure for storing results
►CContinuousWaveletTransform	This class is the base class of the continuous wavelet transformation
CContinuousWaveletTransformNumIntegration	This class computes the continuous wavelet transformation using a marr wavelet
CControlledVocabulary	Representation of a controlled vocabulary
CConvexHull2D	A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling
COPXLDataStructs::CrossLinkSpectrumMatch	The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum in OpenPepXL
CCsiFingerIdMzTabWriter::CsiAdapterHit	Internal structure used in SiriusAdapter that is used for the conversion of the Csi:FingerID output to an mzTab
CCsiFingerIdMzTabWriter::CsiAdapterIdentification
CCsiFingerIdMzTabWriter::CsiAdapterRun
CCsiFingerIdMzTabWriter
CCubicSpline2d	Cubic spline interpolation as described in R.L. Burden, J.D. Faires, Numerical Analysis, 4th ed. PWS-Kent, 1989, ISBN 0-53491-585-X, pp. 126-131
CCV
CCVMappingRule	Representation of a CV Mapping rule used by CVMappings
CCVMappings	Representation of controlled vocabulary mapping rules (for PSI formats)
CCVMappingTerm	Representation of controlled vocabulary term
CCVReference	Controlled Vocabulary Reference
CControlledVocabulary::CVTerm	Representation of a CV term
CCVTerm	Representation of controlled vocabulary term
CSemanticValidator::CVTerm	Representation of a parsed CV term
CEGHFitter1D::Data	Helper struct (contains the size of an area and a raw data container)
CEmgFitter1D::Data	Helper struct (contains the size of an area and a raw data container)
COptimizePeakDeconvolution::Data	Class containing the data needed for optimization
COptimizePick::Data
CTwoDOptimization::Data	Helper struct (contains the size of an area and a raw data container)
CMzIdentMLDOMHandler::DatabaseInput	Struct to hold the information from the DatabaseInput xml tag
CDataFilters::DataFilter	Representation of a peak/feature filter combining FilterType, FilterOperation and a value (either double or String)
CDataFilters	DataFilter array providing some convenience functions
CTransformationModel::DataPoint	Coordinate pair (with optional annotation)
►CDataTabBase	All tabs need to implement this interface
CDIATreeTab	Hierarchical visualization and selection of spectra
CSpectraIDViewTab	Tabular visualization / selection of identified spectra
CSpectraTreeTab	Hierarchical visualization and selection of spectra
CDataValue	Class to hold strings, numeric values, lists of strings and lists of numeric values
CDateTime	DateTime Class
CDaTrait
CMzIdentMLDOMHandler::DBSequence	Struct to hold the information from the DBSequence xml tag
CDecoyGenerator	Methods to generate isobaric decoy sequences for DDA target-decoy searches
CDecoyHelper	Helper class for calculations on decoy proteins
►Cdefault_dfs_visitor
CIDBoostGraph::dfs_ccsplit_visitor	A boost dfs visitor that copies connected components into a vector of graphs
►CDefaultHandler
►CXMLHandler	Base class for XML handlers
CCVMappingFile	Used to load CvMapping files
CConsensusXMLFile	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation
CFeatureXMLFile	This class provides Input/Output functionality for feature maps
CIdXMLFile	Used to load and store idXML files
CMascotXMLHandler	Handler that is used for parsing MascotXML data
CMzDataHandler
CMzIdentMLHandler	XML STREAM handler for MzIdentMLFile
►CMzMLHandler	Handler for mzML file format
►CMSDataWritingConsumer	Consumer class that writes MS data to disk using the mzML format
CNoopMSDataWritingConsumer	Consumer class that perform no operation
CPlainMSDataWritingConsumer	Consumer class that writes MS data to disk using the mzML format
CMzQuantMLHandler	XML handler for MzQuantMLFile
CMzXMLHandler
CPTMXMLHandler	Handler that is used for parsing PTMXML data
►CParamXMLHandler	XML Handler for Param files
CToolDescriptionHandler	XML handler for ToolDescriptionFile
►CSemanticValidator	Semantically validates XML files using CVMappings and a ControlledVocabulary
CMzDataValidator	Semantically validates MzXML files
CMzIdentMLValidator	Semantically validates MzXML files
CMzMLValidator	Semantically validates MzXML files
CMzQuantMLValidator	Semantically validates MzQuantML files
CTraMLValidator	Semantically validates MzXML files
CTraMLHandler	XML handler for TraMLFile
CUnimodXMLHandler	Handler that is used for parsing XTandemXML data
CXQuestResultXMLHandler	XMLHandler for the result files of XQuest
COMSSAXMLFile	Used to load OMSSAXML files
CPepXMLFile	Used to load and store PepXML files
CPepXMLFileMascot	Used to load Mascot PepXML files
CProtXMLFile	Used to load (storing not supported, yet) ProtXML files
CQcMLFile	File adapter for QcML files used to load and store QcML files
CTransformationXMLFile	Used to load and store TransformationXML files
CXTandemXMLFile	Used to load XTandemXML files
►CDefaultParamHandler	A base class for all classes handling default parameters
►CBaseModel< 1 >
►CInterpolationModel	Abstract class for 1D-models that are approximated using linear interpolation
CBiGaussModel	BiGaussian distribution approximated using linear interpolation
CEGHModel	Exponential-Gaussian hybrid distribution model for elution profiles
CEmgModel	Exponentially modified gaussian distribution model for elution profiles
CExtendedIsotopeModel	Extended isotope distribution approximated using linear interpolation
CGaussModel	Normal distribution approximated using linear interpolation
CIsotopeModel	Isotope distribution approximated using linear interpolation
►CBaseModel< 2 >
CProductModel< 2 >	The class template is only implemented for D=2 because we use Peak2D here
►CSignalToNoiseEstimator< MSSpectrum >
CSignalToNoiseEstimatorMeanIterative< Container >	Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities
CSignalToNoiseEstimatorMedian< Container >	Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based)
CAScore	Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the most probable phosphorylation-site(s). For each phosphorylation site a probability score is calculated. The algorithm is implemented according to Beausoleil et al. (Nat. Biotechnol. 2006)
CAbsoluteQuantitation	AbsoluteQuantitation is a class to support absolute or relative quantitation for targeted or untargeted quantitation workflows (e.g., Isotope Dilution Mass Spectrometry)
CAccurateMassSearchEngine	An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB)
►CBaseGroupFinder	The base class of all element group finding algorithms
CLabeledPairFinder	The LabeledPairFinder allows the matching of labeled features (features with a fixed distance)
CQTClusterFinder	A variant of QT clustering for the detection of feature groups
CSimplePairFinder	This class implements a simple point pair finding algorithm
CStablePairFinder	This class implements a pair finding algorithm for consensus features
►CBaseLabeler	Abstract base class for all kinds of labeling techniques
CICPLLabeler	Simulate ICPL experiments
CITRAQLabeler	Simulate iTRAQ experiments
CLabelFreeLabeler	Abstract base class for all kinds of labeling techniques
CO18Labeler	Simulate O-18 experiments
CSILACLabeler	Simulate SILAC experiments
CBaseModel< D >	Abstract base class for all D-dimensional models
►CBaseSuperimposer	The base class of all superimposer algorithms
CPoseClusteringAffineSuperimposer	A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation
CPoseClusteringShiftSuperimposer	A superimposer that uses a voting scheme, also known as pose clustering, to find a good shift transformation
CBasicProteinInferenceAlgorithm	Algorithm class that implements simple protein inference by aggregation of peptide scores. It has multiple parameter options like the aggregation method, when to distinguish peptidoforms, and if you want to use shared peptides ("use_shared_peptides"). First, the best PSM per spectrum is used, then only the best PSM per peptidoform is aggregated. Peptidoforms can optionally be distinguished via the treat_X_separate parameters:
CBayesianProteinInferenceAlgorithm	Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental)
CBernNorm	BernNorm scales the peaks by ranking them and then scaling them according to rank
►CBinnedSpectrumCompareFunctor	Base class for compare functors of BinnedSpectra
CBinnedSharedPeakCount	Compare functor scoring the shared peaks for similarity measurement
CBinnedSpectralContrastAngle	Compare functor scoring the spectral contrast angle for similarity measurement
CBinnedSumAgreeingIntensities	Sum of agreeing intensities for similarity measurement
►CCompNovoIdentificationBase	Run with CompNovoIdentificationBase
CCompNovoIdentification	Run with CompNovoIdentification
CCompNovoIdentificationCID	Run with CompNovoIdentificationCID
►CCompNovoIonScoringBase	Run with CompNovoIonScoringBase
CCompNovoIonScoring	Run with CompNovoIonScoring
CCompNovoIonScoringCID	Run with CompNovoIonScoringCID
►CConsensusIDAlgorithm	Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs)
►CConsensusIDAlgorithmIdentity	Abstract base class for ConsensusID algorithms that compare only identical sequences
CConsensusIDAlgorithmAverage	Calculates a consensus from multiple ID runs by averaging the search scores
CConsensusIDAlgorithmBest	Calculates a consensus from multiple ID runs by taking the best search score
CConsensusIDAlgorithmRanks	Calculates a consensus from multiple ID runs based on the ranks of the search hits
CConsensusIDAlgorithmWorst	Calculates a consensus from multiple ID runs by taking the worst search score (conservative approach)
►CConsensusIDAlgorithmSimilarity	Abstract base class for ConsensusID algorithms that take peptide similarity into account
CConsensusIDAlgorithmPEPIons	Calculates a consensus from multiple ID runs based on PEPs and shared ions
CConsensusIDAlgorithmPEPMatrix	Calculates a consensus from multiple ID runs based on PEPs and sequence similarities
CConsensusMapMergerAlgorithm	Merges identification data in ConsensusMaps
CDBSuitability	This class holds the functionality of calculating the database suitability
CDIAScoring	Scoring of an spectrum at the peak apex of an chromatographic elution peak
CDeNovoAlgorithm	Base class for ion scoring implementation for de novo algorithms
CDeNovoIdentification	Base class for de novo identification
CDeNovoIonScoring	Base class for ion scoring implementation for de novo algorithms
CDeNovoPostScoring	Base class for ion scoring implementation for de novo algorithms
CDetectabilitySimulation	Simulates peptide detectability
CDiaPrescore	Scoring of an spectrum given library intensities of a transition group
CDigestSimulation	Simulates protein digestion
CElutionModelFitter	Helper class for fitting elution models to features
CElutionPeakDetection	Extracts chromatographic peaks from a mass trace
CEmgGradientDescent	Compute the area, background and shape metrics of a peak
CFIAMSDataProcessor	Data processing for FIA-MS data
CFalseDiscoveryRate	Calculates false discovery rates (FDR) from identifications
CFeatureDeconvolution	An algorithm to decharge features (i.e. as found by FeatureFinder)
CFeatureDistance	A functor class for the calculation of distances between features or consensus features
►CFeatureFinderAlgorithm	Abstract base class for FeatureFinder algorithms
CFeatureFinderAlgorithmIsotopeWavelet	Implements the isotope wavelet feature finder
CFeatureFinderAlgorithmMRM	FeatureFinderAlgorithm for MRM experiments
CFeatureFinderAlgorithmPicked	FeatureFinderAlgorithm for picked peaks
CFeatureFinderAlgorithmMetaboIdent
CFeatureFinderIdentificationAlgorithm
CFeatureFinderMultiplexAlgorithm
CFeatureFindingMetabo	Method for the assembly of mass traces belonging to the same isotope pattern, i.e., that are compatible in retention times, mass-to-charge ratios, and isotope abundances
►CFeatureGroupingAlgorithm	Base class for all feature grouping algorithms
CFeatureGroupingAlgorithmKD	A feature grouping algorithm for unlabeled data
CFeatureGroupingAlgorithmLabeled	A map feature grouping algorithm for labeling techniques with two labels
CFeatureGroupingAlgorithmQT	A feature grouping algorithm for unlabeled data
CFeatureGroupingAlgorithmUnlabeled	A map feature grouping algorithm for unlabeled data
►CFilterFunctor	A FilterFunctor extracts some spectrum characteristics for quality assessment
CComplementFilter	Total intensity of peak pairs that could result from complementing fragments of charge state 1
CGoodDiffFilter	GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss
CIntensityBalanceFilter	IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions
CIsotopeDiffFilter	IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks
CNeutralLossDiffFilter	NeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained by a neutral loss
CTICFilter	TICFilter calculates TIC
►CFitter1D	Abstract base class for all 1D-dimensional model fitter
►CLevMarqFitter1D	Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization
CEGHFitter1D	Exponential-Gaussian hybrid distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization
CEmgFitter1D	Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization
►CMaxLikeliFitter1D	Abstract base class for all 1D-model fitters using maximum likelihood optimization
CBiGaussFitter1D	BiGaussian distribution fitter (1-dim.) approximated using linear interpolation
CExtendedIsotopeFitter1D	Extended isotope distribution fitter (1-dim.) approximated using linear interpolation
CGaussFitter1D	Gaussian distribution fitter (1-dim.) approximated using linear interpolation
CIsotopeFitter1D	Isotope distribution fitter (1-dim.) approximated using linear interpolation
CGaussFilter	This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data
CIDDecoyProbability	IDDecoyProbability calculates probabilities using decoy approach
CIDMapper	Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications
CIDMergerAlgorithm	Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but concatenates PSMs. Checks search engine consistency of all inserted runs. It differs from the IDMerger tool, in that it is an algorithm class and it allows inserting multiple peptide hits per peptide sequence (not only the first occurrence)
CIDRipper	Ripping protein/peptide identification according their file origin
CIDScoreSwitcherAlgorithm
CInclusionExclusionList	Provides functionality for writing inclusion or exclusion lists
CIonizationSimulation	Simulates Protein ionization
CIsobaricChannelExtractor	Extracts individual channels from MS/MS spectra for isobaric labeling experiments
CIsobaricQuantifier	Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing
►CIsobaricQuantitationMethod	Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix
CItraqEightPlexQuantitationMethod	ITRAQ 8 plex quantitation to be used with the IsobaricQuantitation
CItraqFourPlexQuantitationMethod	ITRAQ 4 plex quantitation to be used with the IsobaricQuantitation
CTMTElevenPlexQuantitationMethod	TMT 11plex quantitation to be used with the IsobaricQuantitation
CTMTSixPlexQuantitationMethod	TMT 6plex quantitation to be used with the IsobaricQuantitation
CTMTSixteenPlexQuantitationMethod	TMT 16plex quantitation to be used with the IsobaricQuantitation
CTMTTenPlexQuantitationMethod	TMT 10plex quantitation to be used with the IsobaricQuantitation
CIsotopeLabelingMDVs	IsotopeLabelingMDVs is a class to support and analyze isotopic labeling experiments (i.e. MDVs : Mass Distribution Vectors, also known as Mass Isotopomer Distribution (MID))
CKDTreeFeatureMaps	Stores a set of features, together with a 2D tree for fast search
►CLinearResampler	Linear Resampling of raw data
CLinearResamplerAlign	Linear Resampling of raw data with alignment
CLowessSmoothing	LOWESS (locally weighted scatterplot smoothing)
CMRMDecoy	This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object
CMRMFeatureFilter	The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria
CMRMFeatureFinderScoring	The MRMFeatureFinder finds and scores peaks of transitions that co-elute
CMRMFragmentSelection	This class can select appropriate fragment ions of an MS/MS spectrum of a peptide
CMRMMapping	A class to map targeted assays to chromatograms
CMRMTransitionGroupPicker	The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors
CMSPFile	File adapter for MSP files (NIST spectra library)
CMSPGenericFile	Load MSP text file and save it into an `MSExperiment`
CMSSim	Central class for simulation of mass spectrometry experiments
CMapAlignmentAlgorithmIdentification	A map alignment algorithm based on peptide identifications from MS2 spectra
CMapAlignmentAlgorithmPoseClustering	A map alignment algorithm based on pose clustering
CMapAlignmentAlgorithmSpectrumAlignment	A map alignment algorithm based on spectrum similarity (dynamic programming)
CMapAlignmentAlgorithmTreeGuided	A map alignment algorithm based on peptide identifications from MS2 spectra
CMarkerMower	MarkerMower uses PeakMarker to find peaks, those that are not marked get removed
CMascotGenericFile	Read/write Mascot generic files (MGF)
CMascotRemoteQuery	Class which handles the communication between OpenMS and the Mascot server
CMassDecompositionAlgorithm	Mass decomposition algorithm, given a mass it suggests possible compositions
CMassTraceDetection	A mass trace extraction method that gathers peaks similar in m/z and moving along retention time
CMasstraceCorrelator	Correlates individual masstraces found in mass spectrometric maps
CPosteriorErrorProbabilityModel	Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture
CMetaboliteFeatureDeconvolution	An algorithm to decharge small molecule features (i.e. as found by FeatureFinder)
CMetaboliteSpectralMatching
CMorphologicalFilter	This class implements baseline filtering operations using methods from mathematical morphology
CMultiplexDeltaMassesGenerator	Generates complete list of all possible mass shifts due to isotopic labelling
CNLargest	NLargest removes all but the n largest peaks
CNormalizer	Normalizes the peak intensities spectrum-wise
CNucleicAcidSpectrumGenerator	Generates theoretical spectra for nucleic acid sequences
COfflinePrecursorIonSelection	Implements different algorithms for precursor ion selection
COpenPepXLAlgorithm	Search for peptide pairs linked with a labeled cross-linker
COpenPepXLLFAlgorithm	Search for cross-linked peptide pairs in tandem MS spectra
COptimizePeakDeconvolution	This class provides the deconvolution of peak regions using non-linear optimization
CPSLPFormulation	Implements ILP formulation of precursor selection problems
CParentPeakMower	ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions
CPeakIntegrator	Compute the area, background and shape metrics of a peak
►CPeakMarker	PeakMarker marks peaks that seem to fulfill some criterion
CComplementMarker	ComplementMarker marks peak pairs which could represent y - b ion pairs
CIsotopeMarker	IsotopeMarker marks peak pairs which could represent an ion and its isotope
CNeutralLossMarker	NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water, ammonia)
CPeakPickerCWT	This class implements a peak picking algorithm using wavelet techniques
CPeakPickerHiRes	This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width
CPeakPickerIterative	This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data)
CPeakPickerMRM	The PeakPickerMRM finds peaks a single chromatogram
CPeakPickerSH
►CPeakSpectrumCompareFunctor	Base class for compare functors of spectra, that return a similarity value for two spectra
CPeakAlignment	Make a PeakAlignment of two PeakSpectra
CSpectraSTSimilarityScore	Similarity score of SpectraST
CSpectrumAlignmentScore	Similarity score via spectra alignment
CSpectrumCheapDPCorr	SpectrumCheapDPCorr calculates an optimal alignment on stick spectra
CSpectrumPrecursorComparator	SpectrumPrecursorComparator compares just the parent mass of two spectra
CSteinScottImproveScore	Similarity score based of Stein & Scott
CZhangSimilarityScore	Similarity score of Zhang
CPeptideAndProteinQuant	Helper class for peptide and protein quantification based on feature data annotated with IDs
CPeptideIndexing	Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds target/decoy information
►CPlotCanvas	Base class for visualization canvas classes
CPlot1DCanvas	Canvas for visualization of one or several spectra
CPlot2DCanvas	Canvas for 2D-visualization of peak map, feature map and consensus map data
CPlot3DCanvas	Canvas for 3D-visualization of peak map data
CPrecursorIonSelection	This class implements different precursor ion selection strategies
CPrecursorIonSelectionPreprocessing	This class implements the database preprocessing needing for precursor ion selection
CProteinResolver	Helper class for peptide and protein quantification based on feature data annotated with IDs
CProtonDistributionModel	A proton distribution model to calculate the proton distribution over charged peptides
CQuantitativeExperimentalDesign	Merge files according to experimental design
CRTSimulation	Simulates/Predicts retention times for peptides or peptide separation
CRawMSSignalSimulation	Simulates MS signals for a given set of peptides
CRawTandemMSSignalSimulation	Simulates tandem MS signals for a given set of peptides
CSONARScoring	Scoring of an spectrum using SONAR data
CSavitzkyGolayFilter	Computes the Savitzky-Golay filter coefficients using QR decomposition
CScaler	Scaler scales the peak by ranking the peaks and assigning intensity according to rank
►CSignalToNoiseEstimator< Container >	This class represents the abstract base class of a signal to noise estimator
CSignalToNoiseEstimatorMedian< OpenMS::MSChromatogram >
CSignalToNoiseEstimatorMedian< ContainerT >
CSimpleSVM	Simple interface to support vector machines for classification (via LIBSVM)
CSimpleSearchEngineAlgorithm
CSimpleTSGXLMS	Generates theoretical spectra for cross-linked peptides
CSiriusAdapterAlgorithm
CSpectraIDViewTab	Tabular visualization / selection of identified spectra
CSpectraMerger	Merges blocks of MS or MS2 spectra
CSpectraMerger::SpectraDistance_
CSpectrumAlignment	Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) alignment if absolute tolerances are given. Scoring function is the m/z distance between peaks. Intensity does not play a role!
CSpectrumAnnotator	Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options
CSqrtMower	Scales the intensity of peaks to the sqrt
CSvmTheoreticalSpectrumGenerator	Simulates MS2 spectra with support vector machines
CSvmTheoreticalSpectrumGeneratorTrainer	Train SVM models that are used by SvmTheoreticalSpectrumGenerator
CSwathMapMassCorrection	A class containing correction functions for Swath MS maps
CSwathWizardBase	Main window of the SwathWizard tool
CTOFCalibration	This class implements an external calibration for TOF data using external calibrant spectra
CTOPPASBase	Main window of the TOPPAS tool
CTOPPViewBase	Main window of TOPPView tool
CTargetedSpectraExtractor	This class filters, annotates, picks, and scores spectra (e.g., taken from a DDA experiment) based on a target list
CTheoreticalSpectrumGenerator	Generates theoretical spectra for peptides with various options
CTheoreticalSpectrumGeneratorXLMS	Generates theoretical spectra for cross-linked peptides
CThresholdMower	ThresholdMower removes all peaks below a threshold
►CTraceFitter	Abstract fitter for RT profile fitting
CEGHTraceFitter	A RT Profile fitter using an Exponential Gaussian Hybrid background model
CGaussTraceFitter	Fitter for RT profiles using a Gaussian background model
►CTransitionTSVFile	This class supports reading and writing of OpenSWATH transition lists
CTransitionPQPFile	This class supports reading and writing of PQP files
CTwoDOptimization	This class provides the two-dimensional optimization of the picked peak parameters
CWindowMower	WindowMower augments the highest peaks in a sliding or jumping window
CXFDRAlgorithm	Calculates false discovery rate estimates on crosslink identifications
CDeisotoper
CMultiplexDeltaMasses::DeltaMass	Mass shift with corresponding label set
CSvmTheoreticalSpectrumGenerator::DescriptorSet	A set of descriptors for a single training row
►CDigestionEnzyme	Base class for digestion enzymes
CDigestionEnzymeProtein	Representation of a digestion enzyme for proteins (protease)
CDigestionEnzymeRNA	Representation of a digestion enzyme for RNA (RNase)
CDigestionEnzymeDB< DigestionEnzymeType, InstanceType >	Digestion enzyme database (base class)
►CDigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
CProteaseDB	Database for enzymes that digest proteins (proteases)
►CDigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
CRNaseDB	Database for enzymes that digest RNA (RNases)
CIDFilter::DigestionFilter	Is peptide evidence digestion product of some protein
►CDIntervalBase< D >	A base class for D-dimensional interval
CDBoundingBox< 1 >
CDBoundingBox< 2 >
CDRange< 1 >
CDRange< 2 >
CDRange< 3 >
CDBoundingBox< D >	A D-dimensional bounding box
CDRange< D >	A D-dimensional half-open interval
CDistanceMatrix< Value >	A two-dimensional distance matrix, similar to OpenMS::Matrix
CFeatureDistance::DistanceParams_	Structure for storing distance parameters
CColorBrewer::Distinct
►CDocumentIdentifier	Manage source document information
CConsensusMap	A container for consensus elements
►CExperimentalSettings	Description of the experimental settings
CMSExperiment	In-Memory representation of a mass spectrometry experiment
CMSQuantifications
CFeatureMap	A container for features
CDocumentIDTagger	Tags 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 >
CDTAFile	File adapter for DTA files
CEDTAFile	File adapter for Enhanced DTA files
CElement	Representation of an element
CQTCluster::Element
CElementDB	Singleton that stores elements
CEmgGradientDescent_friend
CEmgScoring	Scoring of an elution peak using an exponentially modified gaussian distribution model
CEmpiricalFormula	Representation of an empirical formula
►CEnhancedTabBarWidgetInterface	Widgets that are placed into an EnhancedTabBar must implement this interface
►CPlotWidget	Base class for spectrum widgets
CPlot1DWidget	Widget for visualization of several spectra
CPlot2DWidget	Widget for 2D-visualization of peak map and feature map data
CPlot3DWidget	Widget for 3D-visualization of map data
CTOPPASWidget	Widget visualizing and allowing to edit TOPP pipelines
►CEnzymaticDigestion	Class for the enzymatic digestion of sequences
CProteaseDigestion	Class for the enzymatic digestion of proteins
CRNaseDigestion	Class for the enzymatic digestion of RNAs
CEnzymaticDigestionLogModel	Class for the Log L model of enzymatic digestion of proteins
CEqualInTolerance< CompareType >	Struct for binary predicate to consider equality with a certain tolerance
►CErrorHandler
CXMLValidator	Validator for XML files
CEuclideanSimilarity	CompareFunctor for 2Dpoints
►Cexception	STL class
►Cbad_alloc	STL class
COutOfMemory	Out of memory exception
►Cruntime_error	STL class
►CBaseException	Exception base class
CClusterFunctor::InsufficientInput	Exception thrown if not enough data (<2) is used
CBufferOverflow	Buffer overflow exception
CConversionError	Invalid conversion exception
CDepletedIDPool	Exception used if no more unique document ID's can be drawn from ID pool
CDivisionByZero	Division by zero error exception
CElementNotFound	Element could not be found exception
CFailedAPICall	A call to an external library (other than OpenMS) went wrong
CFileEmpty	File is empty
CFileNameTooLong	Filename is too long to be writable/readable by the filesystem
CFileNotFound	File not found exception
CFileNotReadable	File not readable exception
CFileNotWritable	File not writable exception
CIOException	General IOException
CIllegalArgument	A method or algorithm argument contains illegal values
CIllegalPosition	Invalid 3-dimensional position exception
CIllegalSelfOperation	Illegal self operation exception
CIllegalTreeOperation	Illegal tree operation exception
CIncompatibleIterators	Incompatible iterator exception
CIndexOverflow	Int overflow exception
CIndexUnderflow	Int underflow exception
CInvalidIterator	Invalid iterator exception
CInvalidParameter	Exception indicating that an invalid parameter was handed over to an algorithm
CInvalidRange	Invalid range exception
CInvalidSize	Invalid UInt exception
CInvalidValue	Invalid value exception
CMissingInformation	Not all required information provided
CNotImplemented	Not implemented exception
CNullPointer	Null pointer argument is invalid exception
COutOfGrid	Out of grid exception
COutOfMemory	Out of memory exception
COutOfRange	Out of range exception
CParseError	Parse Error exception
CPostcondition	Postcondition failed exception
CPrecondition	Precondition failed exception
CRequiredParameterNotGiven	A required parameter was not given
CSizeUnderflow	UInt underflow exception
CSqlOperationFailed	SqlOperation failed exception
CUnableToCalibrate	Exception used if an error occurred while calibrating a dataset
CUnableToCreateFile	Unable to create file exception
CUnableToFit	Exception used if an error occurred while fitting a model to a given dataset
CUnregisteredParameter	An unregistered parameter was accessed
CWrongParameterType	A parameter was accessed with the wrong type
CFeatureFinderDefs::NoSuccessor	Exception that is thrown if a method an invalid IndexPair is given
CXMLHandler::EndParsingSoftly	Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file is needed)
CMap< Key, T >::IllegalKey	Map illegal key exception
CUnnormalizedComparator	Exception thrown if clustering is attempted without a normalized compare functor
CExperimentalDesign	Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class
CExperimentalDesignFile	Load an experimental design from a TSV file. (see ExperimentalDesign for details on the supported format)
CExternalProcessMBox	A wrapper around ExternalProcess to conveniently show a MessageBox when an error occurs
CChromatogramExtractorAlgorithm::ExtractionCoordinates
►CFactoryBase	Base class for Factory<T>
CFactory< FactoryProduct >	Returns FactoryProduct* based on the name of the desired concrete FactoryProduct
CFAIMSHelper	Helper 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::FASTAEntry	FASTA 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::FeatureCompare	Comparison functor for features
CFeatureFinderIdentificationAlgorithm::FeatureCompare	Comparison functor for features
CAbsoluteQuantitationStandards::featureConcentration	Structure to hold a single component and its corresponding known concentration
CFeatureFileOptions	Options for loading files containing features
CFeatureFinderIdentificationAlgorithm::FeatureFilterPeptides	Predicate for filtering features by assigned peptides:
CFeatureFinderAlgorithmMetaboIdent::FeatureFilterQuality	Predicate for filtering features by overall quality
CFeatureFinderIdentificationAlgorithm::FeatureFilterQuality	Predicate for filtering features by overall quality:
CFeatureFinderAlgorithmPickedHelperStructs	Wrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes
►CFeatureFinderDefs	The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes
CFeatureFinder	The main feature finder class
CFeatureFinderAlgorithmMRM	FeatureFinderAlgorithm for MRM experiments
CFeatureFinderAlgorithmPicked	FeatureFinderAlgorithm for picked peaks
CFitter1D	Abstract base class for all 1D-dimensional model fitter
CFeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound	Compound in the assay library
CFeatureHypothesis	Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis)
CFeatureMapping
CFeatureMapping::FeatureMappingInfo	Stores information required for preprocessing
CFeatureMapping::FeatureToMs2Indices	Stores preprocessed feature mapping information
CIsotopeWavelet::fi_	Internal union for fast computation of the power function
CFIAMSScheduler
CFile	Basic file handling operations
CFileHandler	Facilitates file handling by file type recognition
CFileMapping	Maps input/output files to filenames for the external program
CFileTypes::FileTypeList	Holds a vector of known file types, e.g. as a way to specify supported input formats
CFileTypes	Centralizes 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< LayerData::DataType >
CFlagSet< TV_STATUS >
CPeptideIndexing::FoundProteinFunctor
CRNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_	Single fragment annotation
CGumbelMaxLikelihoodFitter::Functor< _Scalar, NX, NY >
►CGumbelMaxLikelihoodFitter::Functor< double >
CGumbelMaxLikelihoodFitter::GumbelDistributionFunctor
CFuzzyStringComparator	Fuzzy comparison of strings, tolerates numeric differences
CGammaDistributionFitter::GammaDistributionFitResult	Struct to represent the parameters of a gamma distribution
CGammaDistributionFitter	Implements a fitter for the Gamma distribution
CGaussFilterAlgorithm	This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data
CGaussFitter::GaussFitResult	Struct of parameters of a Gaussian distribution
CGaussFitter	Implements a fitter for Gaussian functions
CSignalToNoiseEstimator< Container >::GaussianEstimate	Protected struct to store parameters my, sigma for a Gaussian distribution
►CLevMarqFitter1D::GenericFunctor
CEGHFitter1D::EGHFitterFunctor
CEmgFitter1D::EgmFitterFunctor
►CTraceFitter::GenericFunctor
CEGHTraceFitter::EGHTraceFunctor
CGaussTraceFitter::GaussTraceFunctor
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
CGlobalExceptionHandler	OpenMS global exception handler
CGradient	Representation of a HPLC gradient
CGridBasedCluster	Basic data structure for clustering
CGridFeature	Representation of a feature in a hash grid
CGridSearch< TupleTypes >
CGUILock	RAII class to disable the GUI and set a busy cursor and go back to the orignal state when this class is destroyed
CGumbelDistributionFitter::GumbelDistributionFitResult	Struct to represent the parameters of a gumbel distribution
CGumbelMaxLikelihoodFitter::GumbelDistributionFitResult	Struct to represent the parameters of a gumbel distribution
CGumbelDistributionFitter	Implements a fitter for the Gumbel distribution
CGumbelMaxLikelihoodFitter	Implements a fitter for the Gumbel distribution
CGzipIfstream	Decompresses 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::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
CHDF5Connector	File adapter for HDF5 files
CHiddenMarkovModel	Hidden Markov Model implementation of PILIS
CHistogram< ValueType, BinSizeType >	Representation of a histogram
CConsensusIDAlgorithm::HitInfo
CHMMState	Hidden Markov Model State class for the Hidden Markov Model
CHost< Pattern< TNeedle, FuzzyAC > >
CHost< Pattern< TNeedle, FuzzyAC > const >
CHPLC	Representation of a HPLC experiment
CHyperScore	An implementation of the X!Tandem HyperScore PSM scoring function
CIBSpectraFile	Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results
CIChromatogramsReader	The interface of read-access to a list of chromatograms
CIChromatogramsWriter
►CIDataFrameWriter
CCSVWriter
CDataMatrix
CIDBoostGraph	Creates and maintains a boost graph based on the OpenMS ID datastructures
CIDConflictResolverAlgorithm	Resolves ambiguous annotations of features with peptide identifications
CIdentificationDataConverter
CMs2IdentificationRate::IdentificationRateData	Structure for storing results
CIDFilter	Collection of functions for filtering peptide and protein identifications
CMzTab::IDMzTabStream
CIDScoreGetterSetter	A class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps
CInclusionExclusionList::IEWindow
►CIFeature
CFeatureOpenMS	An implementation of the OpenSWATH Feature Access interface using OpenMS
CMockFeature	Mock object implementing IFeature
CILPDCWrapper
CIMDataConverter	This class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models
►CIMRMFeature
CMRMFeatureOpenMS	An implementation of the OpenSWATH MRM Feature Access interface using OpenMS
CMockMRMFeature	Mock object implementing IMRMFeature
CIMSAlphabet	Holds 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
CIMSAlphabetTextParser	Implements abstract AlphabetParser to read data from the plain text format
►CIMSDataConsumer	The interface of a consumer of spectra and chromatograms
►CFullSwathFileConsumer	Abstract base class which can consume spectra coming from SWATH experiment stored in a single file
CCachedSwathFileConsumer	On-disk cached implementation of FullSwathFileConsumer
CMzMLSwathFileConsumer	On-disk mzML implementation of FullSwathFileConsumer
CRegularSwathFileConsumer	In-memory implementation of FullSwathFileConsumer
CMSDataAggregatingConsumer	Aggregates spectra by retention time
CMSDataCachedConsumer	Transforming and cached writing consumer of MS data
CMSDataChainingConsumer	Consumer class that passes all consumed data through a set of operations
CMSDataSqlConsumer	A data consumer that inserts MS data into a SQLite database
CMSDataStoringConsumer	Consumer class that simply stores the data
CMSDataTransformingConsumer	Transforming consumer of MS data
CMSDataWritingConsumer	Consumer class that writes MS data to disk using the mzML format
CNoopMSDataConsumer	Consumer class that performs no operation
CIMSElement	Represents a chemical atom with name and isotope distribution
CIMSIsotopeDistribution	Represents a distribution of isotopes restricted to the first K elements
CIMTypes
CIndexedMzMLDecoder	A class to analyze indexedmzML files and extract the offsets of individual tags
CIndexedMzMLFileLoader	A class to load an indexedmzML file
CIndexedMzMLHandler	A low-level class to read an indexedmzML file
CFeatureHandle::IndexLess	Comparator by map and unique id
CPSLPFormulation::IndexLess
CPSLPFormulation::IndexTriple	Struct 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
CFuzzyStringComparator::InputLine	Stores information about the current input line (i.e., stream for the line and the current position in the stream)
►CInputSource
CCompressedInputSource	This class is based on xercesc::LocalFileInputSource
CInRTRange< SpectrumType >	Predicate that determines if a spectrum lies inside/outside a specific retention time range
CInspectInfile	Inspect input file adapter
CInspectOutfile	Representation of an Inspect outfile
CChromatogramPeak::IntensityLess	Comparator by intensity
CPeak1D::IntensityLess
CPeak2D::IntensityLess
CTransformationModelInterpolated::Interpolator	The class defines a generic interpolation technique used in the TransformationModelInterpolated
CTOPPASToolVertex::IOInfo	Stores the information for input/output files/lists
CIonMobilityScoring	A class that calls the ion mobility scoring routines
CCompNovoIonScoringBase::IonScore
CDeNovoIonScoring::IonScore	IonScore
CSvmTheoreticalSpectrumGenerator::IonType	Nested class
►Cios_base	STL class
►Cbasic_ios< Char >	STL class
►Cbasic_istream< Char >	STL class
►Cbasic_ifstream< Char >	STL class
►Cifstream	STL class
CFidHandler	Read-only fid File handler for XMass Analysis
►Cbasic_ostream< Char >	STL class
►Costream	STL class
CLogStream	Log Stream Class
CSVOutStream	Stream class for writing to comma/tab/...-separated values files
CProteinResolver::ISDGroup
CIsEmptySpectrum< SpectrumType >	Predicate that determines if a spectrum is empty
CIDScoreGetterSetter::IsHitType< T >
CIDScoreGetterSetter::IsIDType< T >
►CISignalToNoise
CSignalToNoiseOpenMS< ContainerT >	An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS
CMockSignalToNoise	Mock object implementing ISignalToNoise
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::IsobaricChannelInformation	Summary of an isobaric quantitation channel
CIsobaricIsotopeCorrector	Performs isotope impurity correction on the intensities extracted from an isobaric labeling experiment
CIsobaricNormalizer	Performs median normalization on the extracted ratios of isobaric labeling experiment
CIsobaricQuantifierStatistics	Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion)
►CIsoSpecGeneratorWrapper	Interface for the IsoSpec algorithm - a generator of infinitely-resolved theoretical spectra
CIsoSpecOrderedGeneratorWrapper	Generate the stream of configurations, ordered from most likely to least likely
CIsoSpecThresholdGeneratorWrapper	Provides a threshold-based generator of isotopologues: generates all isotopologues more probable than a given probability threshold
CIsoSpecTotalProbGeneratorWrapper	Generate a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99)
►CIsoSpecWrapper	A convenience class for the IsoSpec algorithm - easier to use than the IsoSpecGeneratorWrapper classes
CIsoSpecThresholdWrapper	A non-generator version of IsoSpecThresholdGeneratorWrapper
CIsoSpecTotalProbWrapper	Create a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99)
CIsotopeCluster	Stores information about an isotopic cluster (i.e. potential peptide charge variants)
CIsotopeDistribution
CIsotopeDistributionCache	Pre-calculate isotope distributions for interesting mass ranges
CFeatureFinderAlgorithmPickedHelperStructs::IsotopePattern	Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked
►CIsotopePatternGenerator	Provides an interface for different isotope pattern generator methods
CCoarseIsotopePatternGenerator	Isotope pattern generator for coarse isotope distributions
CFineIsotopePatternGenerator	Isotope pattern generator for fine isotope distributions
CIsotopeWavelet	Implements 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
CISpectraReader	The interface of read-access to a list of spectra
CISpectraWriter
►CISpectrumAccess	The interface of a mass spectrometry experiment
CSpectrumAccessOpenMS	An implementation of the OpenSWATH Spectrum Access interface using OpenMS
CSpectrumAccessOpenMSCached	An implementation of the Spectrum Access interface using on-disk caching
CSpectrumAccessOpenMSInMemory	An implementation of the OpenSWATH Spectrum Access interface completely in memory
CSpectrumAccessSqMass	An implementation of the Spectrum Access interface using SQL files
►CSpectrumAccessTransforming	An abstract base class implementing a transforming wrapper around spectrum access
CSpectrumAccessQuadMZTransforming	A transforming m/z wrapper around spectrum access using a quadratic equation
CIsZoomSpectrum< SpectrumType >	Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum
►CIterator
CIteratorWrapper< Iterator >	Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi_index_containers
CAASequence::Iterator	Iterator class for AASequence
CNASequence::Iterator	Iterator of NASequence class
►Citerator
CHashGrid< Cluster >::ConstIterator	Constant element iterator for the hash grid
CHashGrid< Cluster >::Iterator	Element iterator for the hash grid
CAreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >	Forward iterator for an area of peaks in an experiment
CIntensityIteratorWrapper< IteratorT >	An iterator wrapper to access peak intensities instead of the peak itself
►Cset< K >::iterator	STL iterator class
CIteratorWrapper< DataQueries::iterator >
CIteratorWrapper< DataProcessingSoftwares::iterator >
►CITransitionGroup
CTransitionGroupOpenMS< SpectrumT, TransitionT >	An implementation of the OpenSWATH Transition Group Access interface using OpenMS
CMockTransitionGroup	Mock object implementing ITransitionGroup
CItraqConstants	Some constants used throughout iTRAQ classes
CJavaInfo	Detect Java and retrieve information
CKDTreeFeatureNode	A node of the kD-tree with pointer to corresponding data and index
CKroenikFile	File adapter for Kroenik (HardKloer sibling) files
CMultiplexDeltaMassesGenerator::Label	Complete label information
►CLayerAnnotatorBase
CLayerAnnotatorAMS
CLayerAnnotatorOSW
CLayerAnnotatorPeptideID
CLayerData	Class that stores the data for one layer
CLayerStack
CLexicographicComparator< Cmp1, Cmp2 >	A wrapper class that combines two comparators lexicographically. Normally you should use the make-function lexicographicComparator() because then you do not need to specify the template arguments
CLibSVMEncoder	Serves 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 >
CLinearRegression	This class offers functions to perform least-squares fits to a straight line model,
CLinearRegressionWithoutIntercept	This class offers functions to perform least-squares fits to a straight line model,
►Clist< T >	STL class
CAnnotations1DContainer	Container for annotations to content of Plot1DCanvas
CListUtils	Collection of utility functions for management of vectors
CLocalLinearMap::LLMParam	Define parameters needed by the Local Linear Map (LLM) model
CLocalLinearMap	Trained Local Linear Map (LLM) model for peak intensity prediction
CInternalCalibration::LockMass	Helper class, describing a lock mass
CLogStreamBuf::LogCacheStruct	Holds a counter of occurrences and an index for the occurrence sequence of the corresponding log message
CLogConfigHandler	The 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_PeptideEvidence	For accession dependent sorting of PeptideEvidences
CPercolatorFeatureSetHelper::lq_ProteinHit	For accession dependent sorting of ProteinHits
►Cmap< K, T >	STL class
CMap< QString, QList< OpenMS::TOPPASResource > >
CMap< UInt, std::vector< const OpenMS::ResidueModification * > >
CMap< OpenMS::String, UInt >
CMap< OpenMS::String, OpenMS::Map< OpenMS::String, UInt > >
CMap< OpenMS::String, OpenMS::SourceFile >
CMap< OpenMS::String, OpenMS::String >
CMap< OpenMS::String, OpenMS::Software >
CMap< Size, OpenMS::String >
CMap< OpenMS::String, IntList >
CMap< Size, std::set< OpenMS::String > >
CMap< const OpenMS::Residue *, char >
CMap< OpenMS::String, std::vector< DataProcessingPtr > >
CMap< OpenMS::String, std::pair< OpenMS::String, OpenMS::String > >
CMap< OpenMS::HMMState *, OpenMS::Map< OpenMS::HMMState *, std::vector< double > > >
CMap< PointType::CoordinateType, DBoundingBox< 1 > >
CMap< OpenMS::String, std::vector< OpenMS::CVMappingRule > >
CMap< OpenMS::String, OpenMS::AASequence >
CMap< OpenMS::HMMState *, OpenMS::Map< OpenMS::HMMState *, double > >
CMap< OpenMS::String, const DigestionEnzymeType * >
CMap< Size, std::vector< double > >
CMap< std::pair< OpenMS::String, OpenMS::String >, bool >
CMap< OpenMS::String, Size >
CMap< OpenMS::String, std::set< OpenMS::String > >
CMap< Size, OpenMS::Map< Size, std::set< OpenMS::String > > >
CMap< OpenMS::HMMState *, OpenMS::Map< OpenMS::HMMState *, Size > >
CMap< OpenMS::HMMState *, OpenMS::Map< OpenMS::HMMState *, std::pair< OpenMS::HMMState *, OpenMS::HMMState * > > >
CMap< OpenMS::HMMState *, std::vector< double > >
CMap< UInt, UInt >
CMap< OpenMS::HMMState *, std::set< OpenMS::HMMState * > >
CMap< OpenMS::EnzymaticDigestionLogModel::BindingSite_, OpenMS::EnzymaticDigestionLogModel::CleavageModel_ >
CMap< OpenMS::String, OpenMS::ControlledVocabulary::CVTerm >
CMap< OpenMS::String, std::vector< OpenMS::CVTerm > >
CMap< OpenMS::String, OpenMS::Map< OpenMS::String, OpenMS::Map< OpenMS::String, UInt > > >
CMap< Size, Size >
CMap< OpenMS::String, OpenMS::Sample >
CMap< OpenMS::String, std::vector< OpenMS::Internal::SemanticValidator::CVTerm > >
CMap< OpenMS::String, OpenMS::HMMState * >
CMap< QString, QString >
CMap< double, std::vector< OpenMS::MassDecomposition > >
CMap< OpenMS::String, OpenMS::Instrument >
CMap< OpenMS::HMMState *, std::pair< OpenMS::HMMState *, OpenMS::HMMState * > >
CMap< OpenMS::String, OpenMS::Map< OpenMS::String, std::pair< OpenMS::String, OpenMS::String > > >
CMap< OpenMS::HMMState *, double >
CMap< char, const OpenMS::Residue * >
CMap< OpenMS::HMMState *, Size >
CMap< char, double >
CMap< Key, T >	Map class based on the STL map (containing several convenience functions)
CMapAlignmentAlgorithmKD	An efficient reference-free feature map alignment algorithm for unlabeled data
►CMapAlignmentEvaluationAlgorithm	Base class for all Caap evaluation algorithms
CMapAlignmentEvaluationAlgorithmPrecision	Caap evaluation algorithm to obtain a precision value
CMapAlignmentEvaluationAlgorithmRecall	Caap evaluation algorithm to obtain a recall value
CMapAlignmentTransformer	This class collects functions for applying retention time transformations to data structures
CMapConversion
CProteinIdentification::Mapping	Two way mapping from ms-run-path to protID|pepID-identifier
CAccurateMassSearchEngine::MappingEntry_
CMappingParam	Filename mappings for all input/output files
CConsensusFeature::MapsLess	Compare by the sets of consensus elements (lexicographically)
CModifiedPeptideGenerator::MapToResidueType
CMapUtilities< MapType >	Utilities for Feature and ConsensusMap
►CMapUtilities< ConsensusMap >
CConsensusMap	A container for consensus elements
►CMapUtilities< FeatureMap >
CFeatureMap	A container for features
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 >
CIntegerMassDecomposer< ValueType, DecompositionValueType >	Implements MassDecomposer interface using algorithm and data structures described in paper "Efficient Mass Decomposition" S. Böcker, Z. Lipták, ACM SAC-BIO, 2004 doi:10.1145/1066677.1066715
CMassDecomposition	Class represents a decomposition of a mass into amino acids
CMassExplainer	Computes 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::MassTrace	Helper struct for mass traces used in FeatureFinderAlgorithmPicked
CMassTrace	A container type that gathers peaks similar in m/z and moving along retention time
CFeatureFinderAlgorithmMetaboIdent::MassTraceBounds	Boundaries 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
Cmean_and_stddev	Functor to compute the mean and stddev of sequence using the std::foreach algorithm
CSysInfo::MemUsage	A convenience class to report either absolute or delta (between two timepoints) RAM usage
CMessagePasserFactory< Label >
CMetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping	MetaboTargetDecoyMassMapping introduces a mapping of target and decoy masses and their respective compound reference using an identifier
CMetaboTargetedAssay	This class provides methods for the extraction of targeted assays for metabolomics
CMetaboTargetedTargetDecoy	Resolve overlapping fragments and missing decoys for experimental specific decoy generation in targeted/pseudo targeted metabolomics
CMetaInfo	A Type-Name-Value tuple class
►CMetaInfoInterface	Interface for classes that can store arbitrary meta information (Type-Name-Value tuples)
CAcquisition	Information about one raw data spectrum that was combined with several other raw data spectra
CAcquisitionInfo	Description of the combination of raw data to a single spectrum
►CCVTermList	Representation of controlled vocabulary term list
CIncludeExcludeTarget	This class stores a SRM/MRM transition
CPrecursor	Precursor meta information
CProduct	Product meta information
CReactionMonitoringTransition	This class stores a SRM/MRM transition
►CSoftware	Description of the software used for processing
CDataProcessingSoftware	Information about software used for data processing
CSourceFile	Description of a file location, used to store the origin of (meta) data
CConfiguration
CContact
CInstrument
►CPeptideCompound	Base class to represent either a peptide or a compound
CCompound	Represents a compound (small molecule)
CPeptide	Represents a peptide (amino acid sequence)
CPrediction
CProtein
CPublication
►CCVTermListInterface	Interface to the controlled vocabulary term list
CInterpretation	Product ion interpretation
CPeptide::Modification
CRetentionTime	This class stores a retention time structure that is used in TargetedExperiment (representing a TraML file)
CTraMLProduct	Represents a product ion
►CChromatogramSettings	Representation of chromatogram settings, e.g. SRM/MRM chromatograms
CMSChromatogram	The representation of a chromatogram
CConsensusMap	A container for consensus elements
CConsensusMap::ColumnHeader	Description of the columns in a consensus map
CContactPerson	Contact person information
CDataProcessing	Description of the applied preprocessing steps
CExperimentalSettings	Description of the experimental settings
CFeatureMap	A container for features
CIdentification	Represents a object which can store the information of an analysisXML instance
CIdentificationData	Representation of spectrum identification results and associated data
CDBSearchParam	Parameters specific to a database search step
CDataProcessingStep	Data processing step that is applied to the data (e.g. database search, PEP calculation, filtering, ConsensusID)
CDataQuery	Search query, e.g. spectrum or feature
CMoleculeParentMatch	Meta data for the association between an identified molecule (e.g. peptide) and a parent molecule (e.g. protein)
CScoreType	Information about a score type
►CScoredProcessingResult	Base class for ID data with scores and processing steps (and meta info)
CIdentifiedCompound
CIdentifiedSequence< SeqType >	Identified sequence (peptide or oligonucleotide)
CMoleculeQueryMatch	Meta data for a search hit (e.g. peptide-spectrum match)
CParentMolecule	Representation of a parent molecule that is identified only indirectly (e.g. a protein)
CParentMoleculeGrouping	Set of groups of ambiguously identified parent molecules (e.g. results of running a protein inference algorithm)
CQueryMatchGroup	: Group of related (co-identified) molecule-query matches
CIdentificationHit	Represents a object which can store the information of an analysisXML instance
CInstrument	Description of a MS instrument
CInstrumentSettings	Description of the settings a MS Instrument was run with
CIonDetector	Description of a ion detector (part of a MS Instrument)
CIonSource	Description of an ion source (part of a MS Instrument)
CMassAnalyzer	Description of a mass analyzer (part of a MS Instrument)
►CMetaInfoDescription	Description of the meta data arrays of MSSpectrum
CFloatDataArray	Float data array class
CIntegerDataArray	Integer data array class
CStringDataArray	String data array class
CPeptideHit	Representation of a peptide hit
CPeptideIdentification	Represents the peptide hits for a spectrum
CProteinHit	Representation of a protein hit
CProteinIdentification	Representation of a protein identification run
CProteinIdentification::SearchParameters	Search parameters of the DB search
►CRichPeak2D	A 2-dimensional raw data point or peak with meta information
►CBaseFeature	A basic LC-MS feature
CConsensusFeature	A consensus feature spanning multiple LC-MS/MS experiments
►CFeature	An LC-MS feature
CMRMFeature	A multi-chromatogram MRM feature
CSample	Meta information about the sample
►CSampleTreatment	Base class for sample treatments (Digestion, Modification, Tagging, ...)
CDigestion	Meta information about digestion of a sample
►CModification	Meta information about chemical modification of a sample
CTagging	Meta information about tagging of a sample e.g. ICAT labeling
CScanWindow	Scan window description
CSpectrumIdentification	Represents a object which can store the information of an analysisXML instance
►CSpectrumSettings	Representation of 1D spectrum settings
CMSSpectrum	The representation of a 1D spectrum
CMetaInfoInterfaceUtils	Utilities operating on containers inheriting from MetaInfoInterface
CMetaInfoRegistry	Registry which assigns unique integer indices to strings
CMetaKeyGetter< T >
CLayerStatisticsDialog::MetaStatsValue_	Struct representing the statistics about one meta information
CMinimumDistance	Basic data structure for distances between clusters
CTraceFitter::ModelData
CModelDescription< D >	Stores the name and parameters of a model
CModificationDefinition	Representation of modification definition
CModificationDefinitionsSet	Representation of a set of modification definitions
CMzIdentMLDOMHandler::ModificationParam	Struct to hold the information from the ModificationParam xml tag
►CModificationsDB	Database which holds all residue modifications from UniMod
CCrossLinksDB
CModifiedNASequenceGenerator
CModifiedPeptideGenerator
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
CMorpheusScore	An implementation of the Morpheus PSM scoring function Inspired by a C# implementation by C. Wenger released under MIT license
CMQEvidence	Builds a MaxQuant Evidence.txt
CMRMBatchFeatureSelector
CMRMFeaturePicker	_MRMFeaturePicker_ defines the structures containing parameters to be used in [MRMTransitionGroupPicker](MRMTransitionGroupPicker) for components and components groups
CMRMFeatureQC	The MRMFeatureQC is a class to handle the parameters and options for MRMFeatureFilter
►CMRMFeatureSelector
►CMRMFeatureSelectorQMIP
CMRMFeatureSelector_test
CMRMFeatureSelectorScore
CMRMIonSeries	Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy
CMRMRTNormalizer	The MRMRTNormalizer will find retention time peptides in data
CMRMScoring	This 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::MSDGroup	Representation of an msd group. Contains peptides, proteins and a pointer to its ISD group
CExperimentalDesign::MSFileSectionEntry
CMsInspectFile	File adapter for MsInspect files
CMSNumpressCoder	Class to encode and decode data encoded with MSNumpress
CMSPGenericFile_friend
CMSstatsFile	File adapter for MSstats files
CMSstatsFile::MSstatsLine_
CMSstatsFile::MSstatsTMTLine_
CMultiGradient	A gradient of multiple colors and arbitrary distances between colors
CMultiplexDeltaMasses	Data structure for mass shift pattern
CMultiplexClustering::MultiplexDistance	Scaled Euclidean distance for clustering
CMultiplexFilteredMSExperiment	Data structure storing all peaks (and optionally their raw data points) of an experiment corresponding to one specific peak pattern
CMultiplexFilteredPeak	Data structure storing a single peak that passed all filters
CMultiplexIsotopicPeakPattern	Data structure for pattern of isotopic peaks
CMultiplexSatelliteCentroided	Data structure storing a single satellite peak
CMultiplexSatelliteProfile	Data structure storing a single satellite data point
CMzIdentMLDOMHandler	XML DOM handler for MzIdentMLFile
CMSChromatogram::MZLess	Comparator for the retention time
CPeak1D::MZLess	Comparator by m/z position
CPeak2D::MZLess	Comparator by m/z position
CMzMLHandlerHelper	Helper for mzML file format
CMzMLSpectrumDecoder	A class to decode input strings that contain an mzML chromatogram or spectrum tag
CMzMLSqliteHandler	Sqlite handler for storing spectra and chromatograms in sqMass format
CMzMLSqliteSwathHandler	Sqlite handler for SWATH data sets
CMzQCFile	File adapter for mzQC files used to load and store mzQC files
CMzTab	Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/
CMzTabAssayMetaData
CMzTabBoolean
CMzTabContactMetaData
CMzTabCVMetaData
CMzTabDouble
CMzTabDoubleList
CMzTabFile	File adapter for MzTab files
CMzTabInstrumentMetaData
CMzTabInteger
CMzTabIntegerList
CMzTabMetaData	All meta data of a mzTab file. Please refer to specification for documentation
CMzTabModification
CMzTabModificationList
CMzTabModificationMetaData
CMzTabMSRunMetaData
CMzTabNucleicAcidSectionRow	NUC - Nucleic acid section (table-based)
CMzTabOligonucleotideSectionRow	OLI - Oligonucleotide section (table-based)
CMzTabOSMSectionRow	OSM - OSM (oligonucleotide-spectrum match) section (table-based)
CMzTabParameter
CMzTabParameterList
CMzTabPeptideSectionRow	PEP - Peptide section (Table based)
CMzTabProteinSectionRow	PRT - Protein section (Table based)
CMzTabPSMSectionRow	PSM - PSM section (Table based)
CMzTabSampleMetaData
CMzTabSmallMoleculeSectionRow	SML Small molecule section (table based)
CMzTabSoftwareMetaData
CMzTabSpectraRef
CMzTabString
CMzTabStringList
CMzTabStudyVariableMetaData
CMZTrafoModel	Create and apply models of a mass recalibration function
CReactionMonitoringTransition::NameLess	Comparator by name
CNASequence	Representation of a nucleic acid sequence
CSplineInterpolatedPeaks::Navigator	Iterator class for access of spline packages
CNeedlemanWunsch	This 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::NoiseEstimator	Class to compute the noise value at a given position
C_Alloc_base< _Tp, _Alloc >::NoLeakAlloc
CNonNegativeLeastSquaresSolver	Wrapper for a non-negative least squares (NNLS) solver
CMSNumpressCoder::NumpressConfig	Configuration class for MSNumpress
COMS_TranslateTableAAToChar_< T >
COMS_TranslateTableByteToAA_< T >
COMS_TranslateTableCharToAA_< T >
COMSSACSVFile	File adapter for OMSSACSV files
COnDiscMSExperiment	Representation of a mass spectrometry experiment on disk
COpenMSBuildInfo	Struct with some static methods to get informations on the build configuration
COpenMSOSInfo
COpenSwath_Ind_Scores
COpenSwath_Scores	A structure to hold the different scores computed by OpenSWATH
COpenSwath_Scores_Usage	A structure to store which scores should be used by the OpenSWATH Algorithm
COpenSwathDataAccessHelper	Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces
COpenSwathHelper	A helper class that is used by several OpenSWATH tools
COpenSwathOSWWriter	Class to write out an OpenSwath OSW SQLite output (PyProphet input)
COpenSwathScoring	A class that calls the scoring routines
COpenSwathTSVWriter	Class to write out an OpenSwath TSV output (mProphet input)
COptimizePick	This class provides the non-linear optimization of the peak parameters
COptimizePick::OptPeakFunctor
COPXLDataStructs
COPXLHelper	Functions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code
COPXLSpectrumProcessingAlgorithms
COSBinaryDataArray	The datastructures used by the OpenSwath interfaces
COSChromatogram	A single chromatogram
COSChromatogramMeta	Identifying information for a chromatogram
COSSpectrum	The structure that captures the generation of a peak list (including the underlying acquisitions)
COSSpectrumMeta	Identifying information for a spectrum
COSWData	Holds all or partial information from an OSW file
COSWFile	This class serves for reading in and writing OpenSWATH OSW files
COSWHierarchy	Hierarchy levels of the OSWData tree
COSWIndexTrace
COSWPeakGroup
COSWPeptidePrecursor	A peptide with a charge state
COSWProtein	A Protein is the highest entity and contains one or more peptides which were found/traced
COSWTransition	High-level meta data of a transition
COverlapDetector	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)
CPairComparatorFirstElement< PairType >	Class for comparison of std::pair using first ONLY e.g. for use with std::sort
CPairComparatorFirstElementMore< PairType >	Class for comparison of std::pair using first ONLY e.g. for use with std::sort
CPairComparatorSecondElement< PairType >	Class for comparison of std::pair using second ONLY e.g. for use with std::sort
CPairComparatorSecondElementMore< PairType >	Class for comparison of std::pair using second ONLY e.g. for use with std::sort
CPairMatcherFirstElement< PairType >	Class for comparison of std::pair using first ONLY e.g. for use with std::sort
CPairMatcherSecondElement< PairType >	Struct for comparison of std::pair using second ONLY e.g. for use with std::sort
CParam	Management and storage of parameters / INI files
CParam::ParamEntry	Parameter entry used to store the actual information inside of a Param entry
CParameterInformation	Struct that captures all information of a command line parameter
CSiriusAdapterAlgorithm::ParameterModifier
►CSiriusAdapterAlgorithm::ParameterSection
CSiriusAdapterAlgorithm::Fingerid
CSiriusAdapterAlgorithm::Passatutto
CSiriusAdapterAlgorithm::Preprocessing
CSiriusAdapterAlgorithm::Project
CSiriusAdapterAlgorithm::Sirius
CParam::ParamIterator	Forward const iterator for the Param class
CParam::ParamNode	Node inside a Param object which is used to build the internal tree
CParamValue	Class to hold strings, numeric values, vectors of strings and vectors of numeric values using the stl types
CParentMoleculeGroup	: Group of ambiguously identified parent molecules (e.g. protein group)
CPattern< TNeedle, FuzzyAC >
CPatternAuxData< TNeedle >
CPatternAuxData< PeptideDB >
CIMSIsotopeDistribution::Peak	Structure that represents an isotope peak - pair of mass and abundance
►CPeak1D	A 1-dimensional raw data point or peak
CPrecursor	Precursor meta information
►CPeak2D	A 2-dimensional raw data point or peak
►CFeatureHandle	Representation of a Peak2D, RichPeak2D or Feature
CFeatureHandle::FeatureHandleMutable_	Helper class returned by FeatureHandle::asMutable(), which see
CRichPeak2D	A 2-dimensional raw data point or peak with meta information
CPeptideHit::PeakAnnotation	Contains annotations of a peak
CPeakIntegrator::PeakArea
CPeakPickerCWT::PeakArea_	Class for the internal peak representation
CPeakIntegrator::PeakBackground
CPeakPickerHiRes::PeakBoundary	Structure for peak boundaries
CPeakCandidate	A small structure to hold peak candidates
CPeakPickerMaxima::PeakCandidate	The PeakCandidate describes the output of the peak picker
CPeakFileOptions	Options for loading files containing peak data
CPeakIndex	Index of a peak or feature
CPeakIntensityPredictor	Predict peak heights of peptides based on Local Linear Map model
CPeakPickerMaxima	This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width
CPeakShape	Internal representation of a peak shape (used by the PeakPickerCWT)
CPeakIntegrator::PeakShapeMetrics
CPeakTypeEstimator	Estimates if the data of a spectrum is raw data or peak data
CPeakWidthEstimator	Rough estimation of the peak width at m/z
►CPenaltyFactors	Class for the penalty factors used during the optimization
CPenaltyFactorsIntensity	Class for the penalty factors used during the optimization
CPepNovoInfile	PepNovo input file adapter
CPepNovoOutfile	Representation of a PepNovo output file
CPeptide
CFeatureFinderIdentificationAlgorithm::PeptideCompare	Comparison functor for (unassigned) peptide IDs
CPeptideAndProteinQuant::PeptideData	Quantitative and associated data for a peptide
CIDFilter::PeptideDigestionFilter	Filter Peptide Hit by its digestion product
CProteinResolver::PeptideEntry	Peptide. First in silico. If experimental is set to true it is MS/MS derived
CMzIdentMLDOMHandler::PeptideEvidence	Struct to hold the PeptideEvidence information
CPeptideEvidence	Representation of a peptide evidence
COPXLHelper::PeptideIDScoreComparator	A comparator for PeptideIdentifications that compares the scores in the first PeptideHit
CPeptideIndexing::PeptideProteinMatchInformation
CPeptideProteinResolution	Resolves shared peptides based on protein scores
CPeptideHit::PepXMLAnalysisResult	Analysis Result (containing search engine / prophet results)
COSWFile::PercolatorFeature
CPercolatorFeatureSetHelper	Percolator feature set and integration helper
CPercolatorOutfile	Class for reading Percolator tab-delimited output files
CCompNovoIdentificationBase::Permut	Simple class to store permutations and a score
CPointerComparator< Cmp >	Wrapper that takes a comparator for `something' and makes a comparator for pointers to `something' out of it. Normally you should use the make-function pointerComparator() because then you do not need to specify the template arguments
CChromatogramPeak::PositionLess	Comparator by position. As this class has dimension 1, this is basically an alias for RTLess
CPeak1D::PositionLess	Comparator by position. As this class has dimension 1, this is basically an alias for MZLess
CPeak2D::PositionLess	Comparator by position. Lexicographical comparison (first RT then m/z) is done
CPeakShape::PositionLess	Comparison of mz_positions
CPpmTrait
CPrecisionWrapper< FloatingPointType >	Wrapper class to implement output with appropriate precision. See precisionWrapper()
CPrecursorCorrection	This class provides methods for precursor correction
CNucleicAcidSearchEngine::PrecursorInfo
CPrecursorMassComparator
CPrecursorPurity	Precursor purity or noise estimation
CSimpleSVM::Prediction	SVM prediction result
CFuzzyStringComparator::PrefixInfo_	Wrapper for the prefix information computed for the failure report
COPXLDataStructs::PreprocessedPairSpectra	The 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::ProductMZLess	Comparator by Product ion MZ
►CProgressLogger	Base class for all classes that want to report their progress
CSignalToNoiseEstimator< MSSpectrum >
CAccurateMassSearchEngine	An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB)
CAverageLinkage	AverageLinkage ClusterMethod
CBaseGroupFinder	The base class of all element group finding algorithms
CBaseSuperimposer	The base class of all superimposer algorithms
CBasicProteinInferenceAlgorithm	Algorithm class that implements simple protein inference by aggregation of peptide scores. It has multiple parameter options like the aggregation method, when to distinguish peptidoforms, and if you want to use shared peptides ("use_shared_peptides"). First, the best PSM per spectrum is used, then only the best PSM per peptidoform is aggregated. Peptidoforms can optionally be distinguished via the treat_X_separate parameters:
CBayesianProteinInferenceAlgorithm	Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental)
CChromatogramExtractor	The ChromatogramExtractor extracts chromatograms from a spectra file
CChromatogramExtractorAlgorithm	The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data
CCompleteLinkage	CompleteLinkage ClusterMethod
CConfidenceScoring
CConsensusMapMergerAlgorithm	Merges identification data in ConsensusMaps
CConsensusXMLFile	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation
CDTA2DFile	DTA2D File adapter
CElutionPeakDetection	Extracts chromatographic peaks from a mass trace
CFASTAFile	This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusual symbols (such as translation end (*)), they will be kept! You can use aggregate methods load() and store() to read/write a set of protein sequences at the cost of memory
CFeatureFinder	The main feature finder class
CFeatureFinderMultiplexAlgorithm
CFeatureFindingMetabo	Method for the assembly of mass traces belonging to the same isotope pattern, i.e., that are compatible in retention times, mass-to-charge ratios, and isotope abundances
CFeatureGroupingAlgorithmKD	A feature grouping algorithm for unlabeled data
CFeatureXMLFile	This class provides Input/Output functionality for feature maps
CGaussFilter	This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data
CGridBasedClustering< Metric >	2D hierarchical clustering implementation optimized for large data sets containing many small clusters i.e. dimensions of clusters << dimension of entire dataset
CIDMergerAlgorithm	Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but concatenates PSMs. Checks search engine consistency of all inserted runs. It differs from the IDMerger tool, in that it is an algorithm class and it allows inserting multiple peptide hits per peptide sequence (not only the first occurrence)
CIdXMLFile	Used to load and store idXML files
►CCachedMzMLHandler	An class that uses on-disk caching to read and write spectra and chromatograms
CMSDataCachedConsumer	Transforming and cached writing consumer of MS data
CInternalCalibration	A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference masses
CIonizationSimulation	Simulates Protein ionization
CLinearResampler	Linear Resampling of raw data
CMRMAssay	Generate assays from a TargetedExperiment
CMRMDecoy	This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object
CMRMFeatureFinderScoring	The MRMFeatureFinder finds and scores peaks of transitions that co-elute
CMRMFeatureQCFile	File adapter for MRMFeatureQC files
CMS2File	MS2 input file adapter
CMSSim	Central class for simulation of mass spectrometry experiments
CMapAlignmentAlgorithmIdentification	A map alignment algorithm based on peptide identifications from MS2 spectra
CMapAlignmentAlgorithmPoseClustering	A map alignment algorithm based on pose clustering
CMapAlignmentAlgorithmSpectrumAlignment	A map alignment algorithm based on spectrum similarity (dynamic programming)
CMapAlignmentAlgorithmTreeGuided	A map alignment algorithm based on peptide identifications from MS2 spectra
CMascotGenericFile	Read/write Mascot generic files (MGF)
CMascotInfile	Mascot input file adapter
CMassTraceDetection	A mass trace extraction method that gathers peaks similar in m/z and moving along retention time
CMasstraceCorrelator	Correlates individual masstraces found in mass spectrometric maps
CMetaboliteSpectralMatching
CMorphologicalFilter	This class implements baseline filtering operations using methods from mathematical morphology
CMultiplexClustering	Clusters results from multiplex filtering
►CMultiplexFiltering	Base class for filtering centroided and profile data for peak patterns
CMultiplexFilteringCentroided	Filters centroided data for peak patterns
CMultiplexFilteringProfile	Filters centroided and profile data for peak patterns
CMzDataFile	File adapter for MzData files
CMzIdentMLFile	File adapter for MzIdentML files
CMzMLFile	File adapter for MzML files
CMzQuantMLFile	File adapter for MzQuantML files
CMzXMLFile	File adapter for MzXML 3.1 files
COpenPepXLAlgorithm	Search for peptide pairs linked with a labeled cross-linker
COpenPepXLLFAlgorithm	Search for cross-linked peptide pairs in tandem MS spectra
►COpenSwathWorkflowBase
COpenSwathCalibrationWorkflow	Execute all steps for retention time and m/z calibration of SWATH-MS data
►COpenSwathWorkflow	Execute all steps in an OpenSwath analysis
COpenSwathWorkflowSonar	Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data)
CPeakPickerCWT	This class implements a peak picking algorithm using wavelet techniques
CPeakPickerHiRes	This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width
CPeakPickerIterative	This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data)
CPeakPickerSH
CPeptideIndexing	Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds target/decoy information
CQcMLFile	File adapter for QcML files used to load and store QcML files
CRawMSSignalSimulation	Simulates MS signals for a given set of peptides
CSVMWrapper	Serves as a wrapper for the libsvm
CSavitzkyGolayFilter	Computes the Savitzky-Golay filter coefficients using QR decomposition
CSignalToNoiseEstimator< Container >	This class represents the abstract base class of a signal to noise estimator
CSimpleSearchEngineAlgorithm
CSingleLinkage	SingleLinkage ClusterMethod
CSpectraMerger	Merges blocks of MS or MS2 spectra
CSwathFile	File adapter for Swath files
CTOFCalibration	This class implements an external calibration for TOF data using external calibrant spectra
CToolDescriptionFile	File adapter for ToolDescriptor files
CTraMLFile	File adapter for HUPO PSI TraML files
CTransitionTSVFile	This class supports reading and writing of OpenSWATH transition lists
CXFDRAlgorithm	Calculates false discovery rate estimates on crosslink identifications
CXMassFile	File adapter for 'XMass Analysis (fid)' files
CXQuestResultXMLFile	Used to load and store xQuest result files
►CProgressLogger::ProgressLoggerImpl	This class represents an actual implementation of a logger
CGUIProgressLoggerImpl	Implements a GUI version of the ProgressLoggerImpl
CProtein
CPeptideAndProteinQuant::ProteinData	Quantitative and associated data for a protein
CProteinResolver::ProteinEntry	Protein from FASTA file
CIDBoostGraph::ProteinGroup	Placeholder for peptides with the same parent proteins or protein groups
CProteinIdentification::ProteinGroup	Bundles multiple (e.g. indistinguishable) proteins in a group
CProteinHit::ProteinHitAccessionHash	Hash of a ProteinHit based on its accession only!
CProteinHit::ProteinHitPtrAccessionHash
CProteinInference	[experimental class] given a peptide quantitation, infer corresponding protein quantities
COPXLDataStructs::ProteinProteinCrossLink	The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL
CPScore	Implementation of the PScore PSM scoring algorithm
CHyperScore::PSMDetail	Compute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match
CPSProteinInference	This 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
CPythonInfo	Detect Python and retrieve information
►CQApplication
CQApplicationTOPP	Extension to the QApplication for running TOPPs GUI tools
►CQCBase	This class serves as an abstract base class for all QC classes
CContaminants	This class is a metric for the QualityControl TOPP tool
CFWHM	QC metric calculating (un)calibrated m/z error
CFeatureSummary
CFragmentMassError
CIdentificationSummary
CMissedCleavages	This class is a metric for the QualityControl TOPP Tool
CMs2IdentificationRate	This class is a metric for the QualityControl-ToppTool
CMs2SpectrumStats	QC metric to determine the number of MS2 scans per MS1 scan over RT
CMzCalibration	QC metric calculating (un)calibrated m/z error
CPSMExplainedIonCurrent
CPeptideMass	QC metric calculating theoretical mass of a peptide sequence
CRTAlignment	Take the original retention time before map alignment and use the alignment's trafoXML for calculation of the new alignment retention times
CSpectrumCount
CTIC
►CQDate
CDate	Date Class
►CQDialog
CDataFilterDialog	Dialog for creating and changing a DataFilter
CFeatureEditDialog	Dialog for editing a feature
CHistogramDialog	Dialog that show a HistogramWidget
CPlot1DPrefDialog	Preferences dialog for Plot1DWidget
CPlot2DPrefDialog	Preferences dialog for Plot2DWidget
CPlot3DPrefDialog	Preferences dialog for Plot3DWidget
CTOPPViewPrefDialog	Preferences dialog for TOPPView
CLayerStatisticsDialog	Dialog showing statistics about the data of the current layer
CListEditor	Editor for editing int, double and string lists (including output and input file lists)
CListFilterDialog	Dialog for creating and changing a DataFilter
CMetaDataBrowser	A meta data visualization widget
CPlot1DGoToDialog	Simple goto/set visible area dialog for exact placement of the viewing window
CPlot2DGoToDialog	GoTo dialog used to zoom to a m/z and retention time range or to a feature
CSaveImageDialog	Dialog for saving an image
CSpectrumAlignmentDialog	Lets the user select two spectra and set the parameters for the spectrum alignment
CTOPPASIOMappingDialog	Dialog which allows to configure the input/output parameter mapping of an edge
CTOPPASInputFileDialog	Dialog which allows to specify an input file
CTOPPASInputFilesDialog	Dialog which allows to specify a list of input files
CTOPPASOutputFilesDialog	Dialog which allows to specify the directory for the output files
CTOPPASToolConfigDialog	TOPP tool configuration dialog
CTOPPASVertexNameDialog	Dialog which allows to change the name of an input/output vertex
CTOPPViewOpenDialog	Dataset opening options for TOPPView
CTheoreticalSpectrumGenerationDialog	Dialog which allows to enter an AA sequence and generates a theoretical spectrum for it
CToolsDialog	TOPP tool selection dialog
►CQFileSystemWatcher
CFileWatcher	Watcher that monitors file changes
►CQGraphicsItem
CTOPPASEdge	An edge representing a data flow in TOPPAS
►CTOPPASVertex	The base class of the different vertex classes
CTOPPASInputFileListVertex	A vertex representing an input file list
CTOPPASMergerVertex	A special vertex that allows to merge several inputs
CTOPPASOutputFileListVertex	A vertex representing an output file list
CTOPPASSplitterVertex	A special vertex that allows to split a list of inputs
CTOPPASToolVertex	A vertex representing a TOPP tool
►CQGraphicsScene
CTOPPASScene	A container for all visual items of a TOPPAS workflow
►CQGraphicsView
CTOPPASWidget	Widget visualizing and allowing to edit TOPP pipelines
►CQItemDelegate
CListEditorDelegate	Internal delegate class
CParamEditorDelegate	Internal delegate class for QTreeWidget
►CQLineEdit
COpenMSLineEdit	Custom QLineEdit which emits a signal when losing focus (such that we can commit its data)
►CQListWidget
CListTable
CLayerListView	Pimped QListView for Layers of a Canvas
►CQMainWindow
CINIFileEditorWindow	Shows the ParamEditor widget in a QMainWindow with a toolbar
CSwathWizardBase	Main window of the SwathWizard tool
CTOPPASBase	Main window of the TOPPAS tool
CTOPPViewBase	Main window of TOPPView tool
►CQMdiArea
CEnhancedWorkspace
►CQObject
CExternalProcess	A wrapper around QProcess to conveniently start an external program and forward its outputs
CMascotRemoteQuery	Class which handles the communication between OpenMS and the Mascot server
CNetworkGetRequest
CRecentFilesMenu	Manages recent files opened by the user and provides a QMenu to go with it
CSignalProvider	Signal mechanism (by deriving from QObject) for classes which are not allowed to have signals themselves
CTOPPASEdge	An edge representing a data flow in TOPPAS
CTOPPASResource	Represents a data resource for TOPPAS workflows
CTOPPASResources	A dictionary mapping string keys to lists of TOPPASResource objects
CTOPPASVertex	The base class of the different vertex classes
CTOPPViewMenu	The file menu items for TOPPView
►CTVControllerBase	Base behavior for different visualizaton modules in TOPPView
CTVDIATreeTabController	Behavior of TOPPView in spectra view mode
CTVIdentificationViewController	Behavior of TOPPView in identification mode
CTVSpectraViewController	Behavior of TOPPView in spectra view mode
►CQOpenGLFunctions_2_0
CPlot3DOpenGLCanvas	OpenGL Canvas for 3D-visualization of map data
►CQOpenGLWidget
CPlot3DOpenGLCanvas	OpenGL Canvas for 3D-visualization of map data
►CQProcess
CFakeProcess	A FakeProcess class
►CQTabBar
CEnhancedTabBar	Convenience tab bar implementation
►CQTableWidget
CTableView	A better QTable for TOPPView, which supports exporting to TSV and conveniently adding data to cells and headers
►CQTabWidget
CDataSelectionTabs	A tabbed view, to browse lists of spectra or identifications
CSwathTabWidget	A multi-tabbed widget for the SwathWizard offering setting of parameters, input-file specification and running Swath and more
CQTCluster	A representation of a QT cluster used for feature grouping
►CQTextEdit
CLogWindow	A log window (QTextEdit) with convenience functions
►CQTreeWidget
CParamTree	QTreeWidget that emits a signal whenever a new row is selected
CTOPPASTreeView	Tree view implementation for the list of TOPP tools
CTreeView	A better QTreeWidget for TOPPView, which supports header context menu and conveniently adding/getting headers names
CQuadraticRegression
CBaseFeature::QualityLess	Compare by quality
CQcMLFile::QualityParameter	Representation of a quality parameter
►CQWidget
CAxisWidget	Widget that represents an axis of a graph
►CBaseVisualizerGUI	A base class for all visualizer classes
CAcquisitionInfoVisualizer	Class that displays all meta information for AcquisitionInfo objects
CAcquisitionVisualizer	Class that displays all meta information for Acquisition objects
CContactPersonVisualizer	Class that displays all meta information for ContactPerson objects
CDataProcessingVisualizer	Class that displays all meta information for DataProcessing objects
CDigestionVisualizer	Class that displays all meta information of digestion objects
CDocumentIdentifierVisualizer	Class that displays all meta information for DocumentIdentifier objects
CExperimentalSettingsVisualizer	Class that displays all meta information for ExperimentalSettings objects
CGradientVisualizer	GradientVisualizer is a visualizer class for objects of type gradient
CHPLCVisualizer	Class that displays all meta information for HPLC objects
CInstrumentSettingsVisualizer	Class that displays all meta information for InstrumentSettings objects
CInstrumentVisualizer	Class that displays all meta information for an MS instrument
CIonDetectorVisualizer	Class that displays all meta information for IonDetector objects
CIonSourceVisualizer	Class that displays all meta information for IonSource objects
CMassAnalyzerVisualizer	Class that displays all meta information for MassAnalyzer objects
CMetaInfoDescriptionVisualizer	Class that displays all meta information for MetaInfoDescription objects
CMetaInfoVisualizer	MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member
CModificationVisualizer	Class that displays all meta information of modification objects
CPeptideHitVisualizer	Class that displays all meta information for PeptideHit objects
CPeptideIdentificationVisualizer	Class that displays all meta information for PeptideIdentification objects
CPrecursorVisualizer	Class that displays all meta information for Precursor objects
CProductVisualizer	Class that displays all meta information for Product objects
CProteinHitVisualizer	Class that displays all meta information for ProteinHit objects
CProteinIdentificationVisualizer	Class that displays all meta information for ProteinIdentification objects
CSampleVisualizer	Class that displays all meta information of sample objects
CScanWindowVisualizer	Class that displays all meta information for ScanWindow objects
CSoftwareVisualizer	Class that displays all meta information for Software objects
CSourceFileVisualizer	Class that displays all meta information for SourceFile objects
CSpectrumSettingsVisualizer	Class that displays all meta information for SpectrumSettings objects
CTaggingVisualizer	Class that displays all meta information of tagging objects
CColorSelector	A widget for selecting a color
CDIATreeTab	Hierarchical visualization and selection of spectra
CHistogramWidget	Widget which can visualize a histogram
CInputFile	A simple widget with a line-edit and a browse button to choose filenames
CFilterList	A widget which shows a list of DataFilter items
CFilterableList	A widget which shows a list of text items, which can be filtered
CInputFileList	A widget shows a list of input files (i.e. existing files on a mounted drive), which allows adding/removing files and supports drag'n'drop from the window manager
CPythonModuleRequirement
CPythonSelector
CMultiGradientSelector	A widget witch allows constructing gradients of multiple colors
COutputDirectory	A simple widget with a line-edit and a browse button to choose filenames
CParamEditor	A GUI for editing or viewing a Param object
CPlotCanvas	Base class for visualization canvas classes
CPlotWidget	Base class for spectrum widgets
CSpectraIDViewTab	Tabular visualization / selection of identified spectra
CSpectraTreeTab	Hierarchical visualization and selection of spectra
CSwathLibraryStats	A multi-tabbed widget for the SwathWizard offering setting of parameters, input-file specification and running Swath and more
CRAIICleanup	Exception-safe way of executing arbitrary code at the end of a scope
CRandomShuffler
CRange	Internal structure to store a lower and upper bound of an m/z range
CRangeManager< D >	Handles the management of a position and intensity range
►CRangeManager< 1 >
CMSChromatogram	The representation of a chromatogram
CMSSpectrum	The representation of a 1D spectrum
►CRangeManager< 2 >
CConsensusMap	A container for consensus elements
CFeatureMap	A container for features
CMSExperiment	In-Memory representation of a mass spectrometry experiment
CPeptideHit::RankLess	Lesser 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 >
CRansacModelLinear	Implementation of a linear RANSAC model fit
►CRansacModel< RansacModelQuadratic >
CRansacModelQuadratic	Implementation of a quadratic RANSAC model fit
CRANSACParam	A simple struct to carry all the parameters required for a RANSAC run
CConsensusFeature::Ratio	Slim struct to feed the need for systematically storing of ratios (
►Creal_policies
CBK_PrecPolicy< T >
►Creal_policies
CStringUtils::real_policies_NANfixed_< T >
CRealMassDecomposer	Handles decomposing of non-integer values/masses over a set of non-integer weights with an error allowed
CBase64::Reinterpreter32_	Internal class needed for type-punning
CBase64::Reinterpreter64_	Internal class needed for type-punning
CResidue	Representation of a residue
CResidueDB	OpenMS 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
CResidueModification	Representation of a modification
CProteinResolver::ResolverResult
CDecoyHelper::Result
CFeatureSummary::Result
CIdentificationSummary::Result
CMorpheusScore::Result	Score and subscores
CTIC::Result
CReverseComparator< Cmp >	Wrapper that reverses (exchanges) the two arguments of a comparator. Normally you should use the make-function reverseComparator() because then you do not need to specify the template arguments
CRibonucleotide	Representation of a ribonucleotide (modified or unmodified)
CRibonucleotideDB	Database of ribonucleotides (modified and unmodified)
CRNPxlFragmentAnnotationHelper	Convenience functions to construct appealing fragment annotation strings and store them as PeptideHit::PeakAnnotation
CRNPxlMarkerIonExtractor
CRNPxlModificationMassesResult
CRNPxlModificationsGenerator
CRNPxlReport	Create report
CRNPxlReportRow	Struct to hold a single report line
CRNPxlReportRowHeader	Create header line
CROCCurve	ROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cutoff values
CMzTabNucleicAcidSectionRow::RowCompare	Comparison operator for sorting rows
CMzTabOligonucleotideSectionRow::RowCompare	Comparison operator for sorting rows
CMzTabOSMSectionRow::RowCompare	Comparison operator for sorting rows
CMzTabPeptideSectionRow::RowCompare	Comparison operator for sorting rows
CMzTabProteinSectionRow::RowCompare	Comparison operator for sorting rows
CMzTabPSMSectionRow::RowCompare	Comparison operator for sorting rows
CChromatogramPeak::RTLess	Comparator by RT position
CMSSpectrum::RTLess	Comparator for the retention time
CMZTrafoModel::RTLess	Comparator by position. As this class has dimension 1, this is basically an alias for MZLess
CPeak2D::RTLess	Comparator by RT position
COSSpectrumMeta::RTLess	Comparator for the retention time
CConfidenceScoring::RTNorm_	Helper for RT normalization (range 0-100)
CFeatureFinderIdentificationAlgorithm::RTRegion	Region in RT in which a peptide elutes:
CAbsoluteQuantitationStandards::runConcentration	Structure to map runs to components to known concentrations
CRWrapper	R-Wrapper Class
CExperimentalDesign::SampleSection
CMs2SpectrumStats::ScanEvent
CPSLPFormulation::ScanLess
CPeptideHit::ScoreLess	Lesser predicate for scores of hits
CProteinHit::ScoreLess	Lesser predicate for scores of hits
CPeptideHit::ScoreMore	Greater predicate for scores of hits
CProteinHit::ScoreMore	Greater predicate for scores of hits
CFeatureFinderAlgorithmPickedHelperStructs::Seed	Helper structure for seeds used in FeatureFinderAlgorithmPicked
CSeedListGenerator	Generate seed lists for feature detection
CMRMFeatureSelector::SelectorParameters
CPrecursorIonSelection::SeqTotalScoreMore	Compare by score
CPeptideHit::SequenceLessComparator	Lesser predicate for (modified) sequence of hits
CSequestInfile	Sequest input file adapter
CSequestOutfile	Representation of a Sequest output file
►Cset< K >	STL class
CIsotopeCluster::ChargedIndexSet	Index set with associated charge estimate
Cshared_xerces_ptr< T >
CSignalToNoiseEstimatorMedianRapid	Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based)
CSimpleOpenMSSpectraFactory	A factory method that returns two ISpectrumAccess implementations
CSimpleTSGXLMS::SimplePeak	A simple struct to represent peaks with mz and charge and sort them easily
CSimpleTSGXLMS::SimplePeakComparator	Comparator to sort SimplePeaks by mz
CSimProtein	Plain data object holding sequence and abundance information on a single protein
CSimRandomNumberGenerator	Wrapper class for random number generators used by the simulation classes
CROCCurve::simsortdec	Predicate for sort()
CSingletonRegistry	Holds pointers to unique instance of a singleton factory
CSiriusMzTabWriter::SiriusAdapterHit	Internal 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::SiriusTargetDecoySpectra	SiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from SIRIUS)
CSiriusAdapterAlgorithm::SiriusTemporaryFileSystemObjects	Struct for temporary folder structure
CConsensusFeature::SizeLess	Compare by size(), the number of consensus elements
CLPWrapper::SolverParam	Struct that holds the parameters of the LP solver
CSpawn< TNeedle >	State of an AC spawn, operating on a trie
CSpecArrayFile	File adapter for SpecArray (.pepList) files
CMzMLFile::SpecInfo
CIDMapper::SpectraIdentificationState	Result of a partitioning by identification state with mapPrecursorsToIdentifications()
CSpectralMatch
CSpectralMatchScoreComparator
CQCBase::SpectraMap	Map to find a spectrum via its NativeID
CSpectrum	The structure that captures the generation of a peak list (including the underlying acquisitions)
CSpectrumAddition	The SpectrumAddition is used to add up individual spectra
CMzMLHandler::SpectrumData	Data necessary to generate a single spectrum
CMzXMLHandler::SpectrumData	Data necessary to generate a single spectrum
CMzIdentMLDOMHandler::SpectrumIdentification	Struct to hold the information from the SpectrumIdentification xml tag
CMzIdentMLDOMHandler::SpectrumIdentificationProtocol	Struct to hold the information from the SpectrumIdentificationProtocol xml tag
►CSpectrumLookup	Helper class for looking up spectra based on different attributes
CSpectrumMetaDataLookup	Helper class for looking up spectrum meta data
CSpectrumMeta	Identifying information for a spectrum
CSpectrumMetaDataLookup::SpectrumMetaData	Meta data of a spectrum
CSplineInterpolatedPeaks	Data structure for spline interpolation of MS1 spectra and chromatograms
CSplinePackage	Fundamental data structure for SplineInterpolatedPeaks
CSqliteConnector	File adapter for Sqlite files
CSqMassFile::SqMassConfig	Configuration class for SqMassFile
CSqMassFile	An 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
CIDBoostGraph::GetPosteriorVisitor
CIDBoostGraph::LabelVisitor	Visits nodes in the boost graph (ptrs to an ID Object) and depending on their type creates a label
CIDBoostGraph::PrintAddressVisitor< CharT >
CIDBoostGraph::SetPosteriorVisitor
CFragmentMassError::Statistics	Structure for storing results: average and variance of all FragmentMassErrors in ppm
CPeptideAndProteinQuant::Statistics	Statistics for processing summary
CPSMExplainedIonCurrent::Statistics	Structure for storing results: average and variance over all PSMs
CStopWatch	This class is used to determine the current process' CPU (user and/or kernel) and wall time
►Cstreambuf
CLogStreamBuf	Stream buffer used by LogStream
CFuzzyStringComparator::StreamElement_	Stores information about characters, numbers, and white spaces loaded from the InputStream
CStreamHandler	Provides a central class to register globally used output streams. Currently supported streams are
CLogStreamBuf::StreamStruct	Holds a stream that is connected to the LogStream. It also includes the minimum and maximum level at which the LogStream redirects messages to this stream
CString< AAcid, Alloc< void > >
CStringListUtils	Utilities operating on lists of Strings
CStringManager
CStringUtils
CStringView	StringView provides a non-owning view on an existing string
CDBSuitability::SuitabilityData	Struct to store results
CSummary	Summary of fitting results
CSummaryStatistics< T >	Helper class to gather (and dump) some statistics from a e.g. vector<double>
CTargetedExperiment::SummaryStatistics
CSVMData	Data structure used in SVMWrapper
CSvmTheoreticalSpectrumGenerator::SvmModelParameterSet	Simple container storing the model parameters required for simulation
CSvmTheoreticalSpectrumGeneratorSet	Loads SvmTheoreticalSpectrumGenerator instances for different charges
CSwathGUILock	RAII class to switch to certain TabWidget, disable the GUI and go back to the orignal Tab when this class is destroyed
CSwathMap	Data structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2
CSwathQC	Quality Control function for OpenSwath
CSwathWindowLoader	Class to read a file describing the Swath Windows
CSysInfo	Some functions to get system information
CTagger	Calculate sequence tags from m/z values
CMetaboTargetedAssay::TargetDecoyGroup	TargetDecoyGroup stores the mz, rt and file number in correspondence to the index of a MetaboTargetedAssay vector
CTargetedExperiment	A description of a targeted experiment containing precursor and production ions
CTargetedExperiment
CFile::TempDir	Class representing a temporary directory
CFile::TemporaryFiles_	Internal helper class, which holds temporary filenames and deletes these files at program exit
►CTextFile	This class provides some basic file handling methods for text files
►CCsvFile	This class handles csv files. Currently only loading is implemented
CAbsoluteQuantitationMethodFile	File adapter for AbsoluteQuantitationMethod files
CMRMFeaturePickerFile	_MRMFeaturePickerFile_ loads components and components groups parameters from a .csv file
CMRMFeatureQCFile	File adapter for MRMFeatureQC files
CFeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern	Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked
CStopWatch::TimeDiff_
►CToolDescriptionInternal	ToolDescription Class
CToolDescription
CToolExternalDetails
CToolHandler
CTOPPASVertex::TOPPASFilenames
►CTOPPBase	Base class for TOPP applications
CNucleicAcidSearchEngine
CSearchEngineBase	Base class for Search Engine Adapters
CTOPPOpenSwathBase
CTOPPGNPSExport
CTOPPASScene::TOPPProcess	Stores the information for a TOPP process
CPrecursorIonSelection::TotalScoreMore	Compare by score
CParam::ParamIterator::TraceInfo	Struct that captures information on entered / left nodes for ParamIterator
CIDDecoyProbability::Transformation_	Struct to be used to store a transformation (used for fitting)
CTransformationDescription	Generic description of a coordinate transformation
►CTransformationModel	Base class for transformation models
CTransformationModelBSpline	B-spline (non-linear) model for transformations
CTransformationModelInterpolated	Interpolation model for transformations
CTransformationModelLinear	Linear model for transformations
CTransformationModelLowess	Lowess (non-linear) model for transformations
CTransformationDescription::TransformationStatistics	Summary 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 >::TransSpectrum	Internally (only by GPUs) used data structure . It allows efficient data exchange between CPU and GPU and avoids unnecessary memory moves. The class is tailored on the isotope wavelet transform and is in general not applicable on similar - but different - situations
CTriqlerFile	File adapter for Triqler files
CTriqlerFile::TriqlerLine_
CTransitionTSVFile::TSVTransition	Internal structure to represent a transition
CTVToolDiscovery	Scans for tools/utils and generates a param for each asynchronously
CTwoDOptimization::TwoDOptFunctor
Cunique_xerces_ptr< T >
CIdentificationSummary::UniqueID
CUniqueIdGenerator	A 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 >
CConsensusMap	A container for consensus elements
►CUniqueIdIndexer< FeatureMap >
CFeatureMap	A container for features
►CUniqueIdInterface	A base class defining a common interface for all classes having a unique id
CConsensusMap	A container for consensus elements
CFeatureHandle	Representation of a Peak2D, RichPeak2D or Feature
CFeatureMap	A container for features
CRichPeak2D	A 2-dimensional raw data point or peak with meta information
CCVTerm::Unit
CUpdateCheck	Helper Functions to perform an update query to the OpenMS REST server
CValueSize< AAcid >
CValueTrait	Trait 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
CMatrix< double >
CMatrix< UInt >
CAcquisitionInfo	Description of the combination of raw data to a single spectrum
CConsensusMap	A container for consensus elements
CFloatDataArray	Float data array class
CIntegerDataArray	Integer data array class
CStringDataArray	String data array class
CFeatureFinderAlgorithmPickedHelperStructs::MassTraces	Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked
CFeatureMap	A container for features
CMSChromatogram	The representation of a chromatogram
CMSSpectrum	The representation of a 1D spectrum
CMatrix< Value >	A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access
CScoreToTgtDecLabelPairs
CVersionInfo::VersionDetails
CVersionInfo	Version information class
CTOPPASVertex::VertexRoundPackage	Info for one edge and round, to be passed to next node
CWeights	Represents a set of weights (double values and scaled with a certain precision their integer counterparts) with a quick access
CWeightWrapper	Encapsulated weight queries to simplify mono vs average weight computation
CInclusionExclusionList::WindowDistance_	Determine distance between two spectra
CXCorrArrayType
COPXLDataStructs::XLPrecursor	The XLPrecursor struct represents a cross-link candidate in the process of filtering candidates by precursor masses in OpenPepXL
COPXLDataStructs::XLPrecursorComparator	The XLPrecursorComparator is a comparator for XLPrecursors, that allows direct comparison of the XLPrecursor precursor mass with double numbers
►CXMLFile	Base class for loading/storing XML files that have a handler derived from XMLHandler
CCVMappingFile	Used to load CvMapping files
CConsensusXMLFile	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation
CFeatureXMLFile	This class provides Input/Output functionality for feature maps
CIdXMLFile	Used to load and store idXML files
CSemanticValidator	Semantically validates XML files using CVMappings and a ControlledVocabulary
CMascotXMLFile	Used to load Mascot XML files
CMzDataFile	File adapter for MzData files
CMzIdentMLFile	File adapter for MzIdentML files
CMzMLFile	File adapter for MzML files
CMzQuantMLFile	File adapter for MzQuantML files
CMzXMLFile	File adapter for MzXML 3.1 files
COMSSAXMLFile	Used to load OMSSAXML files
CPTMXMLFile	Used to load and store PTMXML files
CParamXMLFile	The file pendant of the Param class used to load and store the param datastructure as paramXML
CPepXMLFile	Used to load and store PepXML files
CPepXMLFileMascot	Used to load Mascot PepXML files
CProtXMLFile	Used to load (storing not supported, yet) ProtXML files
CQcMLFile	File adapter for QcML files used to load and store QcML files
CToolDescriptionFile	File adapter for ToolDescriptor files
CTraMLFile	File adapter for HUPO PSI TraML files
CTransformationXMLFile	Used to load and store TransformationXML files
CUnimodXMLFile	Used to load XML files from unimod.org files
CXQuestResultXMLFile	Used to load and store xQuest result files
CXTandemInfile	XTandem input file
CXTandemXMLFile	Used to load XTandemXML files
CXQuestScores	An 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")
CZlibCompression	Compresses and uncompresses data using zlib