OpenMS
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Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 123456]
 ►C_Alloc_base< _Tp, _Alloc >
 C_Alloc_base< _Val, std::allocator< _Node< _Val > > >
 C_Alloc_base< KDTreeFeatureNode, std::allocator< _Node< KDTreeFeatureNode > > >
 ►C_Base_iterator
 C_Bracket_accessor< _Val >
 C_Bracket_accessor< KDTreeFeatureNode >
 ►C_Node_base
 C_Node_compare< _Val, _Acc, _Cmp >
 C_Region< __K, _Val, _SubVal, _Acc, _Cmp >
 CAA
 CAAIndexRepresentation of selected AAIndex properties
 CAASequenceRepresentation of a peptide/protein sequence
 COPXLDataStructs::AASeqWithMassThe AASeqWithMass struct represents a normal peptide with its precomputed mass
 COPXLDataStructs::AASeqWithMassComparatorThe AASeqWithMassComparator is a comparator for AASeqWithMass objects
 CFuzzyStringComparator::AbortComparisonInternal exception class
 CAbsoluteQuantitationMethodAbsoluteQuantitationMethod is a class to hold information about the quantitation method and for applying and/or generating the quantitation method
 CAbsoluteQuantitationStandardsBridges sample-level concentration tables with the FeatureMap output of a feature finder, for building calibration curves used in absolute quantitation
 CAbsoluteQuantitationStandardsFileLoad files containing runConcentration data
 CSiriusMSFile::AccessionInfoSource-file accession metadata of the input mzML, captured for the mzTab-M MS_RUN section
 CAccurateMassSearchResultOne small-molecule hit produced by AccurateMassSearchEngine
 CACNode
 CAcqusHandlerRead-only acqus File handler for XMass Analysis
 CACScoutSpin-off search path through the trie, which can deal with ambiguous AAs and mismatches
 CTOPPViewMenu::ActionRequirement_
 CACTrieAn Aho Corasick trie (a set of nodes with suffix links mainly)
 CACTrieState
 CAdaptiveQuantileResultResult of adaptiveQuantile computation
 CAdductOne elementary adduct contribution to a feature's ionization state
 CAdductCompareComparator for adducts
 CAdductInfoMass-arithmetic helper for ionizing adducts (e.g. [M+H]+, [2M-H]-, [M+2K-H]+)
 CProForma::AdductIonAdduct ion specification for charge state
 CMSstatsFile::AggregatedConsensusInfo
 CTriqlerFile::AggregatedConsensusInfo
 Calways_true< _Tp >
 CProForma::AmbiguousRegionAmbiguous amino acid region
 CPepXMLFile::AminoAcidModification
 CMzIdentMLDOMHandler::AnalysisSoftwareStruct to hold the used analysis software for that file
 CNucleicAcidSearchEngine::AnnotatedHit
 CProSEAlgorithm::AnnotatedHit_Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space
 CSimpleSearchEngineAlgorithm::AnnotatedHit_Compact internal record for one scored peptide candidate against one spectrum
 CAnnotatedMSRunClass for storing MS run data with peptide and protein identifications
 ►CAnnotation1DItemAn abstract class acting as an interface for the different 1D annotation items
 CAnnotationStatistics
 CMassTraceDetection::Apex
 CAppliedProcessingStep
 CArea< N_DIM >
 CArea< 2 >
 CAreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >Forward iterator for an area of peaks in an experiment
 CImzMLHandler::ArrayMeta
 CArrowChromatogramExportConfigConfiguration for Arrow export of chromatogram data
 CArrowSpectraExportConfigConfiguration for Arrow export of spectra data
 CQcMLFile::AttachmentRepresentation of an attachment
 CAxisPainterDraws a coordinate axis. It has only static methods, that's why the constructor is private
 CAxisTickCalculatorCalculates ticks for a given value range
 CBase64Class to encode and decode Base64
 CBaseVisualizer< ObjectType >A base class for all visualizer classes
 ►CBaseVisualizer< Acquisition >
 ►CBaseVisualizer< AcquisitionInfo >
 ►CBaseVisualizer< ContactPerson >
 ►CBaseVisualizer< DataProcessing >
 ►CBaseVisualizer< DocumentIdentifier >
 ►CBaseVisualizer< ExperimentalSettings >
 ►CBaseVisualizer< Gradient >
 ►CBaseVisualizer< HPLC >
 ►CBaseVisualizer< Instrument >
 ►CBaseVisualizer< InstrumentSettings >
 ►CBaseVisualizer< IonDetector >
 ►CBaseVisualizer< IonSource >
 ►CBaseVisualizer< MassAnalyzer >
 ►CBaseVisualizer< MetaInfoDescription >
 ►CBaseVisualizer< MetaInfoInterface >
 ►CBaseVisualizer< PeptideHit >
 ►CBaseVisualizer< PeptideIdentification >
 ►CBaseVisualizer< Precursor >
 ►CBaseVisualizer< Product >
 ►CBaseVisualizer< ProteinHit >
 ►CBaseVisualizer< ProteinIdentification >
 ►CBaseVisualizer< Sample >
 ►CBaseVisualizer< ScanWindow >
 ►CBaseVisualizer< Software >
 ►CBaseVisualizer< SourceFile >
 ►CBaseVisualizer< SpectrumSettings >
 CBasicStatistics< RealT >Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation
 CBasicStatistics< CoordinateType >
 COpenSwathPeptidoformInference::BayesianModelRowCompact Bayesian model row used by the public helper methods
 CBilinearInterpolation< Key, Value >Provides access to bilinearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero
 CMzMLHandlerHelper::BinaryDataRepresentation for binary data in mzML
 CBinaryDataArrayThe datastructures used by the OpenSwath interfaces
 CBinaryTreeNodeElements of a binary tree used to represent a hierarchical clustering process
 ►CBinInputStream
 CBinnedSpectrumThis is a binned representation of a PeakSpectrum
 CBitsetCustom bitset which uses a 32-bit integer to store bits (instead of 8 bytes for std::bitset<32> on Clang/GCC)
 CBSpline< T >
 CBSpline2dB spline interpolation
 CBSpline< double >
 CBSplineSmoothingSplineSmoothing spline implementation using B-spline basis
 CQTCluster::BulkDataClass to store the bulk internal data (neighbors, annotations, etc.)
 CBzip2IfstreamStreaming decompressor for bzip2 (.bz2) files
 ►CCachedmzMLRandom-access reader/writer for the OpenMS on-disk cache format
 CInternalCalibration::CalibrantStats_Statistics when adding peptide calibrants
 CCalibrationDataA helper class, holding all calibration points
 CCalibrationWorkflow::CalibrationResultResults from calibration workflow
 CTOPPOpenSwathBase::CalibrationResultPer-run outputs of the RT / m/z / IM calibration step
 CProSEAlgorithm::CalibrationResult_Result of a calibration pass
 CCentroidOne centroided peak produced by hill detection
 CCentroidTolerancesStructure to hold centroid-based overlap tolerances
 CItraqConstants::ChannelInfoStores information on an iTRAQ channel
 CChannelQCSmall quality control class, holding temporary data for reporting
 CChargePairRepresentation of a (putative) link between two Features, which stem from the same compound but have different charge (including different adduct ions (H+, Na+, ..)
 CTheoreticalSpectrumGenerationDialog::CheckBoxStruct for all information about a check box of an ion
 CChromatogramA single chromatogram
 CMzMLHandler::ChromatogramDataData necessary to generate a single chromatogram
 CChromatogramMetaIdentifying information for a chromatogram
 CChromatogramPeakA 1-dimensional raw data point or peak for chromatograms
 CChromatogramProcessorConvenience entry point that runs MRMFeatureFinderScoring on a list of already-extracted chromatograms
 CChromatogramSchemaSchema for chromatograms in long (one row per data point) format
 CChromatogramSemiWideSchemaSchema for chromatograms in semi-wide (one row per chromatogram, list columns) format
 CChromatogramToolsConversion class to convert chromatograms
 CChromeleonFileLoad Chromeleon HPLC text file and save it into a MSExperiment
 CChromExtractParamsChromatogramExtractor parameters
 CMSSpectrum::ChunkUsed to remember what subsets in a spectrum are sorted already to allow faster sorting of the spectrum
 CMSSpectrum::ChunksContainer for organizing and managing multiple chunks in a spectrum
 CCitationStores Citations for individual TOPP tools
 COPXLDataStructs::CLSMScoreComparatorComparator to sort CrossLinkSpectrumMatches by the main score
 CClusterAnalyzerBundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's)
 ►CClusterFunctorBase class for cluster functors
 CClusterHierarchicalHierarchical clustering with generic clustering functions
 CClusteringGridData structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering
 CClusterProxyKDProxy for a (potential) cluster
 CMzTab::CMMzTabStream
 CCmpHypothesesByScore
 CCmpMassTraceByMZ
 CColorBrewer
 CColorizerColor and style the fonts shown on cout/cerr (or other streams)
 CColorizer::ColorWithUndo_
 CCometModificationHelper struct that represents one Comet variable_modXX entry and supports merging compatible entries
 ►CTargetedSpectraExtractor::ComparatorAbstract base interface for spectral-library scoring strategies consumed by matchSpectrum
 CAccurateMassSearchEngine::CompareEntryAndMass_
 CCompareMzTabMMatchRefData model of MzTabM files. Please see the official MzTabM specification at https://github.com/HUPO-PSI/mzTab/tree/master/specification_document-releases/2_0-Metabolomics-Release
 CCompomerHolds information on an edge connecting two features from a (putative) charge ladder
 CMRMFeatureQC::ComponentGroupPairQCsQuality Controls (QCs) for multiple components (between or within component_groups)
 CMRMFeaturePicker::ComponentGroupParamsStructure to contain information about a component group with its parameters
 CMRMFeatureQC::ComponentGroupQCsQuality Controls (QCs) within a component group
 CMRMFeaturePicker::ComponentParamsStructure to contain information about a single component with its parameters
 CMRMFeatureQC::ComponentQCsQuality Controls (QCs) for individual components
 CSiriusMSFile::CompoundInfoPer-compound metadata accumulated while writing the .ms file
 CMetaboTargetedAssay::CompoundSpectrumPairCompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum
 CMetaboTargetedAssay::CompoundTargetDecoyPairCompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum (target, decoy)
 COpenSwathWorkflowScheduler::ConcurrencyEstimateDerived scheduler limits computed by estimateConcurrency for one extraction/scoring run
 COpenSwathWorkflowScheduler::ConcurrencyLimiterCounting semaphore for paths that still stream one SWATH per worker
 CConditionSingle filter condition (column, operator, values)
 CConnectedComponent
 CConsensusFeatureSchemaSchema for consensus feature table (ConsensusMap features)
 CConsensusMapArrowExportExport ConsensusMap feature data to Apache Arrow format following QPX feature schema
 CConsensusMapArrowIOImport and export ConsensusMap data to/from Apache Arrow format
 CConsensusMapNormalizerAlgorithmMedianAlgorithms of ConsensusMapNormalizer
 CConsensusMapNormalizerAlgorithmQuantileQuantile-normalisation of feature intensities across the maps of a ConsensusMap
 CConsensusMapNormalizerAlgorithmThresholdIntensity normalisation of a ConsensusMap by averaging per-feature intensity ratios against a reference map
 CConsoleUtilsSingleton helper for terminal-width-aware string wrapping in TOPP-tool console output
 CAASequence::ConstIteratorConstIterator for AASequence
 CHashGrid< Cluster >::ConstIteratorConstant element iterator for the hash grid
 CNASequence::ConstIteratorConstIterator of NASequence class
 CConstRefVector< ContainerT >This vector holds pointer to the elements of another container
 ►CConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >ConstIterator for the ConstRefVector
 CFileInfo::ExperimentMeta::Contact
 CMSExperiment::ContainerAdd_< ContainerValueType, addMassTraces >Helper class to add either general data points in set2DData or use mass traces from meta values
 CMSExperiment::ContainerAdd_< ContainerValueType, false >
 CMSExperiment::ContainerAdd_< ContainerValueType, true >
 CContaminants::ContaminantsSummaryResult bundle returned per compute call
 CControlledVocabulary
 CProForma::ConversionIssueDescription of a conversion issue from Peptidoform to AASequence
 CConvexHull2D
 CFileInfo::CorruptionInfo-c (corrupt data) block
 CProForma::CrossLinkGroupCross-link group connecting sites across chains
 COPXLDataStructs::CrossLinkSpectrumMatchThe CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum in OpenPepXL
 CCrossValidationLightweight K-fold / LOO cross-validation utilities and 1-D grid search
 CCubicSpline2dNatural cubic-spline interpolation of a 2D data set
 CCurlInit
 CCV
 CProForma::CvAccessionControlled vocabulary accession for a modification
 CCVMappingRuleRepresentation of a CV Mapping rule used by CVMappings
 CCVMappingsRepresentation of controlled vocabulary mapping rules (for PSI formats)
 CCVMappingTermRepresentation of controlled vocabulary term
 CCVReferenceControlled Vocabulary Reference
 CControlledVocabulary::CVTermRepresentation of a CV term
 CCVTermRepresentation of controlled vocabulary term
 CSemanticValidator::CVTermRepresentation of a parsed CV term
 CEmgFitter1D::DataHelper struct (contains the size of an area and a raw data container)
 CMzIdentMLDOMHandler::DatabaseInputStruct to hold the information from the DatabaseInput xml tag
 CDataFilters::DataFilterRepresentation of a peak/feature filter combining FilterType, FilterOperation and a value (either double or String)
 CDataFiltersDataFilter array providing some convenience functions
 CTransformationModel::DataPointCoordinate pair (with optional annotation)
 ►CDataTabBaseAll tabs need to implement this interface
 CDataValueClass to hold strings, numeric values, lists of strings and lists of numeric values
 CDateDate Class
 CDateTimeDateTime Class
 CDaTrait
 CMzIdentMLDOMHandler::DBSequenceStruct to hold the information from the DBSequence xml tag
 CDBSuitability_friend
 CDDAWorkflowCommonsCommon functions for DDA workflows
 CDeconvolvedSpectrumA class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroup instances representing masses. For MSn n>1, a PeakGroup representing the precursor mass is also added in this class. Properly assigning a precursor mass from the original precursor peak and its deconvolution result is very important in top down proteomics. This assignment is performed here for conventional acquired datasets. But for FLASHIda acquired datasets, the assignment is already done by FLASHIda. So this class simply use the results from FLASHIda log file for assignment. The parsing of FLASHIda log file is done in FLASHDeconv tool class
 CDecoyGeneratorMethods to generate isobaric decoy sequences for DDA target-decoy searches
 CDecoyHelperHelper class for calculations on decoy proteins
 CDecoyHelper::DecoyStatisticsStruct for intermediate results needed for calculations on decoy proteins
 CProSEAlgorithm::DecoyStrategy_Resolved decoy handling for one concrete input database
 CFalseDiscoveryRate::DecoyStringHelperFinds decoy strings in ProteinIdentification runs
 ►Cdefault_dfs_visitor
 ►CDefaultHandler
 ►CDefaultParamHandlerA base class for all classes handling default parameters
 CDeisotoperCollapse isotopic clusters in a centroided peak spectrum to one monoisotopic peak per ion
 CMultiplexDeltaMasses::DeltaMassMass shift with corresponding label set
 COpenSearchModificationAnalysis::DeltaMassEntryStatistics for a single delta mass bin in the histogram
 COpenSearchModificationAnalysis::DeltaMassStatisticsContainer for delta mass statistics table
 CACNode::DepthHitsInternal struct to steal one bit from depth to use as hit indicator
 CFileInfo::DetailInfoDetailed per-spectrum listing (the -d block); kept as pre-rendered lines
 ►CDigestionEnzymeBase class for digestion enzymes
 ►CDigestionEnzymeDataProvider< EnzymeType >Abstract interface for providing digestion enzyme data
 ►CDigestionEnzymeDataProvider< DigestionEnzymeProtein >
 CDigestionEnzymeDB< DigestionEnzymeType, InstanceType >Digestion enzyme database (base class)
 ►CDigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
 ►CDigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
 CIDFilter::DigestionFilterIs peptide evidence digestion product of some protein
 ►CDimBaseA base class for a dimension which represents a certain unit (e.g. RT or m/z). Derived classes implement virtual functions, which receive a well-defined data type, e.g. a Feature, and return the appropriate value for their dimension (the DimRT class would return the RT of the feature). This makes it possible to extract dimensions using a runtime configuration of DimBase instances. Very useful when mapping units (RT, m/z) to axis when plotting etc
 CDimMapper< N_DIM >Allows dynamical switching (at runtime) between a dimension (RT, m/z, int, IM, etc) and X,Y,Z coordinates. You can set either of them, and query the other. The Mapping is stored internally. The unit to which the X,Y,Z coordinates currently mapped onto can also be queried (useful for axis labels etc)
 CDimMapper< 2 >
 ►CDIntervalBase< D >A base class for D-dimensional interval
 CDistanceMatrix< Value >A two-dimensional distance matrix, similar to OpenMS::Matrix
 CFeatureDistance::DistanceParams_Structure for storing distance parameters
 CColorBrewer::Distinct
 ►CDocumentIdentifierManage source document information
 CListUtils::DoubleTolerancePredicate_Predicate to check double equality with a given tolerance
 CDPeak< dimensions >Metafunction to choose among Peak1D respectively Peak2D through a template argument
 CDPosition< D, TCoordinateType >Representation of a coordinate in D-dimensional space
 CDPosition< 1 >
 CDPosition< 2 >
 CDPosition< 2, Int64 >
 CDPosition< 2U >
 CDTAFileFile adapter for DTA files
 CEDTAFile
 CElementRepresentation of an element
 CQTCluster::Element
 CElementDBSingleton that stores elements and isotopes
 CEmgGradientDescent_friend
 CEmgScoringScoring of an elution peak using an exponentially modified gaussian distribution model
 CEmpiricalFormulaRepresentation of an empirical formula
 ►CEnhancedTabBarWidgetInterfaceWidgets that are placed into an EnhancedTabBar must implement this interface
 ►CEnzymaticDigestionClass for the enzymatic digestion of sequences
 CErrorEstimationConfigConfiguration for OpenSwath analyte level inference global and local error estimation
 ►CErrorHandler
 CEuclideanSimilarityCompareFunctor for 2Dpoints
 ►CexceptionSTL class
 CExperimentalDesignRepresentation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class
 CExperimentalDesignFileLoad an experimental design from a TSV file. (see ExperimentalDesign for details on the supported format)
 CFileInfo::ExperimentMetaExperiment / instrument / sample / contact metadata (the -m block, peak files)
 CExposedVector< VectorElement >
 ►CExposedVector< ConsensusFeature >
 ►CExposedVector< Feature >
 ►CExposedVector< PeptideIdentification >
 CExternalProcessA wrapper around boost::process to conveniently start an external program and forward its outputs
 CExternalProcessMBoxA wrapper around ExternalProcess to conveniently show a MessageBox when an error occurs
 CChromatogramExtractorAlgorithm::ExtractionCoordinates
 CFAIMSHelperHelper functions for FAIMS data
 CFASTAContainer< TBackend >Template parameter for vector-based FASTA access
 CFASTAContainer< TFI_File >FASTAContainer<TFI_File> will make FASTA entries available chunk-wise from start to end by loading it from a FASTA file. This avoids having to load the full file into memory. While loading, the container will memorize the file offsets of each entry, allowing to read an arbitrary i'th entry again from disk. If possible, only entries from the currently cached chunk should be queried, otherwise access will be slow
 CFASTAContainer< TFI_Vector >FASTAContainer<TFI_Vector> simply takes an existing vector of FASTAEntries and provides the same interface with a potentially huge speed benefit over FASTAContainer<TFI_File> since it does not need disk access, but at the cost of memory
 CFASTAFile::FASTAEntryFASTA entry type (identifier, description and sequence) The first std::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
 CFileInfo::FastaInfoFASTA specifics
 CBiosaur2Algorithm::FastHillEntryLightweight index entry for fast m/z-based hill lookup
 CFeatureFinderAlgorithmMetaboIdent::FeatureCompareComparison functor for features
 CFeatureFinderIdentificationAlgorithm::FeatureCompareComparison functor for features
 CAbsoluteQuantitationStandards::featureConcentrationOne target component matched to a feature in the corresponding FeatureMap, paired with its known concentration
 CFeatureFileOptionsOptions for loading files containing features
 CFeatureFinderIdentificationAlgorithm::FeatureFilterPeptidesPredicate for filtering features by assigned peptides:
 CFeatureFinderAlgorithmMetaboIdent::FeatureFilterQualityPredicate for filtering features by overall quality
 CFeatureFinderIdentificationAlgorithm::FeatureFilterQualityPredicate for filtering features by overall quality:
 CFeatureFinderAlgorithmPickedHelperStructsWrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes
 CFeatureFinderDefsThe purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes.
 CFeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompoundOne target compound for the FeatureFinderAlgorithmMetaboIdent assay library
 CFeatureHypothesisInternal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis)
 CFileInfo::FeatureInfoFeature / consensus specifics
 CFeatureMapArrowIOImport and export FeatureMap data to/from Apache Arrow format
 CFeatureMappingHelper utilities for matching MS2 spectra to LC-MS features by precursor (m/z, RT)
 CFeatureMapping::FeatureMappingInfoInput bundle: feature maps and a spatial index over them
 CFeatureOverlapFilter
 CFeatureSchemaSchema for LC-MS feature table (FeatureMap features)
 CFeatureMapping::FeatureToMs2IndicesOutput bundle: per-feature MS2 spectrum indices + the list of unassigned MS2 spectra
 CFFIDAlgoExternalIDHandlerClass for handling external peptide identifications in feature finding
 CFIAMSSchedulerBatch driver for FIA-MS analyses. Dispatches each sample of a CSV-described batch to FIAMSDataProcessor
 CDate::Fields
 CDateTime::Fields
 CFileBasic file handling operations
 CFileHandlerFacilitates file handling by file type recognition
 CFileInfoLibrary-level equivalent of the FileInfo tool
 CFileMappingMaps input/output files to filenames for the external program
 CFileInfo::FileMetaGeneral header block (always populated)
 CFileTypeListHolds a vector of known file types, e.g. as a way to specify supported input formats
 CFileTypesCentralizes the file types recognized by FileHandler
 CFileTypeList::FilterElements_Hold filter items (for Qt dialogs) along with their OpenMS type
 CFilterExpressionSimple conjunction/disjunction of conditions
 CFlagSet< ENUM >Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64
 CFlagSet< LayerDataBase::DataType >
 CFlagSet< TV_STATUS >
 CFLASHDeconvFeatureFileFLASHDeconv feature level output *.tsv, *.ms1ft (for Promex), *.feature (for TopPIC) file formats
 CFLASHDeconvSpectrumFileFLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats
 CFLASHHelperClassesWrapper struct for all the structs needed by the FLASHDeconv The following structures/classes are defined: PrecalculatedAveragine, MassFeature, IsobaricQuantities, LogMzPeak, Tag, and DAG for tagging. i) PrecalculatedAveragine - to match observed isotopic envelope against theoretical one, theoretical envelope from averagine model should be quickly calculated. To do so, precalculate averagines for different masses at the beginning of FLASHDeconv runs ii) MassFeature - the feature of the deconvolved masses (instead of m/zs for MS features). iii) IsobaricQuantities - the quantities from isobaric quantification (implemented within FLASHDeconv) iv) LogMzPeak - Log transformed peak from original peak. Contains information such as charge, isotope index, and uncharged mass. v) Tag - the sequence tag generated on deconvolved spectra in FLASHTaggerAlgorithm vi) DAG - the graph for sequence tagging in FLASHTaggerAlgorithm and for proteoform characterization in FLASHExtenderAlgorithm
 CControlledVocabulary::FNV1aHasherEnsure same hash on all platforms (for reproducibility)-
 CProForma::FormulaTagChemical formula with optional charge
 CFragmentIndex::FragmentOne entry in the fragment index
 CNuXLFragmentAnnotationHelper::FragmentAnnotationDetail_Single fragment annotation
 COpenSearchModificationAnalysis::FuzzyDoubleComparatorComparator for approximate comparison of double values
 CFuzzyStringComparatorFuzzy comparison of strings, tolerates numeric differences
 CGammaDistributionFitter::GammaDistributionFitResultStruct to represent the parameters of a gamma distribution
 CGammaDistributionFitterImplements a fitter for the Gamma distribution
 CGaussFilterAlgorithmThis class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data
 CGaussFitter::GaussFitResultStruct of parameters of a Gaussian distribution
 CGaussFitterImplements a fitter for Gaussian functions
 CSignalToNoiseEstimator< Container >::GaussianEstimateProtected struct to store parameters my, sigma for a Gaussian distribution
 ►CLevMarqFitter1D::GenericFunctor
 ►CTraceFitter::GenericFunctorGeneric LM functor with a raw-pointer interface, used to keep Eigen out of the public API
 CIDFilter::GetMatchingItems< HitType, Entry >Builds a map index of data that have a std::string index to find matches and return the objects
 CIDFilter::GetMatchingItems< OpenMS::PeptideEvidence, OpenMS::FASTAFile::FASTAEntry >
 CConfidenceScoring::GLM_Binomial GLM used to map (squared-normalised-RT-diff, intensity-distance) -> [0, 1] confidence
 CGlobalExceptionHandlerOpenMS global exception handler
 CProForma::GlobalModificationGlobal modification applied to specific locations
 CProForma::GlycanCompositionGlycan composition specification
 CGNPSMetaValueFileWriter for the meta-value (.TSV) table consumed by GNPS Feature-Based Molecular Networking
 CGNPSQuantificationFileWriter for the feature-quantification (.TXT) table required by GNPS Feature-Based Molecular Networking
 CGradientRepresentation of a HPLC gradient
 CGravitatorManipulates X or Y component of points in the X-Y plane, by assuming one axis (either X or Y axis) has gravity acting upon it
 CGridBasedClusterBasic data structure for clustering
 CGridFeatureRepresentation of a feature in a hash grid
 CGridSearch< TupleTypes >
 CGUILockRAII class to disable the GUI and set a busy cursor and go back to the original state when this class is destroyed
 CGumbelDistributionFitter::GumbelDistributionFitResultStruct to represent the parameters of a gumbel distribution
 CGumbelMaxLikelihoodFitter::GumbelDistributionFitResultStruct to represent the parameters of a gumbel distribution
 CGumbelDistributionFitterImplements a fitter for the Gumbel distribution
 CGumbelMaxLikelihoodFitterImplements a fitter for the Gumbel distribution
 CGzipIfstreamDecompresses files which are compressed in the gzip format (*.gzip)
 CHasActivationMethod< SpectrumType >Predicate that determines if a spectrum was generated using any activation method given in the constructor list
 CIDFilter::HasDecoyAnnotation< HitType >Is this a decoy hit?
 CIDFilter::HasGoodScore< HitType >Is the score of this hit at least as good as the given value?
 Chash< OpenMS::AASequence >Hash function for OpenMS::AASequence
 Chash< OpenMS::Adduct >
 Chash< OpenMS::AnnotatedMSRun >Hash function for OpenMS::AnnotatedMSRun
 Chash< OpenMS::ChargePair >
 Chash< OpenMS::ChromatogramPeak >
 Chash< OpenMS::ChromatogramSettings >Hash function for OpenMS::ChromatogramSettings
 Chash< OpenMS::Compomer >
 Chash< OpenMS::ConvexHull2D >
 Chash< OpenMS::CVTerm >Hash function for CVTerm
 Chash< OpenMS::CVTerm::Unit >Hash function for CVTerm::Unit
 Chash< OpenMS::CVTermList >Hash function for CVTermList
 Chash< OpenMS::CVTermListInterface >Hash function for CVTermListInterface
 Chash< OpenMS::DataValue >Hash function for DataValue
 Chash< OpenMS::DateTime >
 Chash< OpenMS::DBoundingBox< D > >
 Chash< OpenMS::DigestionEnzyme >Std::hash specialization for DigestionEnzyme
 Chash< OpenMS::DPosition< D, TCoordinateType > >
 Chash< OpenMS::DRange< D > >
 Chash< OpenMS::Element >
 Chash< OpenMS::EmpiricalFormula >Hash function for OpenMS::EmpiricalFormula
 Chash< OpenMS::FeatureHandle >
 Chash< OpenMS::FLASHHelperClasses::LogMzPeak >Hash specialization for FLASHHelperClasses::LogMzPeak
 Chash< OpenMS::FLASHHelperClasses::MassFeature >Hash specialization for FLASHHelperClasses::MassFeature
 Chash< OpenMS::IncludeExcludeTarget >Std::hash specialization for OpenMS::IncludeExcludeTarget
 Chash< OpenMS::Index >
 Chash< OpenMS::IonDetector >Hash function for OpenMS::IonDetector
 Chash< OpenMS::IonSource >
 Chash< OpenMS::IsotopeDistribution >
 Chash< OpenMS::MassAnalyzer >Hash function for OpenMS::MassAnalyzer
 Chash< OpenMS::MetaInfo >
 Chash< OpenMS::MetaInfoInterface >Hash function for MetaInfoInterface
 Chash< OpenMS::MobilityPeak1D >
 Chash< OpenMS::MobilityPeak2D >
 Chash< OpenMS::ModificationDefinition >Hash function for OpenMS::ModificationDefinition
 Chash< OpenMS::NASequence >Hash function for OpenMS::NASequence
 Chash< OpenMS::NuXLFragmentAdductDefinition >Hash function for OpenMS::NuXLFragmentAdductDefinition
 Chash< OpenMS::OPXLDataStructs::ProteinProteinCrossLink >Std::hash specialization for ProteinProteinCrossLink
 Chash< OpenMS::ParamValue >
 Chash< OpenMS::Peak1D >
 Chash< OpenMS::Peak2D >
 Chash< OpenMS::PeakGroup >
 Chash< OpenMS::PeptideEvidence >
 Chash< OpenMS::PeptideHit >Hash function for OpenMS::PeptideHit
 Chash< OpenMS::PeptideHit::PeakAnnotation >Hash function for OpenMS::PeptideHit::PeakAnnotation
 Chash< OpenMS::PeptideIdentification >Hash function for OpenMS::PeptideIdentification
 Chash< OpenMS::Precursor >
 Chash< OpenMS::Product >Hash function for OpenMS::Product
 Chash< OpenMS::ProteinHit >Hash function for OpenMS::ProteinHit
 Chash< OpenMS::ProteinIdentification >Std::hash specialization for ProteinIdentification
 Chash< OpenMS::ProteinIdentification::ProteinGroup >Std::hash specialization for ProteinIdentification::ProteinGroup
 Chash< OpenMS::ProteinIdentification::SearchParameters >Std::hash specialization for ProteinIdentification::SearchParameters
 Chash< OpenMS::ReactionMonitoringTransition >Hash function for ReactionMonitoringTransition
 Chash< OpenMS::Residue >Hash specialization for OpenMS::Residue Hashes all fields used in operator== for consistency
 Chash< OpenMS::ResidueModification >Hash function for OpenMS::ResidueModification
 Chash< OpenMS::Ribonucleotide >Hash function for OpenMS::Ribonucleotide
 Chash< OpenMS::Software >Hash function for OpenMS::Software
 Chash< OpenMS::SpectrumSettings >Hash function for OpenMS::SpectrumSettings
 Chash< OpenMS::TargetedExperimentHelper::Compound >Hash function for TargetedExperimentHelper::Compound
 Chash< OpenMS::TargetedExperimentHelper::Contact >Hash function for TargetedExperimentHelper::Contact
 Chash< OpenMS::TargetedExperimentHelper::CV >Hash function for TargetedExperimentHelper::CV
 Chash< OpenMS::TargetedExperimentHelper::Instrument >Hash function for TargetedExperimentHelper::Instrument
 Chash< OpenMS::TargetedExperimentHelper::Interpretation >Hash function for TargetedExperimentHelper::Interpretation
 Chash< OpenMS::TargetedExperimentHelper::Peptide >Hash function for TargetedExperimentHelper::Peptide
 Chash< OpenMS::TargetedExperimentHelper::PeptideCompound >Hash function for TargetedExperimentHelper::PeptideCompound
 Chash< OpenMS::TargetedExperimentHelper::Prediction >Hash function for TargetedExperimentHelper::Prediction
 Chash< OpenMS::TargetedExperimentHelper::Protein >Hash function for TargetedExperimentHelper::Protein
 Chash< OpenMS::TargetedExperimentHelper::Publication >Hash function for TargetedExperimentHelper::Publication
 Chash< OpenMS::TargetedExperimentHelper::RetentionTime >Hash function for TargetedExperimentHelper::RetentionTime
 Chash< OpenMS::TargetedExperimentHelper::TraMLProduct >Hash function for TargetedExperimentHelper::TraMLProduct
 Chash< OpenSwath::LightCompound >Hash function for LightCompound
 Chash< OpenSwath::LightModification >Hash function for LightModification
 Chash< OpenSwath::LightProtein >Hash function for LightProtein
 Chash< OpenSwath::LightTransition >Hash function for LightTransition
 CHashGrid< Cluster >Container for (2-dimensional coordinate, value) pairs
 CNucleicAcidSearchEngine::HasInvalidLength
 CIDFilter::HasMatchingAccessionImpl< HitType, SetType >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?
 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::HasMinMetaValue< HitType >Predicate to check if a HitType object has a minimum meta value
 CIDFilter::HasNoHits< IdentificationType >Is the list of hits of this peptide/protein ID empty?
 CHasPrecursorCharge< SpectrumType >Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list
 CHasScanMode< SpectrumType >Predicate that determines if a spectrum has a certain scan mode
 CHasScanPolarity< SpectrumType >Predicate that determines if a spectrum has a certain scan polarity
 CHDF5ConnectorFile adapter for HDF5 files
 CBiosaur2Algorithm::HillRepresentation of a single hill (continuous m/z trace across adjacent scans)
 CHistogram< ValueType, BinSizeType >Representation of a histogram
 CFragmentIndex::Hit
 CHit
 CConsensusIDAlgorithm::HitInfo
 CHPLCRepresentation of a HPLC experiment
 CHydrophobicityProfileThis class is used for hydrophobicity profiling of peptides
 CHyperScoreAn implementation of the X!Tandem HyperScore PSM scoring function
 CIBSpectraFileImplements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results
 ►CIChromatogramHandlerAbstract interface for providing chromatograms
 CIChromatogramsReaderThe interface of read-access to a list of chromatograms
 CIChromatogramsWriter
 ►CIDataFrameWriter
 CIDBoostGraphCreates and maintains a boost graph based on the OpenMS ID datastructures
 CIDConflictResolverAlgorithmResolves ambiguous annotations of features with peptide identifications
 CIdentificationDataConverter
 CMs2IdentificationRate::IdentificationRateDataStructure for storing results
 CIDRipper::IdentificationRunsRepresents a set of IdentificationRuns
 CIdentifierMSRunMapperTwo-way mapping from ms-run-path to protID|pepID-identifier
 CFileInfo::IdentInfoIdentification specifics (idXML / mzIdentML)
 CIDFilterCollection of functions for filtering peptide and protein identifications
 CMzTab::IDMzTabStream
 CIDScoreGetterSetterA class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps
 CIDScoreSwitcherAlgorithm::IDSwitchResultStructure holding score switching information for IDScoreSwitcherAlgorithm
 ►CIFeature
 CILPDCWrapperILP-based decharging: pick the maximum-log-score subset of charge-pair edges that yields a consistent per-feature charge assignment
 CIMDataConverterThis class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models
 CMobilityPeak2D::IMLessComparator by IM position
 CMSSpectrum::IMLessComparator for the ion mobility
 CImmoniumIonsInPeptide
 ►CIMRMFeature
 CIMSAlphabetHolds an indexed list of bio-chemical elements used by mass-decomposition algorithms
 ►CIMSAlphabetParser< AlphabetElementType, Container, InputSource >An abstract templatized parser to load the data that is used to initialize Alphabet objects
 ►CIMSDataConsumerThe interface of a consumer of spectra and chromatograms
 CIMSElementRepresents a chemical atom with name and isotope distribution
 CIMSIsotopeDistributionRepresents a distribution of isotopes restricted to the first K elements
 CFeatureFinderIdentificationAlgorithm::IMStatsIon mobility statistics for a peptide in a specific RT region and charge state
 CIMTypes
 CImzMLBinaryIOShared .ibd binary array decode utilities for imzML handlers
 CImzMLMetaDataset-level metadata for imzML mass spectrometry imaging files
 CImzMLSpectrumIndexPer-spectrum binary index entry for an imzML dataset
 CImzMLWriterWriter for imzML 1.1.0 files (.imzML + companion .ibd)
 CIndentedStreamClass for writing data which spans multiple lines with an indentation for each line (all except the first)
 CIndex
 CIndexedMzMLDecoderA class to analyze indexedmzML files and extract the offsets of individual tags
 CIndexedMzMLFileLoaderA class to load an indexedmzML file
 CIndexedMzMLHandlerA low-level class to read an indexedmzML file
 CFeatureHandle::IndexLessComparator by map and unique id
 CProForma::InfoTagInfo tag for arbitrary text annotations
 CInIntensityRange< PeakType >Predicate that determines if a peak lies inside/outside a specific intensity range
 CINIUpdater
 CInMSLevelRange< SpectrumType >Predicate that determines if a spectrum lies inside/outside a specific MS level set
 CInMzRange< PeakType >Predicate that determines if a peak lies inside/outside a specific m/z range
 CInPrecursorMZRange< SpectrumType >Predicate that determines if a spectrum's precursor is within a certain m/z range
 CInputFileInformation about input files that were processed
 CFuzzyStringComparator::InputLineStores information about the current input line (i.e., stream for the line and the current position in the stream)
 ►CInputSource
 CInRTRange< SpectrumType >Predicate that determines if a spectrum lies inside/outside a specific retention time range
 CInspectInfileInspect input file adapter
 CInspectOutfile
 CIntensityIteratorWrapper< IteratorT >An iterator wrapper to access peak intensities instead of the peak itself
 CChromatogramPeak::IntensityLessComparator by intensity
 CMobilityPeak1D::IntensityLess
 CMobilityPeak2D::IntensityLess
 CPeak1D::IntensityLess
 CPeak2D::IntensityLess
 CTransformationModelInterpolated::InterpolatorThe class defines a generic interpolation technique used in the TransformationModelInterpolated
 CTOPPASToolVertex::IOInfoStores the information for input/output files/lists
 CIonIdentityMolecularNetworkingHelpers for the Ion Identity Molecular Networking (IIMN) workflow on GNPS
 CIonImageDense W x H grid of ion intensities with a per-pixel mask
 CIonMobilityScoringA class that calls the ion mobility scoring routines
 CFragmentIndex::IonOffsetsPrecomputed ion-type mass offsets (from Residue::getInternalTo*Ion formulas)
 ►Cios_baseSTL class
 ►CIPeptideIdsAbstract base class which defines an interface for PeptideIdentifications
 CIPFAlignmentRowAlignment-group membership for cross-run IPF signal propagation
 CIPFPrecursorProbabilityRowPrecursor-layer posterior error probability used by IPF
 CIPFPrecursorRowPeak-group and precursor evidence for peptidoform inference
 CIPFResultRowFinal peptidoform inference result row
 CIPFTransitionRowTransition-layer evidence for peptidoform inference
 CCalibrationWorkflow::IrtExperimentsPrepared iRT experiments ready for calibration
 CIsEmptySpectrum< SpectrumType >Predicate that determines if a spectrum is empty
 CIDScoreGetterSetter::IsHitType< T >
 CIDScoreGetterSetter::IsIDType< T >
 ►CISignalToNoise
 CIsInCollisionEnergyRange< SpectrumType >Predicate that determines if an MSn spectrum was generated with a collision energy in the given range
 CIsInIsolationWindow< SpectrumType >Predicate that determines if the isolation window covers ANY of the given m/z values
 CIsInIsolationWindowSizeRange< SpectrumType >Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range
 CIsobaricQuantitationMethod::IsobaricChannelInformationSummary of an isobaric quantitation channel
 CIsobaricIsotopeCorrectorPerforms isotope impurity correction on intensities extracted from isobaric labeling experiments
 CIsobaricNormalizerPerforms median normalization on the extracted ratios of isobaric labeling experiment
 CIsobaricQuantifierStatisticsStatistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion)
 CFLASHHelperClasses::IsobaricQuantitiesIsobaric quantities
 CIsoelectricPoint
 ►CIsoSpecGeneratorWrapperInterface for the IsoSpec algorithm - a generator of infinitely-resolved theoretical spectra
 ►CIsoSpecWrapperA convenience class for the IsoSpec algorithm - easier to use than the IsoSpecGeneratorWrapper classes
 CBiosaur2Algorithm::IsotopeCandidateCandidate isotope peak that can be associated with a monoisotopic hill
 CIsotopeClusterStores information about an isotopic cluster (i.e. potential peptide charge variants)
 CIsotopeDistribution
 CFeatureFinderAlgorithmPickedHelperStructs::IsotopePatternHelper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked
 ►CIsotopePatternGeneratorProvides an interface for different isotope pattern generator methods
 CProForma::IsotopeReplacementIsotope replacement for stable isotope labeling
 CISpectraReaderThe interface of read-access to a list of spectra
 CISpectraWriter
 ►CISpectrumAccessThe interface of a mass spectrometry experiment
 CIsZoomSpectrum< SpectrumType >Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum
 ►Citerator
 ►CIterator
 ►Citerator
 CAASequence::IteratorIterator class for AASequence
 CHashGrid< Cluster >::IteratorElement iterator for the hash grid
 CNASequence::IteratorIterator of NASequence class
 ►Cset< K >::iteratorSTL iterator class
 ►CITransitionGroup
 CItraqConstantsSome constants used throughout iTRAQ classes
 CJavaInfoDetect Java and retrieve information
 CKDTreeFeatureNodeLightweight kd-tree entry: a back-pointer to a KDTreeFeatureMaps and the index of one feature in it
 CKernelDensityEstimationKernel Density Estimation utilities using FFT-based methods
 CKroenikFileFile adapter for Kroenik (HardKloer sibling) files
 CMultiplexDeltaMassesGenerator::LabelComplete label information
 CProForma::LabelLabel for cross-links, branches, or ambiguous grouping
 CProForma::LabileModificationLabile modification that may be lost during fragmentation
 ►CLayerAnnotatorBase
 ►CLayerDataDefs
 CLayerStack
 ►CLayerStatisticsCompute summary statistics (count/min/max/avg) about a container, e.g. intensity, charge, meta values, ..
 ►CLayerStoreDataBase class to store either the currently visible or all data of a canvas
 CLevelContextInferenceShared OpenSwath analysis context inference for peptide, protein, and gene rows
 CLevelContextInferenceConfigConfiguration for peptide-, protein-, and gene-level context inference
 CLevelContextInputRowCompact level-context input row independent of file format
 CLevelContextResultRowFinal level-context result row
 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< KeyType >
 CLinearRegressionThis class offers functions to perform least-squares fits to a straight line model, \( Y(c,x) = c_0 + c_1 x \)
 CModifiedSincSmoother::LinearRegressionHelper class for weighted linear regression
 CLinearRegressionWithoutInterceptThis class offers functions to perform least-squares fits to a straight line model, \( Y(c,x) = c_0 + c_1 x \)
 ►Clist< T >STL class
 CListUtilsCollection of utility functions for management of vectors
 CInternalCalibration::LockMassHelper class, describing a lock mass
 CLogStreamBuf::LogCacheStructHolds a counter of occurrences and an index for the occurrence sequence of the corresponding log message
 CLogConfigHandlerThe LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream
 CFLASHHelperClasses::LogMzPeakLog transformed peak. After deconvolution, all necessary information from deconvolution such as charge and isotope index is stored
 CLogSinkGuardRAII guard that temporarily removes a stream from a LogStream and re-inserts it on scope exit
 CLogStreamNotifierSink-side hook that is notified whenever a LogStream flushes a complete message
 CLooper< param_index, grid_size, EvalResult, Tuple, TupleTypes >
 CLooper< grid_size, grid_size, EvalResult, Tuple, TupleTypes... >
 CLooper< param_index, grid_size, EvalResult, Tuple, FirstTupleType, TupleTypes... >
 CSimpleTSGXLMS::LossIndex
 CTheoreticalSpectrumGeneratorXLMS::LossIndex
 CLPWrapperA wrapper class for linear programming (LP) solvers
 CPercolatorFeatureSetHelper::lq_PeptideEvidenceFor accession dependent sorting of PeptideEvidences
 CPercolatorFeatureSetHelper::lq_ProteinHitFor accession dependent sorting of ProteinHits
 CMapAlignmentAlgorithmKDAn efficient reference-free feature map alignment algorithm for unlabeled data
 ►CMapAlignmentEvaluationAlgorithmBase class for all Caap evaluation algorithms
 CMapAlignmentTransformerThis class collects functions for applying retention time transformations to data structures
 CFileInfo::FeatureInfo::MapColumn
 CMapConversionStatic helpers that convert between the three OpenMS container types (PeakMap, FeatureMap, ConsensusMap)
 CAccurateMassSearchEngine::MappingEntry_
 CMappingParamFilename mappings for all input/output files
 CScores::Maps_Holds the static score type lookup maps (thread-safe via C++11 function-local static)
 CConsensusFeature::MapsLessCompare by the sets of consensus elements (lexicographically)
 CModifiedPeptideGenerator::MapToResidueTypeCached mapping ResidueModification* -> already-instantiated modified Residue*
 CMapUtilities< MapType >Utilities for Feature and ConsensusMap
 ►CMapUtilities< ConsensusMap >
 ►CMapUtilities< FeatureMap >
 ►CMassDecomposer< ValueType, DecompositionValueType >An interface to handle decomposing of integer values/masses over a set of integer weights (alphabet)
 CMassDecomposer< long unsigned int, unsigned int >
 CMassDecompositionClass represents a decomposition of a mass into amino acids
 CProForma::MassDeltaMass delta modification with optional source hint
 CMassExplainerComputes empirical formulas for given mass differences using a set of allowed elements
 CFLASHHelperClasses::MassFeatureMass feature (Deconvolved masses in spectra are traced by Mass tracing to generate mass features - like LC-MS features)
 CIMSAlphabet::MassSortingCriteria_Private class-functor to sort out elements in mass ascending order
 CFeatureFinderAlgorithmPickedHelperStructs::MassTraceHelper struct for mass traces used in FeatureFinderAlgorithmPicked
 CMassTraceA container type that gathers peaks similar in m/z and moving along retention time
 CFeatureFinderAlgorithmMetaboIdent::MassTraceBoundsBoundaries for a mass trace in a feature
 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
 CWNetMatcher::MatchResultResult of a pairwise matching
 CMatrix< Value >A 2D matrix class with efficient buffer access for NumPy interoperability
 CMatrix< double >
 CMatrix< int >
 CMatrix< XCorrArrayType >
 Cmean_and_stddevFunctor to compute the mean and stddev of sequence using the std::foreach algorithm
 CSysInfo::MemUsageA convenience class to report either absolute or delta (between two timepoints) RAM usage
 CMessagePasserFactory< Label >
 CMetaboTargetedTargetDecoy::MetaboTargetDecoyMassMappingMetaboTargetDecoyMassMapping introduces a mapping of target and decoy masses and their respective compound reference using an identifier
 CMetaboTargetedAssayThis class provides methods for the extraction of targeted assays for metabolomics
 CMetaboTargetedTargetDecoyResolve overlapping fragments and missing decoys for experimental specific decoy generation in targeted/pseudo targeted metabolomics
 CMetaInfoA Type-Name-Value tuple class
 ►CMetaInfoInterfaceInterface for classes that can store arbitrary meta information (Type-Name-Value tuples)
 CMetaInfoInterfaceUtilsUtilities operating on containers inheriting from MetaInfoInterface
 CMetaInfoRegistryRegistry which assigns unique integer indices to strings
 CMetaKeyGetter< T >
 CMinimumDistanceBasic data structure for distances between clusters
 CMobilityPeak1D::MobilityLessComparator by mobility position
 CMobilityPeak1DA 1-dimensional raw data mobility point or peak. The unit (ms, 1/K_0, etc) is implicit
 CMobilityPeak2DA 2-dimensional raw data point or peak
 CMobilogramParquetConsumerWrites Mobilograms (ion-mobility traces) to a Parquet file using a PyProphet-compatible-like schema
 CTraceFitter::ModelDataHelper bundle passed to functors so they can read both the traces and the weighting flag
 CModelDescription< D >Stores the name and parameters of a model
 CProForma::ModificationA modification with one or more alternative tags
 ►CModificationDataProviderInterface for providing ResidueModification data to ModificationsDB
 CModificationDefinition
 CModificationDefinitionsSet
 CMzIdentMLDOMHandler::ModificationParamStruct to hold the information from the ModificationParam xml tag
 COpenSearchModificationAnalysis::ModificationPatternStores details of a modification pattern found in the data
 ►CModificationsDBDatabase which holds all residue modifications from UniMod
 COpenSearchModificationAnalysis::ModificationSummaryData structure for modification summary output
 CModifiedNASequenceGeneratorGenerator of modified nucleic-acid sequences for fixed and variable modification placement
 CModifiedPeptideGeneratorGenerate fixed- and variable-modification variants of an AASequence, lock-free
 CProForma::ModifiedRangeModified sequence range with shared modifications
 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
 CFragmentIndex::ModSlotA candidate modification slot for a specific peptide
 CMonosaccharideDB::MonosaccharideStructure representing a monosaccharide
 CMonosaccharideDBSingleton database of monosaccharides for glycan notation
 CMorpheusScoreAn implementation of the Morpheus PSM scoring function Inspired by a C# implementation by C. Wenger released under MIT license
 CMQExporterHelper::MQCommonOutputs
 CMQEvidenceBuilds a MaxQuant Evidence.txt
 CMQExporterHelperHelper class for common functions and NON trivial values needed for exporting MaxQuant outputs
 CMQMsmsBuilds a MaxQuant msms.txt
 CMRMBatchFeatureSelectorBatch processing wrapper for MRMFeatureSelector
 CMRMFeaturePickerMRMFeaturePicker defines the structures containing parameters to be used in MRMTransitionGroupPicker for components and components groups
 CMRMFeatureQCThe MRMFeatureQC is a class to handle the parameters and options for MRMFeatureFilter
 ►CMRMFeatureSelectorA base class for selection of MRM Features through Linear Programming optimization
 CMRMFileMinimal SRM/MRM file loader returning a single SwathMap wrapping the chromatogram container
 CMRMIonSeriesGenerate theoretical fragment ion series for use in MRMAssay and MRMDecoy
 CMRMRTNormalizerThe MRMRTNormalizer will find retention time peptides in data
 CMRMScoringThis class implements different scores for peaks found in SRM/MRM
 CMRMTransitionGroup< ChromatogramType, TransitionType >The representation of a group of transitions in a targeted proteomics experiment
 CMRMTransitionGroup< SpectrumT, TransitionT >
 CMS2AdductsOfSinglePrecursorAdduct
 CMSExperimentArrowExportExport MSExperiment data to Apache Arrow format
 CExperimentalDesign::MSFileSectionEntry
 CMSImagingExperimentIn-memory model for a 2D imaging mass spectrometry dataset
 CMSImagingGeometryPixel grid metadata and (x, y) -> spectrum_index lookup for MSI data
 CMSImagingRegionA spatial region within an MSI dataset, in global pixel coordinates
 CMsInspectFile
 CMSNumpressCoderClass to encode and decode data encoded with MSNumpress
 CMSPGenericFile_friend
 CMSstatsFileFile adapter for MSstats files
 CMSstatsFile::MSstatsLine_
 CMSstatsFile::MSstatsTMTLine_
 CProSEAlgorithm::MultiFileSearchResultMulti-file search result bundle
 CMultiGradientA gradient of multiple colors and arbitrary distances between colors
 CMultipleTestingStatistical functions for multiple testing correction
 CMultiplexDeltaMassesData structure for mass shift pattern
 CMultiplexClustering::MultiplexDistanceScaled Euclidean distance for clustering
 CMultiplexFilteredMSExperimentData structure storing all peaks (and optionally their raw data points) of an experiment corresponding to one specific peak pattern
 CMultiplexFilteredPeakData structure storing a single peak that passed all filters
 CMultiplexIsotopicPeakPatternData structure for pattern of isotopic peaks
 CMultiplexSatelliteCentroidedData structure storing a single satellite peak
 CMultiplexSatelliteProfileData structure storing a single satellite data point
 CNuXLModificationMassesResult::MyStringLengthCompareComparator that orders strings primarily by length (shortest first) and lexicographically within the same length
 CMzIdentMLDOMHandlerXML DOM handler for MzIdentMLFile
 CMobilityPeak2D::MZLessComparator by m/z position
 CMSChromatogram::MZLessComparator for the precursor m/z time
 CPeak1D::MZLessComparator by m/z position
 CPeak2D::MZLessComparator by m/z position
 CMzMLHandlerHelperHelper for mzML file format
 CMzMLSpectrumDecoderA class to decode input strings that contain an mzML chromatogram or spectrum tag
 CMzMLSqliteHandlerSqlite handler for storing spectra and chromatograms in sqMass format
 CMzMLSqliteSwathHandlerRead-only accessor for SWATH/DIA spectrum indices stored in an sqMass file
 CMzPAFParser and writer for mzPAF (Peak Annotation Format) notation
 CMzPAFAnnotationA single mzPAF peak annotation
 CMzPAFMassDeltaMass delta in an mzPAF annotation
 CMzPAFNeutralLossNeutral loss in an mzPAF annotation
 CMzPAFPeakAnnotationsMultiple mzPAF annotations for a single peak
 CMzQCFileFile adapter for mzQC files used to load and store mzQC files
 CMzTabAssayMetaData
 ►CMzTabBase
 CMzTabBoolean
 CMzTabContactMetaData
 CMzTabCVMetaData
 CMzTabDouble
 CMzTabDoubleList
 CMzTabFileFile adapter for MzTab files
 CFileInfo::MzTabInfoMzTab specifics
 CMzTabInstrumentMetaData
 CMzTabInteger
 CMzTabIntegerList
 CMzTabMAssayMetaDataMztabM Assay Metadata
 CMzTabMDatabaseMetaDataMztabM Database Metadata
 CMzTabMetaDataAll meta data of a mzTab file. Please refer to specification for documentation
 CMzTabMFileFile adapter for MzTab-M files
 CMzTabMMetaDataMztabM Metadata
 CMzTabMMSRunMetaDataMztabM MSRun Metadata
 CMzTabModificationData model of MzTab files
 CMzTabModificationList
 CMzTabModificationMetaData
 CMzTabMSmallMoleculeEvidenceSectionRowSME Small molecule evidence section (mztab-m)
 CMzTabMSmallMoleculeFeatureSectionRowSMF Small molecule feature section (mztab-m)
 CMzTabMSmallMoleculeSectionRowSML Small molecule section (mztab-m)
 CMzTabMSRunMetaData
 CMzTabMStudyVariableMetaDataMztabM StudyVariable Metadata
 CMzTabNucleicAcidSectionRowNUC - Nucleic acid section (table-based)
 CMzTabOligonucleotideSectionRowOLI - Oligonucleotide section (table-based)
 CMzTabOSMSectionRowOSM - OSM (oligonucleotide-spectrum match) section (table-based)
 CMzTabParameter
 CMzTabParameterList
 CMzTabPeptideSectionRowPEP - Peptide section (Table based)
 CMzTabProteinSectionRowPRT - Protein section (Table based)
 CMzTabPSMSectionRowPSM - PSM section (Table based)
 CMzTabSampleMetaData
 CMzTabSmallMoleculeSectionRowSML Small molecule section (table based)
 CMzTabSoftwareMetaData
 CMzTabSpectraRef
 CMzTabString
 CMzTabStringList
 CMzTabStudyVariableMetaData
 CMZTrafoModelCreate and apply models of a mass recalibration function
 CProForma::NamedModNamed modification with optional CV prefix hint
 CFileInfo::NamedStatsOne named SummaryStatistics block; title is the label used in both renderers
 CReactionMonitoringTransition::NameLessComparator by name
 CNASequenceRepresentation of a nucleic acid sequence
 CSplineInterpolatedPeaks::NavigatorIterator class for access of spline packages
 CNeedlemanWunschGlobal-alignment similarity score for two amino-acid sequences using the Needleman-Wunsch algorithm
 CQTCluster::Neighbor
 CNeighborSeqSubset-neighbor peptide search: find peptides from a wider pool (typically a FASTA digest) that are spectral neighbors of a smaller "relevant" peptide set, useful when only part of a complex sample is of interest
 CNeighborSeq::NeighborStatsStatistics of how many neighbors were found per reference peptide
 CNetworkConvenience wrapper around NetworkGetRequest for one-shot HTTP/HTTPS downloads
 CNetworkGetRequestSynchronous HTTP GET request backed by libcurl
 CSignalToNoiseEstimatorMedianRapid::NoiseEstimatorClass to compute the noise value at a given position
 C_Alloc_base< _Tp, _Alloc >::NoLeakAlloc
 CNonNegativeLeastSquaresSolverWrapper around the Lawson-Hanson non-negative least squares (NNLS) Fortran routine
 CMSNumpressCoder::NumpressConfigConfiguration class for MSNumpress
 CNuXLAnnotateAndLocatePost-scoring step of the OpenNuXL pipeline: annotates fragment-ion peaks of each candidate hit and localises the NA cross-link to a residue
 CNuXLAnnotatedHit
 CNuXLConstantsIndex positions of the per-peak IntegerDataArrays used by the OpenNuXL pipeline
 CNuXLDeisotoperDeisotoping of nucleotide cross-link mass spectra
 CNuXLFDRClass-separated FDR calculation for nucleic-acid cross-links (NuXL)
 CNuXLFragmentAdductDefinition
 CNuXLFragmentAnnotationHelperConvenience functions to construct appealing fragment annotation strings and store them as PeptideHit::PeakAnnotation
 CNuXLFragmentIonGeneratorAugments a peptide-cross-link fragment spectrum with NuXL-specific ions that TheoreticalSpectrumGenerator does not produce
 CNuXLLinearRescore
 CNuXLMarkerIonExtractor
 CNuXLModificationMassesResultResult of NuXLModificationsGenerator::initModificationMassesNA — empirical formulas with their monoisotopic mass and the disambiguating nucleotide-composition lookup
 CNuXLModificationsGeneratorEnumerator of precursor-adduct masses for NuXL cross-link searches
 CNuXLParameterParsing
 CNuXLProteinReportProtein report
 CNuXLReportCreate PSM report
 CNuXLReportRowStruct to hold a single report line
 CNuXLReportRowHeaderCreate header line
 CNuXLRTPrediction
 COMSSACSVFile
 COnDiscImzMLExperimentRandom-access, on-disc reader for imzML mass spectrometry imaging datasets
 COnDiscMSExperimentRepresentation of a mass spectrometry experiment on disk
 COpenMSBuildInfoBuild-configuration accessors: build type, OpenMP availability, and OpenMP thread count
 COpenMSOSInfoSnapshot of the runtime operating system: name, version, and pointer-width architecture
 COpenSearchModificationAnalysis::OpenSearchAnalysisResultCombined result of open search modification analysis
 COpenSearchModificationAnalysisUtility class for analyzing modification patterns in open search results
 ►COpenSwath_Ind_ScoresA structure to hold the individual scores computed for unique ion signatures (UIS) scores for the Inference of Peptidoforms (IPF) workflow
 COpenSwath_ScoresA structure to hold the different scores computed by OpenSWATH
 COpenSwath_Scores_UsageA structure to store which scores should be used by the OpenSWATH Algorithm
 COpenSwathDataAccessHelperSeveral helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces
 COpenSwathExportFilterConfigShared filter configuration for OpenSWATH export readers
 COpenSwathExportRowFiltered feature-level row used by results and matrix exports
 COpenSwathFeatureScoreRowFeature-level scored row for Parquet export
 COpenSwathFeatureScoreTableFeature-level Parquet export table with dynamically discovered FEATURE_MS1 / FEATURE_MS2 columns
 COpenSwathGeneInferenceOpenSwath gene-level context inference
 COpenSwathHelperA helper class that is used by several OpenSWATH tools
 COpenSwathMatrixExportConfigConfiguration for matrix exports
 COpenSwathMatrixExporterBuild and write OpenSWATH quantification matrices
 COpenSwathOSWParquetReaderReader for OpenSwath OSW Parquet output
 COpenSwathOSWParquetWriter
 COpenSwathOSWWriterClass to write out an OpenSwath OSW SQLite output (PyProphet input)
 COpenSwathParquetExportConfigConfiguration for scored feature Parquet exports
 COpenSwathParquetExporterWrite scored OpenSWATH feature and transition tables to Parquet
 COpenSwathPeptideInferenceOpenSwath peptide-level context inference
 COpenSwathPeptidoformInferenceOpenSwath inference of peptidoforms (IPF)
 COpenSwathProteinInferenceOpenSwath protein-level context inference
 COpenSwathQuantMatrixDense matrix representation used by matrix exports
 COpenSwathResultsExportConfigConfiguration for user-facing feature results exports
 COpenSwathResultsExporterWrite filtered OpenSWATH feature results to TSV or Parquet
 COpenSwathScoring
 COpenSwathTransitionScoreRowTransition-level scored row for optional Parquet export
 COpenSwathTransitionScoreTableTransition-level Parquet export table with dynamically discovered FEATURE_TRANSITION columns
 COpenSwathWorkflowSchedulerPlans memory-bounded OpenSwathWorkflow work waves and exposes a small concurrency-limiter pair
 CFileInfo::OptionsWhat to compute (mirrors the CLI flags; lets callers opt into expensive work)
 COpenSwathWorkflowScheduler::OptionsMemory and concurrency knobs used by wave planning and batch sizing
 COPXLDataStructsNamespace-style container holding the data types shared across the OpenPepXL cross-linking pipeline
 COPXLHelperFunctions needed by OpenPepXL to reduce duplicated code
 COPXLSpectrumProcessingAlgorithmsSpectrum preprocessing and theoretical-vs-experimental peak alignment helpers used by the OpenPepXL cross-link search engines
 COSBinaryDataArrayThe datastructures used by the OpenSwath interfaces
 COSChromatogramA single chromatogram
 COSChromatogramMetaIdentifying information for a chromatogram
 COSSpectrumThe structure that captures the generation of a peak list (including the underlying acquisitions)
 COSSpectrumMetaIdentifying information for a spectrum
 COpenSwathOSWWriter::OSWDataBuffered OSW table rows ready for insertion through prepared statements
 COSWDataHolds all or partial information from an OSW file
 COSWFeaturePrecursorSchemaSchema for OpenSWATH feature-level precursor intensity table
 COSWFeatureSchemaSchema for OpenSWATH feature scoring results table
 COSWFeatureTransitionSchemaSchema for OpenSWATH per-transition feature scoring results table
 COSWFileThis class serves for reading in and writing OpenSWATH OSW files
 COSWHierarchyHierarchy levels of the OSWData tree
 COSWIndexTraceIndex path into the OSWData tree from the root down to a specific node
 COSWPeakGroupA peak group (also called feature) is defined on a small RT range (leftWidth to rightWidth) in a group of extracted transitions (chromatograms)
 COSWPeptidePrecursorA peptide with a charge state
 COSWPrecursorSchemaSchema for OpenSWATH precursor (peptide query) table
 COSWProteinA Protein is the highest entity and contains one or more peptides which were found/traced
 COSWRunSchemaSchema for OpenSWATH run metadata table
 COSWTransitionHigh-level meta-data of one fragment-ion transition referenced by an OSWPeakGroup
 COSWTransitionSchemaSchema for OpenSWATH transition (fragment ion) table
 COpenSwathOSWWriter::OSWValueTyped OSW cell value used for direct SQLite binding
 COverlapDetectorA heuristic: Given a set of levels (rows), try to add items at to topmost row which does not overlap an already placed item in this row (according to its x-coordinate)
 ►CPainterBaseAn empty base class with some static convenience functions
 Cpair_hashSimple hash function for Scoring::pos2D
 CAnnotatedMSRun::PairIterator< T1, T2 >Iterator for pairs of spectra and peptide identifications
 CAreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::Param
 CParamManagement and storage of parameters / INI files
 CParamCTDFileSerializes a Param class in paramCTD file format. Note: only storing is currently possible
 CParamCWLFileExports .cwl files
 CParam::ParamEntryParameter entry used to store the actual information inside of a Param entry
 CParameterInformationStruct that captures all information of a command line parameter
 CParam::ParamIteratorForward const iterator for the Param class
 CParamJSONFileLoad from JSON (in a Common Workflow Language (CWL) compatible way) into the Param class
 CParam::ParamNodeNode inside a Param object which is used to build the internal tree
 CParams
 CParamValueClass to hold strings, numeric values, vectors of strings and vectors of numeric values using the stl types
 CParentGroup: Group of ambiguously identified parent sequences (e.g. protein group)
 CParquetFileShared utilities for reading, writing, and packaging Parquet-based file formats
 CParquetFilterTyped filter builder for parquet-backed datasets
 CParquetFilterBuilderFluent builder for ParquetFilter objects
 CParquetWriteConfigConfiguration for Parquet file writing
 CParseErrorThrows filename and message if test is false
 CBiosaur2Algorithm::PatternCandidateInternal representation of a candidate isotope pattern
 CIMSIsotopeDistribution::PeakStructure that represents an isotope peak - pair of mass and abundance
 ►CPeak1DA 1-dimensional raw data point or peak
 ►CPeak2DA 2-dimensional raw data point or peak
 CPeptideHit::PeakAnnotationContains annotations of a peak
 CPeakIntegrator::PeakArea
 CPeakIntegrator::PeakBackground
 CPeakPickerHiRes::PeakBoundaryStructure for peak boundaries
 CMassTraceDetection::PeakCandidateEncapsulates peak finding logic for both up and down directions
 CPeakCandidateA small structure to hold peak candidates
 CPeakFileOptionsOptions for loading files containing peak data
 CPeakGroupClass describing a deconvolved mass. A mass contains multiple (LogMz) peaks of different charges and isotope indices. PeakGroup is the set of such peaks representing a single monoisotopic mass. PeakGroup also contains features that define the quality of it. It is used for PeakGroupScoring calculation. DeconvolvedSpectrum consists of PeakGroups
 COpenSwathOSWParquetReader::PeakGroupFeatureScoresResult
 CPeakGroupScoringScoring functions for PeakGroup. For now, only Qscore has been implemented. For Qscore, the weight vector has been determined by logistic regression. In the future, other technique such as deep learning would be used
 CPeakIndexIndex of a peak or feature
 CFileInfo::PeakInfoPeak-file (MSExperiment) specifics
 CPeakPickerMobilogram::PeakPositionsStruct to hold peak positions
 CPeakIntegrator::PeakShapeMetrics
 CPeakTypeEstimatorEstimates if the data of a spectrum is raw data or peak data
 CPeakWidthEstimatorRough estimation of the peak width at m/z
 CPEFFCustomKeyDefRepresents a custom key definition from the PEFF header
 CPEFFDatabaseMetadataMetadata from a PEFF database header section
 CPEFFDisulfideBondRepresents a disulfide bond annotation in PEFF
 CPEFFEntryRepresents a single entry in a PEFF file with all annotations
 CPEFFModificationRepresents a PEFF modification annotation
 CPEFFProcessedRegionRepresents a PEFF processed region (signal peptide, transit peptide, etc.)
 CPEFFVariantComplexRepresents a complex PEFF variant (insertion, deletion, or substitution of multiple amino acids)
 CPEFFVariantSimpleRepresents a simple PEFF variant (single amino acid substitution)
 CIdentificationDataConverter::PepIDCompareFunctor for ordering peptide IDs by RT and m/z (if available)
 CPepNovoInfile
 CPepNovoOutfileRepresentation of a PepNovo output file
 CFragmentIndex::PeptideCompact descriptor of a peptide instance held by the FragmentIndex
 CPeptide
 CFeatureFinderIdentificationAlgorithm::PeptideCompareComparison functor for (unassigned) peptide IDs
 CPeptideAndProteinQuant::PeptideDataQuantitative and associated data for a peptide
 CIDFilter::PeptideDigestionFilterFilter Peptide Hit by its digestion product
 CMzIdentMLDOMHandler::PeptideEvidenceStruct to hold the PeptideEvidence information
 CPeptideEvidenceRepresentation of a peptide evidence
 CBiosaur2Algorithm::PeptideFeatureAggregated properties of a detected peptide feature
 CIDMapper::PeptideIdentificationListStateResult of a partitioning by identification state with mapPrecursorsToIdentifications()
 COPXLHelper::PeptideIDScoreComparatorA comparator for PeptideIdentifications that compares the scores in the first PeptideHit
 CPeptideProteinResolutionResolves shared peptides based on protein scores
 CProForma::PeptidoformA single peptidoform (one peptide chain)
 CPeptidoformInferenceConfigConfiguration for peptidoform inference
 CProForma::PeptidoformIonA peptidoform ion (one or more chains with optional charge)
 CPeptideHit::PepXMLAnalysisResultAnalysis Result (containing search engine / prophet results)
 COSWFile::PercolatorFeature
 CPercolatorFeatureSetHelperPercolator feature set and integration helper
 CPercolatorInfileClass for storing Percolator tab-delimited input files
 CPercolatorModelTrained Percolator model: averaged SVM weights in raw feature space
 CPercolatorOutfileClass for reading Percolator tab-delimited output files
 CPi0ResultResult of pi0 estimation for multiple testing correction
 CPickerPoolShared
 CMSImagingGeometry::PixelA pixel in the imaging grid, linked to one spectrum in the experiment
 CIsoelectricPoint::PkaValuesInternal struct holding pKa values for a given scale
 CProForma::PositionConstraintPosition constraint specifying allowed residues for a modification
 CChromatogramPeak::PositionLessComparator by position. As this class has dimension 1, this is basically an alias for RTLess
 CMobilityPeak1D::PositionLessComparator by position. As this class has dimension 1, this is basically an alias for MobilityLess
 CMobilityPeak2D::PositionLessComparator by position. Lexicographical comparison (first IM then m/z) is done
 CPeak1D::PositionLessComparator by position. As this class has dimension 1, this is basically an alias for MZLess
 CPeak2D::PositionLessComparator by position. Lexicographical comparison (first RT then m/z) is done
 COpenSwathPeptidoformInference::PosteriorRowPosterior probability row returned by applyBM
 CPpmTrait
 CTransitionPQPFile::PQPSqlQueryInfoHolds information about a PQP SQL query and optional column availability
 CFLASHHelperClasses::PrecalculatedAveraginePre-binned averagine isotope-distribution cache used by FLASHDeconv for fast cosine-similarity scoring
 CPrecisionWrapper< FloatingPointType >Wrapper class to implement output with appropriate precision. See precisionWrapper()
 CPrecursorCorrectionThis class provides methods for precursor correction
 CNucleicAcidSearchEngine::PrecursorInfo
 CPrecursorMassComparatorStrict-weak ordering on MSSpectrum by the first precursor's m/z (ascending). Convenient as a sort predicate when building a precursor-m/z-indexed spectral library
 CPrecursorPurityPrecursor purity or noise estimation
 CSimpleSVM::PredictionSVM/SVR prediction result
 CFuzzyStringComparator::PrefixInfo_Wrapper for the prefix information computed for the failure report
 COPXLDataStructs::PreprocessedPairSpectraThe PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spectra to each other
 CProbablePhosphoSites
 CFileInfo::ProcessingStepOne data-processing step (the -p block)
 CReactionMonitoringTransition::ProductMZLessComparator by Product ion MZ
 CProFormaProForma v2 peptidoform notation parser and data structures
 ►CProgressLoggerBase class for all classes that want to report their progress
 ►CProgressLogger::ProgressLoggerImplThis class represents an actual implementation of a logger
 CLayerDataDefs::ProjectionDataResult of computing a projection on X and Y axis in a 2D Canvas; see LayerDataBase::getProjection()
 CProtein
 CPeptideAndProteinQuant::ProteinDataQuantitative and associated data for a protein
 CIDBoostGraph::ProteinGroupIndistinguishable protein groups (size, nr targets, score)
 CProteinIdentification::ProteinGroupBundles multiple (e.g. indistinguishable) proteins in a group
 CProteinGroupArrowExportExport protein group data to Apache Arrow format following QPX pg schema
 CProteinGroupSchemaSchema for protein group (indistinguishable group) results table
 CProteinHit::ProteinHitAccessionHashHash of a ProteinHit based on its accession only!
 CProteinHit::ProteinHitPtrAccessionHash
 CProteinIdentificationArrowIOImport and export ProteinIdentification data to/from Apache Arrow format
 CProteinModificationSummaryMap a protein position to all observed modifications and associated statistics
 COPXLDataStructs::ProteinProteinCrossLinkThe ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL
 CProteinSchemaSchema for protein identification results table
 CPScoreImplementation of the PScore PSM scoring algorithm
 CPSMArrowIORead and write OpenMS identification data as a parquet bundle (.idparquet)
 CHyperScore::PSMDetailCompute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match
 CPSMSchemaSchema for peptide-spectrum match (PSM) results table
 COpenSearchModificationAnalysis::PTMEntryStatistics for a mapped PTM
 COpenSearchModificationAnalysis::PTMStatisticsContainer for PTM statistics table
 CPrecursorPurity::PurityScores
 CIsobaricChannelExtractor::PurityState_Small struct to capture the current state of the purity computation
 CPythonInfoDetect Python and retrieve information
 ►CQApplication
 ►CQCBaseThis class serves as an abstract base class for all QC classes
 ►CQDialog
 ►CQFileSystemWatcher
 ►CQGraphicsItem
 ►CQGraphicsScene
 ►CQGraphicsView
 ►CQItemDelegate
 ►CQLineEdit
 ►CQListWidget
 ►CQMainWindow
 ►CQMdiArea
 ►CQObject
 ►CQOpenGLFunctions_2_0
 ►CQOpenGLWidget
 ►CQProcess
 CQPXFeatureSchemaSchema for QPX feature view (quantms Parquet eXchange format)
 CQPXFileExport PSM (Peptide Spectrum Match) data to Apache Arrow format following QPX PSM schema
 CQPXPgSchemaSchema for QPX protein group export (quantms Parquet eXchange format, pg table)
 CQPXPSMSchemaSchema for QPX PSM export (quantms Parquet eXchange format, PSM table)
 ►CQTabBar
 ►CQTableWidget
 ►CQTabWidget
 CQTClusterA representation of a QT cluster used for feature grouping
 ►CQTextEdit
 ►CQTreeWidget
 CQuadraticRegressionEstimates model parameters for a quadratic equation
 CBaseFeature::QualityLessCompare by quality
 CQcMLFile::QualityParameterRepresentation of a quality parameter
 CQvalueQvalue : contains functions to calculate Qvalues from deconvolution quality score (Qscore) defined in PeakGroupScoring
 ►CQWidget
 CRAIICleanupException-safe way of executing arbitrary code at the end of a scope
 CRandomShuffler
 CFileInfo::RangeOne [min,max] interval for a single dimension; present==false => "<none>"
 CRangeInternal structure to store a lower and upper bound of an m/z range
 ►CRangeBaseBase class for a simple range with minimum and maximum
 ►CRangeBases
 CFileInfo::RangesMSExperiment carries four range categories; non-MSExperiment maps fill only combined
 CFileInfo::RangeSetFour range dimensions FileInfo reports for a map / spectrum group
 CRangeStats< VALUE_TYPE >Struct representing the statistics about a set of values
 CRangeStatsTypeOrigin and name of a statistic
 CRankDataRank items (1-based) with SciPy-like tie handling
 CPeptideHit::RankLessLesser predicate for scores of hits
 CRANSAC< TModelType >This class provides a generic implementation of the RANSAC outlier detection algorithm. Is implemented and tested after the SciPy reference: http://wiki.scipy.org/Cookbook/RANSAC
 CRansacModel< ModelT >Generic plug-in template base class using 'Curiously recurring template pattern' (CRTP) to allow for arbitrary RANSAC models (e.g. linear or quadratic fits)
 ►CRansacModel< RansacModelLinear >
 ►CRansacModel< RansacModelQuadratic >
 CRANSACParamA simple struct to carry all the parameters required for a RANSAC run
 CConsensusFeature::RatioSlim struct to feed the need for systematically storing of ratios
 ►Creal_policies
 ►Creal_policies
 CRealMassDecomposerDecomposes a real-valued mass over a real-valued alphabet of Weights, within a configurable absolute mass error
 CIdentificationData::RefTranslatorStructure that maps references of corresponding objects after copying
 ►CRefVariant
 CBase64::Reinterpreter32_Internal class needed for type-punning
 CBase64::Reinterpreter64_Internal class needed for type-punning
 CRescoreInputInput to domain-agnostic Percolator::rescore
 CRescoreOutputOutput from Percolator::rescore. Aligned 1:1 with RescoreInput::features
 CResidueRepresentation of an amino acid residue
 CResidueDBOpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called
 CResidueModificationRepresentation of a modification on an amino acid residue
 CDecoyHelper::Result
 CFalseDiscoveryRate::DecoyStringHelper::ResultFinds the most common decoy string in the accessions of proteins. Checks for suffix and prefix and some common decoy strings. Only successful if more than 30% had a common string
 CFeatureSummary::Result
 CFileInfo::ResultMaster result aggregate
 CIdentificationSummary::Result
 CMorpheusScore::ResultScore and subscores
 CTIC::ResultComputed Total Ion Current trace plus stability counters
 CRibonucleotideRepresentation of a ribonucleotide (modified or unmodified)
 ►CRibonucleotideDataProviderInterface for providing Ribonucleotide data to RibonucleotideDB
 CRibonucleotideDBDatabase of ribonucleotides (modified and unmodified)
 CRibonucleotideEntryHolds a Ribonucleotide together with optional ambiguity codes
 CIDRipper::RipFileContentRepresents the content of an IDRipper output file
 CIDRipper::RipFileIdentifierIdentifies an IDRipper output file
 CIDRipper::RipFileIdentifierIdxComparatorProvides a 'less' operation for RipFileIdentifiers that ignores the out_basename and origin_fullname members
 CROCCurveROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cutoff values
 COpenSwathOSWParquetReader::RowSingle extracted row combining feature + precursor + run metadata
 CMzTabNucleicAcidSectionRow::RowCompareComparison operator for sorting rows
 CMzTabOligonucleotideSectionRow::RowCompareComparison operator for sorting rows
 CMzTabOSMSectionRow::RowCompareComparison operator for sorting rows
 CMzTabPeptideSectionRow::RowCompareComparison operator for sorting rows
 CMzTabProteinSectionRow::RowCompareComparison operator for sorting rows
 CMzTabPSMSectionRow::RowCompareComparison operator for sorting rows
 CChromatogramPeak::RTLessComparator by RT position
 CMobilogram::RTLessComparator for the RT of the mobilogram
 CMSSpectrum::RTLessComparator for the retention time
 CMZTrafoModel::RTLessComparator by position. As this class has dimension 1, this is basically an alias for MZLess
 CPeak2D::RTLessComparator by RT position
 COSSpectrumMeta::RTLessComparator for the retention time
 CConfidenceScoring::RTNorm_Map RT values into the [0, 100] interval using min/max RT of the assay library
 CFeatureFinderIdentificationAlgorithm::RTRegionRegion in RT in which a peptide elutes:
 CAbsoluteQuantitationStandards::runConcentrationOne (sample, target, internal-standard, concentration) entry as provided by the user
 CProSEAlgorithm::RunStatisticsPer-run identification statistics for the end-of-search report
 CRWrapperR-Wrapper Class
 CExperimentalDesign::SampleSection
 CMs2SpectrumStats::ScanEvent
 CScopedResamplingWarningSuppressionInternal RAII guard for temporary resampling warning suppression
 COpenSwathWorkflowScheduler::ScopedSlotRAII slot guard for ConcurrencyLimiter — acquires on construction, releases on destruction
 CPeptideHit::ScoreLessLesser predicate for scores of hits
 CProteinHit::ScoreLessLesser predicate for scores of hits
 CPeptideHit::ScoreMoreGreater predicate for scores of hits
 CProteinHit::ScoreMoreGreater predicate for scores of hits
 CScoresUtility class for score type handling in identification and quantification workflows
 CIDScoreSwitcherAlgorithm::ScoreSearchResultStructure to hold score detection results for any ScoreType.
 CProSEAlgorithm::SearchContextPrepared per-database state shared across multiple spectrum files
 CSearchParamsSchemaSchema for search engine parameters and settings table
 CProSEAlgorithm::SearchResultComprehensive search result including modification analysis
 CFeatureFinderAlgorithmPickedHelperStructs::SeedHelper structure for seeds used in FeatureFinderAlgorithmPicked
 CSeedListGeneratorGenerate seed lists for feature detection
 CMRMFeatureSelector::SelectorParameters
 CPeptideHit::SequenceChargeEqualEquality functor for PeptideHit based on sequence and charge
 CPeptideHit::SequenceChargeHashHash functor for PeptideHit based on sequence and charge
 CSequenceCoverageCompute sequence coverage of a protein by peptide sequences
 CProForma::SequenceElementA single amino acid with its modifications
 CPeptideHit::SequenceLessComparatorLesser predicate for (modified) sequence of hits
 CSequestInfile
 CSequestOutfileRepresentation of a Sequest output file
 ►Cset< K >STL class
 Cshared_xerces_ptr< T >
 CProSEAlgorithm::SharedSearchStatsConfiguration, database and fragment-index facts shared across all input files of one ProSE invocation
 CSignalToNoiseEstimatorMedianRapidEstimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based)
 CSimpleOpenMSSpectraFactoryA factory method that returns two ISpectrumAccess implementations
 CSimpleTSGXLMS::SimplePeakA simple struct to represent peaks with mz and charge and sort them easily
 CSimpleTSGXLMS::SimplePeakComparatorComparator to sort SimplePeaks by mz
 CROCCurve::simsortdecPredicate for sort()
 CSiriusFragmentAnnotation
 CSiriusMSFileWrites a SIRIUS .ms file from an MSExperiment, optionally enriched with feature/adduct/formula annotations
 CSiriusFragmentAnnotation::SiriusTargetDecoySpectraSiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from SIRIUS)
 CConsensusFeature::SizeLessCompare by size(), the number of consensus elements
 CLPWrapper::SolverParamStruct that holds the parameters of the LP solver
 CSparseVector< _Scalar, _Flags, _StorageIndex >
 CSpecArrayFileFile adapter for SpecArray (.pepList) files
 CImzMLHandler::SpecIMS
 CMzMLFile::SpecInfo
 CSpectralMatchOne library-search match record: the observed spectrum, the matching DB spectrum, the score, and the metabolite metadata copied from the hit
 CSpectralMatchScoreComparatorStrict-weak ordering on SpectralMatch by hyperscore (descending — top-scoring match comes first when sorted)
 CSpectraLongSchemaSchema for spectra in long (one row per peak) format
 CQCBase::SpectraMapMap to find a spectrum via its NativeID
 CSpectraSemiWideSchemaSchema for spectra in semi-wide (one row per spectrum, list columns for peaks) format
 CSpectrumThe structure that captures the generation of a peak list (including the underlying acquisitions)
 CSpectrumAdditionThe SpectrumAddition is used to add up individual spectra
 CMzMLHandler::SpectrumDataData necessary to generate a single spectrum
 CMzXMLHandler::SpectrumDataData necessary to generate a single spectrum
 CMzIdentMLDOMHandler::SpectrumIdentificationStruct to hold the information from the SpectrumIdentification xml tag
 CMzIdentMLDOMHandler::SpectrumIdentificationProtocolStruct to hold the information from the SpectrumIdentificationProtocol xml tag
 ►CSpectrumLookupHelper class for looking up spectra based on different attributes
 CFragmentIndex::SpectrumMatchMatch between a query peak and an entry in the DB
 CFragmentIndex::SpectrumMatchesTopNContainer for SpectrumMatch. Also keeps count of total number of candidates and total number of matches
 CSpectrumMetaIdentifying information for a spectrum
 CSpectrumMetaDataLookup::SpectrumMetaDataMeta data of a spectrum
 CSpectrumNativeIDParserParser for extracting scan numbers from spectrum native IDs
 CSplineInterpolatedPeaksData structure for spline interpolation of MS1 spectra and chromatograms
 CSplinePackageFundamental data structure for SplineInterpolatedPeaks
 CSqliteConnectorFile adapter for Sqlite files
 CSqMassFile::SqMassConfigCompression / metadata options used when reading or writing an sqMass file
 CSqMassFileRead and write mass-spectrometry data in the on-disk sqMass (SQLite) format
 Csquared_difference< _Tp, _Dist >
 Csquared_difference< typename _Acc::result_type, typename _Acc::result_type >
 Csquared_difference_counted< _Tp, _Dist >
 ►Cstatic_visitor
 CFragmentMassError::StatisticsStructure for storing results: average and variance of all FragmentMassErrors in ppm
 CPeptideAndProteinQuant::StatisticsStatistics for processing summary
 CProteinModificationSummary::StatisticsBasic modification statistic
 CPSMExplainedIonCurrent::StatisticsStructure for storing results: average and variance over all PSMs
 CStatsCounterSimple counting struct, for non-numerical occurrences of meta-values
 CIdentificationDataConverter::StepOptCompareFunctor for ordering StepOpt (by date of the steps, if available):
 CStopWatchThis class is used to determine the current process' CPU (user and/or kernel) and wall time
 COpenSwathOSWWriter::OSWValue::Storage
 ►Cstreambuf
 CFuzzyStringComparator::StreamElement_Stores information about characters, numbers, and white spaces loaded from the InputStream
 CStreamHandlerProvides a central class to register globally used output streams. Currently supported streams are
 CLogStreamBuf::StreamStructHolds a stream that is connected to the LogStream. It also includes the minimum and maximum level at which the LogStream redirects messages to this stream
 CStringListUtilsUtilities operating on lists of Strings
 CStringManager
 CStringUtilsHelper
 CDBSuitability::SuitabilityDataStruct to store results
 CMSExperiment::SumIntensityReductionCalculates the sum of intensities for a range of elements
 CLayerDataDefs::ProjectionData::Summary
 CSummarySummary of fitting results
 CSummaryStatistics< T >Helper class to gather (and dump) some statistics from a e.g. vector<double>
 CTargetedExperiment::SummaryStatistics
 CSummaryStatistics< std::vector< double > >
 CSwathMapData structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2
 CSwathQCQuality Control function for OpenSwath
 CSwathWindowLoader
 CSysInfoSome functions to get system information
 CTaggerCalculate sequence tags from m/z values
 CMetaboTargetedAssay::TargetDecoyGroupTargetDecoyGroup stores the mz, rt and file number in correspondence to the index of a MetaboTargetedAssay vector
 CTargetedDataFileLoader
 CTargetedExperimentA description of a targeted experiment containing precursor and production ions
 CTargetedExperiment
 CFile::TempDirClass representing a temporary directory
 CFile::TemporaryFiles_Internal helper class, which holds temporary filenames and deletes these files at program exit
 ►CTextFile
 CFeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePatternHelper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked
 CStopWatch::TimeDiff_
 ►CToolDescriptionInternalToolDescription Class
 CToolExternalDetails
 CToolHandler
 CToolInfoA struct to pass information about the tool as one parameter
 CTOPPASVertex::TOPPASFilenames
 ►CTOPPBaseBase class for TOPP applications
 CTOPPASScene::TOPPProcessStores the information for a TOPP process
 CMassTraceDetection::TraceExtensionStateEncapsulates trace extension state
 CParam::ParamIterator::TraceInfoStruct that captures information on entered / left nodes for ParamIterator
 CIDDecoyProbability::Transformation_Struct to be used to store a transformation (used for fitting)
 CTransformationDescriptionGeneric description of a coordinate transformation
 ►CTransformationModelBase class for transformation models
 CTransformationDescription::TransformationStatisticsSummary statistics before/after applying the transformation. For deviations before/after transformation, the percentiles 100, 99, 95, 90, 75, 50, 25 are returned
 COpenSwathOSWParquetReader::TransitionFeaturesResultResult container for transition-level features
 CTransitionFlagsPacked boolean flags for transitions Reduces memory from 4 bytes (4 separate bools) to 1 byte
 CMRMFeatureFinderScoring::TransitionGroupCacheCache of transition-group invariant data to avoid per-feature recomputation
 CDiaPrescore::TransitionGroupTheoreticalSpectrumCacheCached transition-group-specific theoretical spectrum used by the DIA prescore
 CTransitionHelper
 CTransitionParquetFileRead OpenSwath Parquet library input (.oswpq) into LightTargetedExperiment
 CTriqlerFileFile adapter for Triqler files
 CTriqlerFile::TriqlerLine_
 CTransitionTSVFile::TSVTransitionInternal structure to represent a transition
 CTVToolDiscoveryScans for tools and generates a param for each asynchronously
 Cunique_xerces_ptr< T >
 CIdentificationSummary::UniqueID
 CUniqueIdGeneratorA generator for unique ids
 CUniqueIdIndexer< T >A base class for containers with elements derived from UniqueIdInterface. This adds functionality to convert a unique id into an index into the container
 ►CUniqueIdIndexer< ConsensusMap >
 ►CUniqueIdIndexer< FeatureMap >
 ►CUniqueIdInterfaceA base class defining a common interface for all classes having a unique id
 CCVTerm::Unit
 CProForma::UnlocalisedModUnlocalised modification with optional occurrence count
 COpenSwathOSWParquetReader::UnscoredResultResult container for an unscored table
 CUpdateCheckHelper Functions to perform an update query to the OpenMS REST server
 CUSIUtility class for handling Universal Spectrum Identifiers (USI)
 CFileInfo::ValidationInfo-v (schema/semantic validation) and -i (indexed mzML) blocks
 CValidationResultResult of schema validation containing validity flag and error messages
 CValueTraitTrait for MatchedIterator to find pairs with a certain distance, which is computed directly on the value_type of the container
 CFragmentIndex::VarModEntryEntry in the per-AA variable modification lookup table
 CVecLowPrecision< T >
 ►Cvector< T >STL class
 CVersionInfo::VersionDetailsParsed semver-style version: major.minor.patch with an optional pre-release identifier
 CVersionInfoVersion information class
 CTOPPASVertex::VertexRoundPackageInfo for one edge and round, to be passed to next node
 COpenSwathWorkflowScheduler::WaveA wave: a group of SWATH indices (into the original swath_maps vector) that may be resident at the same time. Populated by planWaves
 CWeightsPairs an alphabet of double-valued masses with the scaled integer weights derived from them
 CWNetMatcherPairwise point-set matching using Wasserstein optimal transport
 CXCorrArrayType
 CXICParquetFile::XICAnalyteAnalyte metadata container
 CXICParquetFile::XICChromatogramLightweight chromatogram container for XIC parquet rows
 CXICParquetFileReader for OpenSWATH chromatogram Parquet files (.xic)
 CXICParquetFile::XICRunInfoUnique run information (run_id, source_file)
 CXICSchemaSchema for extracted ion chromatogram (XIC) data table
 CXIMParquetFile::XIMAnalyteAnalyte metadata container
 CXIMParquetFile::XIMMobilogramLightweight mobilogram container for XIM parquet rows
 CXIMParquetFileReader for OpenSWATH mobilogram Parquet files (.xim)
 CXIMParquetFile::XIMRunInfoUnique run information (run_id, source_file)
 CXIMSchemaSchema for extracted ion mobilogram (XIM) data table
 COPXLDataStructs::XLPrecursorThe XLPrecursor struct represents a cross-link candidate in the process of filtering candidates by precursor masses in OpenPepXL
 COPXLDataStructs::XLPrecursorComparatorThe XLPrecursorComparator is a comparator for XLPrecursors, that allows direct comparison of the XLPrecursor precursor mass with double numbers
 ►CXMLFileBase class for loading and storing XML files via Xerces, with optional schema validation and transparent gzip / bzip2 / zip decompression on load
 CXQuestScoresAn implementation of the scores for cross-link identification from the xQuest algorithm (O. Rinner et al., 2008, "Identification of cross-linked peptides from large sequence databases")
 CZipArchiveFileSmall libzip-based helpers for working with ZIP archives
 CZipIfstreamStreaming reader for the single non-directory entry of a ZIP archive
 CZipRandomAccessFileFactory to obtain an Arrow RandomAccessFile for a named entry inside a zip archive (or a direct file when the archive path is a directory)
 CZlibCompressionCompresses and uncompresses arbitrary byte buffers using zlib