Namespace List

Here is a list of all namespaces with brief descriptions:

[detail level 1234]

Narrow
►NEigen
CSparseVector
►Neol_bspline
CBSpline
NH5
NIsoSpec
►NKDTree
►C_Alloc_base
CNoLeakAlloc
C_Base_iterator
C_Bracket_accessor
C_Iterator
C_Node
C_Node_base
C_Node_compare
C_Region
Calways_true
CKDTree
Csquared_difference
Csquared_difference_counted
►Nms
►Nnumpress
NMSNumpress
►NOpenMS	Main OpenMS namespace
NArrowIOHelpers	Public helpers for writing and concatenating Arrow tables to Parquet files
►NArrowSchemaValidation	Utilities for validating Arrow table schemas against expected definitions
CValidationResult	Result of schema validation containing validity flag and error messages
NCometNativeIDRemapper	Rewrite spectrum native IDs to a monotonic "index=N" form and translate PSM references back
►NConstants	Mathematical and physical constants namespace
NUserParam
►NDataArrays
CFloatDataArray	Float data array class
CIntegerDataArray	Integer data array class
CStringDataArray	Std::string data array class
Ndetail
►NDetail
CMetaKeyGetter
NDIAHelpers
►NException	Exception namespace
CBaseException	Exception base class
CBufferOverflow	Buffer overflow exception
CConversionError	Invalid conversion exception
CDepletedIDPool	Exception used if no more unique document ID's can be drawn from ID pool
CDivisionByZero	Division by zero error exception
CElementNotFound	Element could not be found exception
CExternalExecutableNotFound	External executable (e.g. comet.exe) not found exception
CFailedAPICall	A call to an external library (other than OpenMS) went wrong
CFileEmpty	File is empty
CFileNameTooLong	Filename is too long to be writable/readable by the filesystem
CFileNotFound	File not found exception
CFileNotReadable	File not readable exception
CFileNotWritable	File not writable exception
CGlobalExceptionHandler	OpenMS global exception handler
CIllegalArgument	A method or algorithm argument contains illegal values
CIllegalPosition	Invalid 3-dimensional position exception
CIllegalSelfOperation	Illegal self operation exception
CIllegalTreeOperation	Illegal tree operation exception
CIncompatibleIterators	Incompatible iterator exception
CIndexOverflow	Int overflow exception
CIndexUnderflow	Int underflow exception
CInternalToolError	A tool or algorithm which was called internally raised an exception
CInvalidFileType	Invalid file type exception
CInvalidIterator	Invalid iterator exception
CInvalidParameter	Exception indicating that an invalid parameter was handed over to an algorithm
CInvalidRange	Invalid range exception
CInvalidSize	Invalid UInt exception
CInvalidValue	Invalid value exception
CIOException	General IOException
CMissingInformation	Not all required information provided
CNotImplemented	Not implemented exception
CNotSorted	Array not sorted exception
CNullPointer	Null pointer argument is invalid exception
COutOfGrid	Out of grid exception
COutOfMemory	Out of memory exception
COutOfRange	Out of range exception
CParseError	Parse Error exception
CPostcondition	Postcondition failed exception
CPrecondition	Precondition failed exception
CRequiredParameterNotGiven	A required parameter was not given
CSizeUnderflow	UInt underflow exception
CSqlOperationFailed	SqlOperation failed exception
CUnableToCalibrate	Exception used if an error occurred while calibrating a dataset
CUnableToCreateFile	Unable to create file exception
CUnableToFit	Exception used if an error occurred while fitting a model to a given dataset
CUnregisteredParameter	An unregistered parameter was accessed
CWrongParameterType	A parameter was accessed with the wrong type
NFastLowessSmoothing	LOWESS (locally weighted scatterplot smoothing)
►NGUIHelpers
►CColorBrewer
CDistinct
CGUILock	RAII class to disable the GUI and set a busy cursor and go back to the original state when this class is destroyed
COverlapDetector	A 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)
NHelpers
►NIdentificationDataInternal
CAdductCompare	Comparator for adducts
CAppliedProcessingStep
CDBSearchParam	Parameters specific to a database search step
CIdentifiedCompound
CIdentifiedMolecule	Variant type holding Peptide/Compound/Oligo references and convenience functions
CIdentifiedSequence	Representation of an identified sequence (peptide or oligonucleotide)
CInputFile	Information about input files that were processed
CIteratorWrapper	Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi_index_containers
CObservation	Representation of an observation, e.g. a spectrum or feature, in an input data file
CObservationMatch	Representation of a search hit (e.g. peptide-spectrum match)
CObservationMatchGroup	: Group of related (co-identified) input matches
CParentGroup	: Group of ambiguously identified parent sequences (e.g. protein group)
CParentGroupSet	Set of groups of ambiguously identified parent sequences (e.g. results of running a protein inference algorithm)
CParentMatch	Meta data for the association between an identified molecule (e.g. peptide) and a parent sequence (e.g. protein)
CParentSequence	Representation of a parent sequence that is identified only indirectly (e.g. a protein)
CProcessingSoftware	Information about software used for data processing
CProcessingStep	Data processing step that is applied to the data (e.g. database search, PEP calculation, filtering, ConsensusID)
CScoredProcessingResult	Base class for ID data with scores and processing steps (and meta info)
CScoreType	Information about a score type
►Nims
►CIMSAlphabet	Holds an indexed list of bio-chemical elements used by mass-decomposition algorithms
CMassSortingCriteria_	Private class-functor to sort out elements in mass ascending order
CIMSAlphabetParser	An abstract templatized parser to load the data that is used to initialize Alphabet objects
CIMSAlphabetTextParser	Implements abstract AlphabetParser to read data from the plain text format
CIMSElement	Represents a chemical atom with name and isotope distribution
►CIMSIsotopeDistribution	Represents a distribution of isotopes restricted to the first K elements
CPeak	Structure that represents an isotope peak - pair of mass and abundance
CIntegerMassDecomposer	Implements MassDecomposer interface using algorithm and data structures described in paper "Efficient Mass Decomposition" S. Böcker, Z. Lipták, ACM SAC-BIO, 2004 doi:10.1145/1066677.1066715
CMassDecomposer	An interface to handle decomposing of integer values/masses over a set of integer weights (alphabet)
CRealMassDecomposer	Decomposes a real-valued mass over a real-valued alphabet of Weights, within a configurable absolute mass error
CWeights	Pairs an alphabet of double-valued masses with the scaled integer weights derived from them
►NInterfaces
CBinaryDataArray	The datastructures used by the OpenSwath interfaces
CChromatogram	A single chromatogram
CChromatogramMeta	Identifying information for a chromatogram
CIChromatogramsReader	The interface of read-access to a list of chromatograms
CIChromatogramsWriter
CIMSDataConsumer	The interface of a consumer of spectra and chromatograms
CISpectraReader	The interface of read-access to a list of spectra
CISpectraWriter
CSpectrum	The structure that captures the generation of a peak list (including the underlying acquisitions)
CSpectrumMeta	Identifying information for a spectrum
►NInternal	Namespace used to hide implementation details from users
NClassTest	Namespace for class tests
►NPASEFHillCentroider
CCentroid	One centroided peak produced by hill detection
CParams
NSqliteHelper
CAcqusHandler	Read-only acqus File handler for XMass Analysis
►CAreaIterator	Forward iterator for an area of peaks in an experiment
CParam
CCachedMzMLHandler	An class that uses on-disk caching to read and write spectra and chromatograms
CConsensusXMLHandler	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation
CDIntervalBase	A base class for D-dimensional interval
CFeatureXMLHandler	This class provides Input/Output functionality for feature maps
CFFIDAlgoExternalIDHandler	Class for handling external peptide identifications in feature finding
CFidHandler	Read-only fid File handler for XMass Analysis
CFileMapping	Maps input/output files to filenames for the external program
CFilterableList	A widget which shows a list of text items, which can be filtered
CFilterList	A widget which shows a list of DataFilter items
►CIDBoostGraph	Creates and maintains a boost graph based on the OpenMS ID datastructures
Cdfs_ccsplit_visitor	A boost dfs visitor that copies connected components into a vector of graphs
CGetPosteriorVisitor	Visits nodes in the boost graph (either ptrs to an ID Object or some lightweight surrogates) and depending on their type gets the score (usually the posterior)
CGetScoreTgTVisitor	Visits nodes in the boost graph (either ptrs to an ID Object or some lightweight surrogates) and depending on their type gets the score (usually the posterior) plus if it is a decoy or a target
CLabelVisitor	Visits nodes in the boost graph (ptrs to an ID Object) and depending on their type creates a label e.g. for printing to dot format
CPrintAddressVisitor	Visits nodes in the boost graph (ptrs to an ID Object) and depending on their type prints the address. For debugging purposes only
CProteinGroup	Indistinguishable protein groups (size, nr targets, score)
CSetPosteriorVisitor	Visits nodes in the boost graph (either ptrs to an ID Object or some lightweight surrogates) and depending on their type sets the posterior Don't forget to set higherScoreBetter and score names in the parent ID objects
CIdentification
CIdentificationHit	Represents a object which can store the information of an analysisXML instance
►CImzMLHandler	SAX2 handler for imzML 1.1.0 files, extending OpenMS MzMLHandler
CArrayMeta
CSpecIMS
CImzMLWriter	Writer for imzML 1.1.0 files (.imzML + companion .ibd)
CIndexedMzMLHandler	A low-level class to read an indexedmzML file
CInputFileList	A widget shows a list of input files (i.e. existing files on a mounted drive), which allows adding/removing files and supports drag'n'drop from the window manager
CIntensityIteratorWrapper	An iterator wrapper to access peak intensities instead of the peak itself
CListEditorDelegate	Internal delegate class
CListTable
CLooper
CLooper< grid_size, grid_size, EvalResult, Tuple, TupleTypes... >
CLooper< param_index, grid_size, EvalResult, Tuple, FirstTupleType, TupleTypes... >
CMappingParam	Filename mappings for all input/output files
CMascotXMLHandler	Handler that is used for parsing MascotXML data
CMessagePasserFactory
CMzDataHandler
CMzDataValidator	Semantic validator for mzData files
►CMzIdentMLDOMHandler	XML DOM handler for MzIdentMLFile
CAnalysisSoftware	Struct to hold the used analysis software for that file
CDatabaseInput	Struct to hold the information from the DatabaseInput xml tag
CDBSequence	Struct to hold the information from the DBSequence xml tag
CModificationParam	Struct to hold the information from the ModificationParam xml tag
CPeptideEvidence	Struct to hold the PeptideEvidence information
CSpectrumIdentification	Struct to hold the information from the SpectrumIdentification xml tag
CSpectrumIdentificationProtocol	Struct to hold the information from the SpectrumIdentificationProtocol xml tag
CMzIdentMLHandler	XML STREAM handler for MzIdentMLFile
CMzIdentMLValidator	Semantic validator for mzIdentML files
►CMzMLHandler	Handler for mzML file format
CChromatogramData	Data necessary to generate a single chromatogram
CSpectrumData	Data necessary to generate a single spectrum
►CMzMLHandlerHelper	Helper for mzML file format
CBinaryData	Representation for binary data in mzML
CMzMLSqliteHandler	Sqlite handler for storing spectra and chromatograms in sqMass format
CMzMLSqliteSwathHandler	Read-only accessor for SWATH/DIA spectrum indices stored in an sqMass file
CMzMLValidator	Semantic validator for mzML files
►CMzXMLHandler
CSpectrumData	Data necessary to generate a single spectrum
COMSFileLoad	Helper class for loading .oms files (SQLite format)
COMSFileStore	Helper class for storing .oms files (SQLite format)
COpenMSBuildInfo	Build-configuration accessors: build type, OpenMP availability, and OpenMP thread count
COpenMSLineEdit	Custom QLineEdit which emits a signal when losing focus (such that we can commit its data)
COpenMSOSInfo	Snapshot of the runtime operating system: name, version, and pointer-width architecture
CParamEditorDelegate	Internal delegate class for QTreeWidget
CParamTree	QTreeWidget that emits a signal whenever a new row is selected
CParamXMLHandler	XML Handler for Param files
CPlot1DPrefDialog	Preferences dialog for Plot1DWidget
CPlot2DPrefDialog	Preferences dialog for Plot2DWidget
CPlot3DPrefDialog	Preferences dialog for Plot3DWidget
CPTMXMLHandler	Handler that is used for parsing PTMXML data
CSAX2HandlerAdapter	Adapts an OpenMS XMLHandler to the Xerces SAX2 DefaultHandler interface
CScopedResamplingWarningSuppression	Internal RAII guard for temporary resampling warning suppression
►CSemanticValidator	Semantically validates XML files using CVMappings and a ControlledVocabulary
CCVTerm	Representation of a parsed CV term
Cshared_xerces_ptr
CSpectrumIdentification
CSqliteConnectorFriend
CStringManager	Helper class for XML parsing that handles the conversions of Xerces strings
CToolDescription
CToolDescriptionHandler	XML handler for ToolDescriptionFile
CToolDescriptionInternal	ToolDescription Class
CToolExternalDetails
CTOPPViewPrefDialog	Preferences dialog for TOPPView
CTraMLHandler	XML handler for TraMLFile
CTraMLValidator	Semantically validates MzXML files
CUnimodXMLHandler	Handler that is used for parsing XTandemXML data
CUniProtXMLHandler	SAX handler for UniProtKB XML <entry> documents
Cunique_xerces_ptr
CXMLAttributes	Xerces-free, lightweight view over the attribute list of an XML element
CXMLFile	Base class for loading and storing XML files via Xerces, with optional schema validation and transparent gzip / bzip2 / zip decompression on load
►CXMLHandler	Base class for XML handlers
CEndParsingSoftly	Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file is needed)
CXQuestResultXMLHandler	XMLHandler for the result files of XQuest
REvaluator
►NLogger	Log streams
CLogSinkGuard	RAII guard that temporarily removes a stream from a LogStream and re-inserts it on scope exit
CLogStream	Log Stream Class
►CLogStreamBuf	Stream buffer used by LogStream
CLogCacheStruct	Holds a counter of occurrences and an index for the occurrence sequence of the corresponding log message
CStreamStruct	Holds a stream that is connected to the LogStream. It also includes the minimum and maximum level at which the LogStream redirects messages to this stream
CLogStreamNotifier	Sink-side hook that is notified whenever a LogStream flushes a complete message
►NMath	Math namespace
CAdaptiveQuantileResult	Result of adaptiveQuantile computation
CBasicStatistics	Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation
CBilinearInterpolation	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
CBSplineSmoothingSpline	Smoothing spline implementation using B-spline basis
►CGammaDistributionFitter	Implements a fitter for the Gamma distribution
CGammaDistributionFitResult	Struct to represent the parameters of a gamma distribution
►CGaussFitter	Implements a fitter for Gaussian functions
CGaussFitResult	Struct of parameters of a Gaussian distribution
►CGumbelDistributionFitter	Implements a fitter for the Gumbel distribution
CGumbelDistributionFitResult	Struct to represent the parameters of a gumbel distribution
►CGumbelMaxLikelihoodFitter	Implements a fitter for the Gumbel distribution
CGumbelDistributionFitResult	Struct to represent the parameters of a gumbel distribution
CHistogram	Representation of a histogram
CKernelDensityEstimation	Kernel Density Estimation utilities using FFT-based methods
CLinearInterpolation	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
CLinearRegression	This class offers functions to perform least-squares fits to a straight line model, \( Y(c,x) = c_0 + c_1 x \)
CLinearRegressionWithoutIntercept	This class offers functions to perform least-squares fits to a straight line model, \( Y(c,x) = c_0 + c_1 x \)
CMultipleTesting	Statistical functions for multiple testing correction
CPi0Result	Result of pi0 estimation for multiple testing correction
CPosteriorErrorProbabilityModel	Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture
CQuadraticRegression	Estimates model parameters for a quadratic equation
CRandomShuffler
CRankData	Rank items (1-based) with SciPy-like tie handling
CRANSAC	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	Generic plug-in template base class using 'Curiously recurring template pattern' (CRTP) to allow for arbitrary RANSAC models (e.g. linear or quadratic fits)
CRansacModelLinear	Implementation of a linear RANSAC model fit
CRansacModelQuadratic	Implementation of a quadratic RANSAC model fit
CRANSACParam	A simple struct to carry all the parameters required for a RANSAC run
►CROCCurve	ROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cutoff values
Csimsortdec	Predicate for sort()
CSummaryStatistics	Helper class to gather (and dump) some statistics from a e.g. vector<double>
►NML
CPeptDeepInputBatch	Flat tensor buffers and dimensions for a PeptDeep ONNX batch
CPeptDeepInputBuilder	Shared featurization for PeptDeep RT, CCS, and MS2 ONNX predictors
CPeptDeepInputConfig	Sequence-padding policy for PeptDeep ONNX inputs
NMRMTransitionGroupPickerMeta
NNNLS
NNuXLPresets
NStringConversions
NStringUtils
►NTargetedExperimentHelper	This class stores helper structures that are used in multiple classes of the TargetedExperiment (e.g. ReactionMonitoringTransition and IncludeExcludeTarget)
CCompound	Represents a compound (small molecule)
CConfiguration
CContact
CCV
CInstrument
CInterpretation	Product ion interpretation
►CPeptide	Represents a peptide (amino acid sequence)
CModification
CPeptideCompound	Base class to represent either a peptide or a compound
CPrediction
CProtein
CPublication
CRetentionTime	This class stores a retention time structure that is used in TargetedExperiment (representing a TraML file)
CTraMLProduct	Represents a product ion
NTest
CAA
CAAIndex	Representation of selected AAIndex properties
►CAASequence	Representation of a peptide/protein sequence
CConstIterator	ConstIterator for AASequence
CIterator	Iterator class for AASequence
CAbsoluteQuantitation	AbsoluteQuantitation is a class to support absolute or relative quantitation for targeted or untargeted quantitation workflows (e.g., Isotope Dilution Mass Spectrometry)
CAbsoluteQuantitationMethod	AbsoluteQuantitationMethod is a class to hold information about the quantitation method and for applying and/or generating the quantitation method
CAbsoluteQuantitationMethodFile	File adapter for AbsoluteQuantitationMethod files
►CAbsoluteQuantitationStandards	Bridges sample-level concentration tables with the FeatureMap output of a feature finder, for building calibration curves used in absolute quantitation
CfeatureConcentration	One target component matched to a feature in the corresponding FeatureMap, paired with its known concentration
CrunConcentration	One (sample, target, internal-standard, concentration) entry as provided by the user
CAbsoluteQuantitationStandardsFile	Load files containing runConcentration data
►CAccurateMassSearchEngine	An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB)
CCompareEntryAndMass_
CMappingEntry_
CAccurateMassSearchResult	One small-molecule hit produced by AccurateMassSearchEngine
►CACNode
CDepthHits	Internal struct to steal one bit from depth to use as hit indicator
CAcquisition	Information about one raw data spectrum that was combined with several other raw data spectra
CAcquisitionInfo	Description of the combination of raw data to a single spectrum
CAcquisitionInfoVisualizer	Class that displays all meta information for AcquisitionInfo objects
CAcquisitionVisualizer	Class that displays all meta information for Acquisition objects
CACScout	Spin-off search path through the trie, which can deal with ambiguous AAs and mismatches
CACTrie	An Aho Corasick trie (a set of nodes with suffix links mainly)
CACTrieState
CAdduct	One elementary adduct contribution to a feature's ionization state
CAdductInfo	Mass-arithmetic helper for ionizing adducts (e.g. [M+H]+, [2M-H]-, [M+2K-H]+)
►CAnnotatedMSRun	Class for storing MS run data with peptide and protein identifications
CPairIterator	Iterator for pairs of spectra and peptide identifications
CAnnotation1DCaret	An annotation item which paints a set of carets on the canvas
CAnnotation1DDistanceItem	An annotation item which represents a measured distance between two peaks
CAnnotation1DItem	An abstract class acting as an interface for the different 1D annotation items
CAnnotation1DPeakItem	A peak annotation item
CAnnotation1DTextItem	An annotation item which represents an arbitrary text on the canvas
CAnnotation1DVerticalLineItem	An annotation item which represents a vertical line (or more precisely a line along the gravity axis, i.e. it could also be horizontal) and text label on top
CAnnotations1DContainer	Container for annotations to content of Plot1DCanvas
CAnnotationStatistics
CArea
CArrowChromatogramExportConfig	Configuration for Arrow export of chromatogram data
CArrowSpectraExportConfig	Configuration for Arrow export of spectra data
CAScore	Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the most probable phosphorylation-site(s). For each phosphorylation site a probability score is calculated. The algorithm is implemented according to Beausoleil et al. (Nat. Biotechnol. 2006)
CAverageLinkage	AverageLinkage ClusterMethod
CAxisPainter	Draws a coordinate axis. It has only static methods, that's why the constructor is private
CAxisTickCalculator	Calculates ticks for a given value range
CAxisWidget	Widget that represents an axis of a graph
►CBase64	Class to encode and decode Base64
CReinterpreter32_	Internal class needed for type-punning
CReinterpreter64_	Internal class needed for type-punning
►CBaseFeature	A basic LC-MS feature
CQualityLess	Compare by quality
CBaseGroupFinder	The base class of all element group finding algorithms
CBaseModel	Abstract base class for 1-dimensional models
CBaseSuperimposer	The base class of all superimposer algorithms
CBaseVisualizer	A base class for all visualizer classes
CBaseVisualizerGUI	A base class for all visualizer classes
CBasicProteinInferenceAlgorithm	Simple protein inference by aggregation of per-peptide PSM scores
CBayesianProteinInferenceAlgorithm	Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental)
CBiGaussFitter1D	BiGaussian distribution fitter (1-dim.) approximated using linear interpolation
CBiGaussModel
CBinaryTreeNode	Elements of a binary tree used to represent a hierarchical clustering process
CBinnedSharedPeakCount	Compare functor scoring the shared peaks for similarity measurement
CBinnedSpectralContrastAngle	Compare functor scoring the spectral contrast angle for similarity measurement
CBinnedSpectrum	This is a binned representation of a PeakSpectrum
CBinnedSpectrumCompareFunctor	Base class for compare functors of BinnedSpectra
CBinnedSumAgreeingIntensities	Sum of agreeing intensities for similarity measurement
►CBiosaur2Algorithm	Implementation of the Biosaur2 feature detection workflow for LC-MS1 data
CFastHillEntry	Lightweight index entry for fast m/z-based hill lookup
CHill	Representation of a single hill (continuous m/z trace across adjacent scans)
CIsotopeCandidate	Candidate isotope peak that can be associated with a monoisotopic hill
CPatternCandidate	Internal representation of a candidate isotope pattern
CPeptideFeature	Aggregated properties of a detected peptide feature
CBitset	Custom bitset which uses a 32-bit integer to store bits (instead of 8 bytes for std::bitset<32> on Clang/GCC)
CBSpline2d	B spline interpolation
CBuiltInProteaseDataProvider	Data provider for built-in protease definitions
CBzip2Ifstream	Streaming decompressor for bzip2 (.bz2) files
CBzip2InputStream	Implements the BinInputStream class of the xerces-c library in order to read bzip2 compressed XML files
CCachedmzML	Random-access reader/writer for the OpenMS on-disk cache format
CCachedSwathFileConsumer	On-disk cached implementation of FullSwathFileConsumer
CCalibrationData	A helper class, holding all calibration points
►CCalibrationWorkflow	Orchestrates calibration workflows for OpenSWATH analysis
CCalibrationResult	Results from calibration workflow
CIrtExperiments	Prepared iRT experiments ready for calibration
CCentroidTolerances	Structure to hold centroid-based overlap tolerances
CChannelQC	Small quality control class, holding temporary data for reporting
CChargePair	Representation of a (putative) link between two Features, which stem from the same compound but have different charge (including different adduct ions (H+, Na+, ..)
CChromatogramExtractor	The ChromatogramExtractor extracts chromatograms (intensity vs retention time) from mass spectrometry data
►CChromatogramExtractorAlgorithm	The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data
CExtractionCoordinates
►CChromatogramPeak	A 1-dimensional raw data point or peak for chromatograms
CIntensityLess	Comparator by intensity
CPositionLess	Comparator by position. As this class has dimension 1, this is basically an alias for RTLess
CRTLess	Comparator by RT position
CChromatogramProcessor	Convenience entry point that runs MRMFeatureFinderScoring on a list of already-extracted chromatograms
CChromatogramRangeManager	Range manager for chromatograms
CChromatogramSchema	Schema for chromatograms in long (one row per data point) format
CChromatogramSemiWideSchema	Schema for chromatograms in semi-wide (one row per chromatogram, list columns) format
CChromatogramSettings	Representation of chromatogram settings, e.g. SRM/MRM chromatograms
CChromatogramTools	Conversion class to convert chromatograms
CChromeleonFile	Load Chromeleon HPLC text file and save it into a MSExperiment
CChromExtractParams	ChromatogramExtractor parameters
CCitation	Stores Citations for individual TOPP tools
CClusterAnalyzer	Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's)
►CClusterFunctor	Base class for cluster functors
CInsufficientInput	Exception thrown if not enough data (<2) is used
CClusterHierarchical	Hierarchical clustering with generic clustering functions
CClusteringGrid	Data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering
CClusterProxyKD	Proxy for a (potential) cluster
CCmpHypothesesByScore
CCmpMassTraceByMZ
CCoarseIsotopePatternGenerator	Isotope pattern generator for coarse isotope distributions
►CColorizer	Color and style the fonts shown on cout/cerr (or other streams)
CColorWithUndo_
CColorSelector	A widget for selecting a color
CCometModification	Helper struct that represents one Comet variable_modXX entry and supports merging compatible entries
CCompareMzTabMMatchRef	Data 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
CCompleteLinkage	CompleteLinkage ClusterMethod
CCompomer	Holds information on an edge connecting two features from a (putative) charge ladder
CCompressedInputSource	Xerces InputSource that opens a bzip2-, zip- or gzip-compressed file on demand
CCondition	Single filter condition (column, operator, values)
►CConfidenceScoring	Confidence scoring for SRM/MRM/PRM features against a targeted assay library
CGLM_	Binomial GLM used to map (squared-normalised-RT-diff, intensity-distance) -> [0, 1] confidence
CRTNorm_	Map RT values into the [0, 100] interval using min/max RT of the assay library
CConnectedComponent
►CConsensusFeature	A consensus feature spanning multiple LC-MS/MS experiments
CMapsLess	Compare by the sets of consensus elements (lexicographically)
CRatio	Slim struct to feed the need for systematically storing of ratios
CSizeLess	Compare by size(), the number of consensus elements
CConsensusFeatureSchema	Schema for consensus feature table (ConsensusMap features)
►CConsensusIDAlgorithm	Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs)
CHitInfo
CConsensusIDAlgorithmAverage	Calculates a consensus from multiple ID runs by averaging the search scores
CConsensusIDAlgorithmBest	Calculates a consensus from multiple ID runs by taking the best search score
CConsensusIDAlgorithmIdentity	Abstract base class for ConsensusID algorithms that compare only identical sequences
CConsensusIDAlgorithmPEPIons	Calculates a consensus from multiple ID runs based on PEPs and shared ions
CConsensusIDAlgorithmPEPMatrix	Calculates a consensus from multiple ID runs based on PEPs and sequence similarities
CConsensusIDAlgorithmRanks	Calculates a consensus from multiple ID runs based on the ranks of the search hits
CConsensusIDAlgorithmSimilarity	Abstract base class for ConsensusID algorithms that take peptide similarity into account
CConsensusIDAlgorithmWorst	Calculates a consensus from multiple ID runs by taking the worst search score (conservative approach)
►CConsensusMap	A container for consensus elements
CColumnHeader	Description of the columns in a consensus map
CConsensusMapArrowExport	Export ConsensusMap feature data to Apache Arrow format following QPX feature schema
CConsensusMapArrowIO	Import and export ConsensusMap data to/from Apache Arrow format
CConsensusMapMergerAlgorithm	Merges identification data in ConsensusMaps
CConsensusMapNormalizerAlgorithmMedian	Algorithms of ConsensusMapNormalizer
CConsensusMapNormalizerAlgorithmQuantile	Quantile-normalisation of feature intensities across the maps of a ConsensusMap
CConsensusMapNormalizerAlgorithmThreshold	Intensity normalisation of a ConsensusMap by averaging per-feature intensity ratios against a reference map
CConsensusXMLFile	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation
CConsoleUtils	Singleton helper for terminal-width-aware string wrapping in TOPP-tool console output
►CConstRefVector	This vector holds pointer to the elements of another container
CConstRefVectorConstIterator	ConstIterator for the ConstRefVector
CConstRefVectorIterator	Mutable iterator for the ConstRefVector
CContactPerson	Contact person information
CContactPersonVisualizer	Class that displays all meta information for ContactPerson objects
►CContaminants	QualityControl metric: flag PSMs whose peptide sequences match a user-supplied contaminants FASTA (e.g. cRAP) after digestion
CContaminantsSummary	Result bundle returned per compute call
►CControlledVocabulary
CCVTerm	Representation of a CV term
CFNV1aHasher	Ensure same hash on all platforms (for reproducibility)-
CConvexHull2D
CCrossLinksDB	Process-wide singleton database of cross-linking modifications
CCrossValidation	Lightweight K-fold / LOO cross-validation utilities and 1-D grid search
CCsvFile	This class handles csv files. Currently only loading is implemented
CCubicSpline2d	Natural cubic-spline interpolation of a 2D data set
CCurlInit
CCVMappingFile	Used to load CvMapping files
CCVMappingRule	Representation of a CV Mapping rule used by CVMappings
CCVMappings	Representation of controlled vocabulary mapping rules (for PSI formats)
CCVMappingTerm	Representation of controlled vocabulary term
CCVReference	Controlled Vocabulary Reference
►CCVTerm	Representation of controlled vocabulary term
CUnit
CCVTermList	Representation of controlled vocabulary term list
CCVTermListInterface	Interface to the controlled vocabulary term list
CDataFilterDialog	Dialog for creating and changing a DataFilter
►CDataFilters	DataFilter array providing some convenience functions
CDataFilter	Representation of a peak/feature filter combining FilterType, FilterOperation and a value (either double or String)
CDataProcessing	Description of the applied preprocessing steps
CDataProcessingVisualizer	Class that displays all meta information for DataProcessing objects
CDataSelectionTabs	A tabbed view, to browse lists of spectra or identifications
CDataTabBase	All tabs need to implement this interface
CDataValue	Class to hold strings, numeric values, lists of strings and lists of numeric values
►CDate	Date Class
CFields
►CDateTime	DateTime Class
CFields
CDaTrait
CDBoundingBox	A D-dimensional bounding box
►CDBSuitability	This class holds the functionality of calculating the database suitability
CSuitabilityData	Struct to store results
CDBSuitability_friend
CDDAWorkflowCommons	Common functions for DDA workflows
CDeconvolvedSpectrum	A 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
CDecoyGenerator	Methods to generate isobaric decoy sequences for DDA target-decoy searches
►CDecoyHelper	Helper class for calculations on decoy proteins
CDecoyStatistics	Struct for intermediate results needed for calculations on decoy proteins
CResult
CDefaultChromHandler	Dispatching chromatogram handler that picks SRM/MRM or DIA at runtime based on the input maps
CDefaultParamHandler	A base class for all classes handling default parameters
CDeisotoper	Collapse isotopic clusters in a centroided peak spectrum to one monoisotopic peak per ion
CDIAChromHandler	IChromatogramHandler implementation for DIA / SWATH / PRM / PASEF-DIA acquisitions, where chromatograms are extracted from full-scan MS2 data rather than being directly acquired as SRM/MRM traces
►CDiaPrescore	Scoring of an spectrum given library intensities of a transition group
CTransitionGroupTheoreticalSpectrumCache	Cached transition-group-specific theoretical spectrum used by the DIA prescore
CDIAScoring	Scoring of an spectrum at the peak apex of an chromatographic elution peak
CDIATreeTab	Hierarchical visualization and selection of spectra
CDigestionEnzyme	Base class for digestion enzymes
CDigestionEnzymeDataProvider	Abstract interface for providing digestion enzyme data
CDigestionEnzymeDB	Digestion enzyme database (base class)
CDigestionEnzymeProtein	Representation of a digestion enzyme for proteins (protease)
CDigestionEnzymeRNA	Representation of a digestion enzyme for RNA (RNase)
CDimBase	A 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
CDimIM	Dimension implementation for ion mobility values
CDimINT	Dimension implementation for intensity values
CDimMapper	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)
CDimMZ	Dimension implementation for m/z values
CDimRT	Dimension implementation for retention time values
CDistanceMatrix	A two-dimensional distance matrix, similar to OpenMS::Matrix
CDocumentIdentifier	Manage source document information
CDocumentIdentifierVisualizer	Class that displays all meta information for DocumentIdentifier objects
CDPeak	Metafunction to choose among Peak1D respectively Peak2D through a template argument
CDPosition	Representation of a coordinate in D-dimensional space
CDRange	A D-dimensional half-open interval
CDTA2DFile	DTA2D File adapter
CDTAFile	File adapter for DTA files
CEDTAFile
►CEGHTraceFitter	A RT Profile fitter using an Exponential Gaussian Hybrid background model
CEGHTraceFunctor
CElement	Representation of an element
CElementDB	Singleton that stores elements and isotopes
CElutionModelFitter	Helper class for fitting elution models to features
CElutionPeakDetection	Extracts chromatographic peaks from a mass trace
►CEmgFitter1D	Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization
CData	Helper struct (contains the size of an area and a raw data container)
CEgmFitterFunctor
CEmgGradientDescent	Fit peaks to an Exponentially Modified Gaussian (EMG) model using gradient descent
CEmgGradientDescent_friend
CEmgModel
CEmgScoring	Scoring of an elution peak using an exponentially modified gaussian distribution model
CEmpiricalFormula	Representation of an empirical formula
CEnhancedTabBar	Convenience tab bar implementation
CEnhancedTabBarWidgetInterface	Widgets that are placed into an EnhancedTabBar must implement this interface
CEnhancedWorkspace
CEnzymaticDigestion	Class for the enzymatic digestion of sequences
CEnzymeXMLDataProvider	Data provider that loads digestion enzymes from an XML file
CErrorEstimationConfig	Configuration for OpenSwath analyte level inference global and local error estimation
CEuclideanSimilarity	CompareFunctor for 2Dpoints
►CExperimentalDesign	Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class
CMSFileSectionEntry
CSampleSection
CExperimentalDesignFile	Load an experimental design from a TSV file. (see ExperimentalDesign for details on the supported format)
CExperimentalSettings	Description of the experimental settings
CExperimentalSettingsVisualizer	Class that displays all meta information for ExperimentalSettings objects
CExposedVector
CExtendedIsotopeFitter1D	Extended isotope distribution fitter (1-dim.) approximated using linear interpolation
CExtendedIsotopeModel
CExternalProcess	A wrapper around boost::process to conveniently start an external program and forward its outputs
CExternalProcessMBox	A wrapper around ExternalProcess to conveniently show a MessageBox when an error occurs
CFAIMSHelper	Helper functions for FAIMS data
CFakeProcess	A FakeProcess class
►CFalseDiscoveryRate	Calculates false discovery rates (FDR) from identifications
►CDecoyStringHelper	Finds decoy strings in ProteinIdentification runs
CResult	Finds 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
CFASTAContainer	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	This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusual symbols (such as translation end (*)), they will be kept! You can use aggregate methods load() and store() to read/write a set of protein sequences at the cost of memory
CFASTAEntry	FASTA 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
CFeature	An LC-MS feature
CFeatureDeconvolution	An algorithm to decharge features (i.e. as found by FeatureFinder)
►CFeatureDistance	A functor class for the calculation of distances between features or consensus features
CDistanceParams_	Structure for storing distance parameters
CFeatureEditDialog	Dialog for editing a feature
CFeatureFileOptions	Options for loading files containing features
CFeatureFinderAlgorithm	Abstract base class for FeatureFinder algorithms
►CFeatureFinderAlgorithmMetaboIdent
CFeatureCompare	Comparison functor for features
CFeatureFilterQuality	Predicate for filtering features by overall quality
CFeatureFinderMetaboIdentCompound	One target compound for the FeatureFinderAlgorithmMetaboIdent assay library
CMassTraceBounds	Boundaries for a mass trace in a feature
CFeatureFinderAlgorithmPicked	FeatureFinderAlgorithm for picked peaks
►CFeatureFinderAlgorithmPickedHelperStructs	Wrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes
CIsotopePattern	Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked
CMassTrace	Helper struct for mass traces used in FeatureFinderAlgorithmPicked
CMassTraces	Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked
CSeed	Helper structure for seeds used in FeatureFinderAlgorithmPicked
CTheoreticalIsotopePattern	Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked
►CFeatureFinderDefs	The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes.
CNoSuccessor	Exception that is thrown if a method an invalid IndexPair is given
►CFeatureFinderIdentificationAlgorithm	ID-guided MS1 feature finder; the algorithm behind FeatureFinderIdentification
CFeatureCompare	Comparison functor for features
CFeatureFilterPeptides	Predicate for filtering features by assigned peptides:
CFeatureFilterQuality	Predicate for filtering features by overall quality:
CIMStats	Ion mobility statistics for a peptide in a specific RT region and charge state
CPeptideCompare	Comparison functor for (unassigned) peptide IDs
CRTRegion	Region in RT in which a peptide elutes:
CFeatureFinderMultiplexAlgorithm	Identification-free quantitative feature finder for SILAC / Dimethyl / ICPL-style label-pair experiments
CFeatureFindingMetabo	Method for the assembly of mass traces belonging to the same isotope pattern, i.e., that are compatible in retention times, mass-to-charge ratios, and isotope abundances
CFeatureGroupingAlgorithm	Base class for all feature grouping algorithms
CFeatureGroupingAlgorithmKD	A feature grouping algorithm for unlabeled data
CFeatureGroupingAlgorithmLabeled	A map feature grouping algorithm for labeling techniques with two labels
CFeatureGroupingAlgorithmQT	A feature grouping algorithm for unlabeled data
CFeatureGroupingAlgorithmUnlabeled	A map feature grouping algorithm for unlabeled data
CFeatureGroupingAlgorithmWNet	A feature grouping algorithm using Wasserstein optimal transport
►CFeatureHandle	Representation of a Peak2D, RichPeak2D or Feature
CFeatureHandleMutable_	Helper class returned by FeatureHandle::asMutable(), which see
CIndexLess	Comparator by map and unique id
CFeatureHypothesis	Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis)
CFeatureMap	A container for features
CFeatureMapArrowIO	Import and export FeatureMap data to/from Apache Arrow format
►CFeatureMapping	Helper utilities for matching MS2 spectra to LC-MS features by precursor (m/z, RT)
CFeatureMappingInfo	Input bundle: feature maps and a spatial index over them
CFeatureToMs2Indices	Output bundle: per-feature MS2 spectrum indices + the list of unassigned MS2 spectra
CFeatureOpenMS	An implementation of the OpenSWATH Feature Access interface using OpenMS
CFeatureOverlapFilter
CFeatureSchema	Schema for LC-MS feature table (FeatureMap features)
►CFeatureSummary
CResult
CFeatureXMLFile	This class provides Input/Output functionality for feature maps
CFIAMSDataProcessor	Data processing pipeline for one Flow Injection Analysis MS (FIA-MS) sample
CFIAMSScheduler	Batch driver for FIA-MS analyses. Dispatches each sample of a CSV-described batch to FIAMSDataProcessor
►CFile	Basic file handling operations
COpenMSDataPath_	Bundles the resolved OpenMS data path with a human-readable description of where it was found (for diagnostics)
CTempDir	Class representing a temporary directory
CTemporaryFiles_	Internal helper class, which holds temporary filenames and deletes these files at program exit
CFileHandler	Facilitates file handling by file type recognition
►CFileInfo	Library-level equivalent of the FileInfo tool
CCorruptionInfo	-c (corrupt data) block
CDetailInfo	Detailed per-spectrum listing (the -d block); kept as pre-rendered lines
►CExperimentMeta	Experiment / instrument / sample / contact metadata (the -m block, peak files)
CContact
CFastaInfo	FASTA specifics
►CFeatureInfo	Feature / consensus specifics
CMapColumn
CFileMeta	General header block (always populated)
CIdentInfo	Identification specifics (idXML / mzIdentML)
CMzTabInfo	MzTab specifics
CNamedStats	One named SummaryStatistics block; title is the label used in both renderers
COptions	What to compute (mirrors the CLI flags; lets callers opt into expensive work)
CPeakInfo	Peak-file (MSExperiment) specifics
CProcessingStep	One data-processing step (the -p block)
CRange	One [min,max] interval for a single dimension; present==false => "<none>"
CRanges	MSExperiment carries four range categories; non-MSExperiment maps fill only combined
CRangeSet	Four range dimensions FileInfo reports for a map / spectrum group
CResult	Master result aggregate
CValidationInfo	-v (schema/semantic validation) and -i (indexed mzML) blocks
►CFileTypeList	Holds a vector of known file types, e.g. as a way to specify supported input formats
CFilterElements_	Hold filter items (for Qt dialogs) along with their OpenMS type
CFileTypes	Centralizes the file types recognized by FileHandler
CFileWatcher	Watcher that monitors file changes
CFilterExpression	Simple conjunction/disjunction of conditions
CFineIsotopePatternGenerator	Isotope pattern generator for fine isotope distributions
CFitter1D	Abstract base class for all 1D-dimensional model fitter
CFlagSet	Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64
CFLASHDeconvAlgorithm	FLASHDeconv algorithm: ultrafast mass deconvolution algorithm for top down mass spectrometry dataset From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps: i) decharging and select candidate masses - speed up via binning ii) collecting isotopes from the candidate masses and deisotoping - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups)
CFLASHDeconvFeatureFile	FLASHDeconv feature level output *.tsv, *.ms1ft (for Promex), *.feature (for TopPIC) file formats
CFLASHDeconvSpectrumFile	FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats
►CFLASHHelperClasses	Wrapper 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
CIsobaricQuantities	Isobaric quantities
CLogMzPeak	Log transformed peak. After deconvolution, all necessary information from deconvolution such as charge and isotope index is stored
CMassFeature	Mass feature (Deconvolved masses in spectra are traced by Mass tracing to generate mass features - like LC-MS features)
CPrecalculatedAveragine	Pre-binned averagine isotope-distribution cache used by FLASHDeconv for fast cosine-similarity scoring
►CFragmentIndex	Generates from a set of Fasta files a 2D-datastructure which stores all theoretical masses of all b and y ions from all peptides generated from the Fasta file. The datastructure is build such that on one axis the fragments are sorted by their own mass and the axis by the mass of their precursor/protein. The FI has two options: Bottom-up and Top Down. In later digestion is skiped and the fragments have a direct reference to the mass of the proteins instead of digested peptides
CFragment	One entry in the fragment index
CHit
CIonOffsets	Precomputed ion-type mass offsets (from Residue::getInternalTo*Ion formulas)
CModSlot	A candidate modification slot for a specific peptide
CPeptide	Compact descriptor of a peptide instance held by the FragmentIndex
CSpectrumMatch	Match between a query peak and an entry in the DB
CSpectrumMatchesTopN	Container for SpectrumMatch. Also keeps count of total number of candidates and total number of matches
CVarModEntry	Entry in the per-AA variable modification lookup table
►CFragmentMassError
CStatistics	Structure for storing results: average and variance of all FragmentMassErrors in ppm
CFullSwathFileConsumer	Abstract base class which can consume spectra coming from SWATH experiment stored in a single file
►CFuzzyStringComparator	Fuzzy comparison of strings, tolerates numeric differences
CAbortComparison	Internal exception class
CInputLine	Stores information about the current input line (i.e., stream for the line and the current position in the stream)
CPrefixInfo_	Wrapper for the prefix information computed for the failure report
CStreamElement_	Stores information about characters, numbers, and white spaces loaded from the InputStream
CFWHM	QC metric calculating (un)calibrated m/z error
CGaussFilter	This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data
CGaussFilterAlgorithm	This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data
CGaussFitter1D	Gaussian distribution fitter (1-dim.) approximated using linear interpolation
CGaussModel	Normal distribution approximated using linear interpolation
►CGaussTraceFitter	Fitter for RT profiles using a Gaussian background model
CGaussTraceFunctor
CGNPSMetaValueFile	Writer for the meta-value (.TSV) table consumed by GNPS Feature-Based Molecular Networking
CGNPSMGFFile	Writer for the consensus-spectrum MGF file consumed by GNPS Feature-Based / Ion-Identity Molecular Networking
CGNPSQuantificationFile	Writer for the feature-quantification (.TXT) table required by GNPS Feature-Based Molecular Networking
CGradient	Representation of a HPLC gradient
CGradientVisualizer	GradientVisualizer is a visualizer class for objects of type gradient
CGravitator	Manipulates 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
CGridBasedCluster	Basic data structure for clustering
CGridBasedClustering	2D hierarchical clustering implementation optimized for large data sets containing many small clusters i.e. dimensions of clusters << dimension of entire dataset
CGridFeature	Representation of a feature in a hash grid
CGridSearch
CGUIProgressLoggerImpl	Implements a GUI version of the ProgressLoggerImpl
CGzipIfstream	Decompresses files which are compressed in the gzip format (*.gzip)
CGzipInputStream	Implements the BinInputStream class of the xerces-c library in order to read gzip compressed XML files
CHasActivationMethod	Predicate that determines if a spectrum was generated using any activation method given in the constructor list
►CHashGrid	Container for (2-dimensional coordinate, value) pairs
CConstIterator	Constant element iterator for the hash grid
CIterator	Element iterator for the hash grid
CHasMetaValue	Predicate that determines if a class has a certain metavalue
CHasPrecursorCharge	Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list
CHasScanMode	Predicate that determines if a spectrum has a certain scan mode
CHasScanPolarity	Predicate that determines if a spectrum has a certain scan polarity
CHDF5Connector	File adapter for HDF5 files
CHistogramDialog	Dialog that show a HistogramWidget
CHistogramWidget
CHit
CHPLC	Representation of a HPLC experiment
CHPLCVisualizer	Class that displays all meta information for HPLC objects
CHydrophobicityProfile	This class is used for hydrophobicity profiling of peptides
►CHyperScore	An implementation of the X!Tandem HyperScore PSM scoring function
CPSMDetail	Compute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match
CIBSpectraFile	Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results
CIChromatogramHandler	Abstract interface for providing chromatograms
CIDConflictResolverAlgorithm	Resolves ambiguous annotations of features with peptide identifications
►CIDDecoyProbability	IDDecoyProbability calculates probabilities using decoy approach
CTransformation_	Struct to be used to store a transformation (used for fitting)
►CIdentificationData
CModifyMultiIndexAddProcessingStep	Helper functor for adding processing steps to elements in a boost::multi_index_container structure
CModifyMultiIndexAddScore	Helper functor for adding scores to elements in a boost::multi_index_container structure
CModifyMultiIndexRemoveParentMatches	Helper functor for removing invalid parent matches from elements in a boost::multi_index_container structure
CRefTranslator	Structure that maps references of corresponding objects after copying
►CIdentificationDataConverter
CPepIDCompare	Functor for ordering peptide IDs by RT and m/z (if available)
CStepOptCompare	Functor for ordering StepOpt (by date of the steps, if available):
►CIdentificationSummary
CResult
CUniqueID
CIdentifierMSRunMapper	Two-way mapping from ms-run-path to protID|pepID-identifier
►CIDFilter	Collection of functions for filtering peptide and protein identifications
CDigestionFilter	Is peptide evidence digestion product of some protein
CGetMatchingItems	Builds a map index of data that have a std::string index to find matches and return the objects
CHasDecoyAnnotation	Is this a decoy hit?
CHasGoodScore	Is the score of this hit at least as good as the given value?
CHasMatchingAccessionImpl	Given a list of protein accessions, do any occur in the annotation(s) of this hit?
CHasMaxMetaValue	Does a meta value of this hit have at most the given value?
CHasMetaValue	Is a meta value with given key and value set on this hit?
CHasMinMetaValue	Predicate to check if a HitType object has a minimum meta value
CHasNoHits	Is the list of hits of this peptide/protein ID empty?
CPeptideDigestionFilter	Filter Peptide Hit by its digestion product
►CIDMapper	Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications
CPeptideIdentificationListState	Result of a partitioning by identification state with mapPrecursorsToIdentifications()
CIDMergerAlgorithm	Algorithm for merging multiple protein and peptide identification runs
►CIDRipper	Ripping protein/peptide identification according their file origin
CIdentificationRuns	Represents a set of IdentificationRuns
CRipFileContent	Represents the content of an IDRipper output file
CRipFileIdentifier	Identifies an IDRipper output file
CRipFileIdentifierIdxComparator	Provides a 'less' operation for RipFileIdentifiers that ignores the out_basename and origin_fullname members
►CIDScoreGetterSetter	A class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps
CIsHitType
CIsIDType
►CIDScoreSwitcherAlgorithm	This class is used to switch identification scores within identification or consensus feature maps
CIDSwitchResult	Structure holding score switching information for IDScoreSwitcherAlgorithm
CScoreSearchResult	Structure to hold score detection results for any ScoreType.
CIdXMLFile	Used to load and store idXML files
CILPDCWrapper	ILP-based decharging: pick the maximum-log-score subset of charge-pair edges that yields a consistent per-feature charge assignment
CIMDataConverter	This class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models
CIMTypes
CImzMLBinaryIO	Shared .ibd binary array decode utilities for imzML handlers
CImzMLFile	File adapter for imzML 1.1.0 mass spectrometry imaging data
CImzMLMeta	Dataset-level metadata for imzML mass spectrometry imaging files
CImzMLSpectrumIndex	Per-spectrum binary index entry for an imzML dataset
CIncludeExcludeTarget	This class stores a SRM/MRM transition
CIndentedStream	Class for writing data which spans multiple lines with an indentation for each line (all except the first)
CIndex
CIndexedMzMLDecoder	A class to analyze indexedmzML files and extract the offsets of individual tags
CIndexedMzMLFileLoader	A class to load an indexedmzML file
CINIFileEditorWindow	Shows the ParamEditor widget in a QMainWindow with a toolbar
CInIntensityRange	Predicate that determines if a peak lies inside/outside a specific intensity range
CINIUpdater
CInMemoryDataProvider	Data provider that serves pre-built modifications from memory
CInMemoryDigestionEnzymeDataProvider	In-memory data provider for digestion enzymes (primarily for testing)
CInMemoryRibonucleotideDataProvider	Data provider that serves pre-built ribonucleotides from memory
CInMSLevelRange	Predicate that determines if a spectrum lies inside/outside a specific MS level set
CInMzRange	Predicate that determines if a peak lies inside/outside a specific m/z range
CInPrecursorMZRange	Predicate that determines if a spectrum's precursor is within a certain m/z range
CInputFile	A simple widget with a line-edit and a browse button to choose filenames
CInRTRange	Predicate that determines if a spectrum lies inside/outside a specific retention time range
CInspectInfile	Inspect input file adapter
CInspectOutfile
CInstrument	Description of a MS instrument
CInstrumentSettings	Description of the settings a MS Instrument was run with
CInstrumentSettingsVisualizer	Class that displays all meta information for InstrumentSettings objects
CInstrumentVisualizer	Class that displays all meta information for an MS instrument
CInteractiveSplashScreen	A QSplashScreen which stays responsive and can be dismissed early by the user
►CInternalCalibration	A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference masses
CCalibrantStats_	Statistics when adding peptide calibrants
CLockMass	Helper class, describing a lock mass
CInterpolationModel	Abstract class for 1D-models that are approximated using linear interpolation
CIonDetector	Description of a ion detector (part of a MS Instrument)
CIonDetectorVisualizer	Class that displays all meta information for IonDetector objects
CIonIdentityMolecularNetworking	Helpers for the Ion Identity Molecular Networking (IIMN) workflow on GNPS
CIonImage	Dense W x H grid of ion intensities with a per-pixel mask
CIonMobilityScoring	A class that calls the ion mobility scoring routines
CIonSource	Description of an ion source (part of a MS Instrument)
CIonSourceVisualizer	Class that displays all meta information for IonSource objects
CIPeptideIds	Abstract base class which defines an interface for PeptideIdentifications
CIPFAlignmentRow	Alignment-group membership for cross-run IPF signal propagation
CIPFPrecursorProbabilityRow	Precursor-layer posterior error probability used by IPF
CIPFPrecursorRow	Peak-group and precursor evidence for peptidoform inference
CIPFResultRow	Final peptidoform inference result row
CIPFTransitionRow	Transition-layer evidence for peptidoform inference
CIsEmptySpectrum	Predicate that determines if a spectrum is empty
CIsInCollisionEnergyRange	Predicate that determines if an MSn spectrum was generated with a collision energy in the given range
CIsInIsolationWindow	Predicate that determines if the isolation window covers ANY of the given m/z values
CIsInIsolationWindowSizeRange	Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range
►CIsobaricChannelExtractor	Extracts individual channels from MS/MS spectra for isobaric labeling experiments
CPurityState_	Small struct to capture the current state of the purity computation
CIsobaricIsotopeCorrector	Performs isotope impurity correction on intensities extracted from isobaric labeling experiments
CIsobaricNormalizer	Performs median normalization on the extracted ratios of isobaric labeling experiment
CIsobaricQuantifier	Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing
CIsobaricQuantifierStatistics	Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion)
►CIsobaricQuantitationMethod	Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix
CIsobaricChannelInformation	Summary of an isobaric quantitation channel
►CIsoelectricPoint
CPkaValues	Internal struct holding pKa values for a given scale
CIsoSpecGeneratorWrapper	Interface for the IsoSpec algorithm - a generator of infinitely-resolved theoretical spectra
CIsoSpecOrderedGeneratorWrapper	Generate the stream of configurations, ordered from most likely to least likely
CIsoSpecThresholdGeneratorWrapper	Provides a threshold-based generator of isotopologues: generates all isotopologues more probable than a given probability threshold
CIsoSpecThresholdWrapper	A non-generator version of IsoSpecThresholdGeneratorWrapper
CIsoSpecTotalProbGeneratorWrapper	Generate a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99)
CIsoSpecTotalProbWrapper	Create a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99)
CIsoSpecWrapper	A convenience class for the IsoSpec algorithm - easier to use than the IsoSpecGeneratorWrapper classes
►CIsotopeCluster	Stores information about an isotopic cluster (i.e. potential peptide charge variants)
CChargedIndexSet	Index set with associated charge estimate
CIsotopeDistribution
CIsotopeFitter1D	Isotope distribution fitter (1-dim.) approximated using linear interpolation
CIsotopeLabelingMDVs	IsotopeLabelingMDVs is a class to support and analyze isotopic labeling experiments (i.e. MDVs : Mass Distribution Vectors, also known as Mass Isotopomer Distribution (MID))
CIsotopeModel
CIsotopePatternGenerator	Provides an interface for different isotope pattern generator methods
CIsZoomSpectrum	Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum
►CItraqConstants	Some constants used throughout iTRAQ classes
CChannelInfo	Stores information on an iTRAQ channel
CItraqEightPlexQuantitationMethod	ITRAQ 8 plex quantitation to be used with the IsobaricQuantitation
CItraqFourPlexQuantitationMethod	ITRAQ 4 plex quantitation to be used with the IsobaricQuantitation
CJavaInfo	Detect Java and retrieve information
CKDTreeFeatureMaps	Pools features from multiple maps into a single 2D kd-tree on (RT, m/z) for fast range queries
CKDTreeFeatureNode	Lightweight kd-tree entry: a back-pointer to a KDTreeFeatureMaps and the index of one feature in it
CKroenikFile	File adapter for Kroenik (HardKloer sibling) files
CLabeledPairFinder	The LabeledPairFinder allows the matching of labeled features (features with a fixed distance)
CLayerAnnotatorAMS
CLayerAnnotatorBase
CLayerAnnotatorOSW
CLayerAnnotatorPeptideID
CLayerData1DBase	Base class for all 1D layers, a special case of LayerData
CLayerData1DChrom
CLayerData1DIonMobility
CLayerData1DPeak
CLayerDataBase	Class that stores the data for one layer
CLayerDataChrom	Class that stores the data for one layer of type Chromatogram
CLayerDataConsensus	Class that stores the data for one layer of type ConsensusMap
►CLayerDataDefs
►CProjectionData	Result of computing a projection on X and Y axis in a 2D Canvas; see LayerDataBase::getProjection()
CSummary
CLayerDataFeature	Class that stores the data for one layer of type FeatureMap
CLayerDataIdent	Class that stores the data for one layer of type PeptideIdentifications
CLayerDataIonMobility	Class that stores the data for one layer of type IonMobility
CLayerDataPeak	Class that stores the data for one layer of type PeakMap
CLayerListView	Pimped QListView for Layers of a Canvas
CLayerStack
CLayerStatistics	Compute summary statistics (count/min/max/avg) about a container, e.g. intensity, charge, meta values, ..
CLayerStatisticsConsensusMap	Computes statistics and distributions for a PeakMap
CLayerStatisticsDialog	Dialog showing statistics about the data of the current layer
CLayerStatisticsFeatureMap	Computes statistics and distributions for a PeakMap
CLayerStatisticsIdent	Computes statistics and distributions for a vector<PeptideIdentifications>
CLayerStatisticsPeakMap	Computes statistics and distributions for a PeakMap
CLayerStoreData	Base class to store either the currently visible or all data of a canvas
CLayerStoreDataConsensusMapAll	Visitor which can save a full ConsensusMap; subsequently the data can be stored to a file
CLayerStoreDataConsensusMapVisible	Visitor which can save a visible piece of data; subsequently the data can be stored to a file
CLayerStoreDataFeatureMapAll	Visitor which can save a full FeatureMap; subsequently the data can be stored to a file
CLayerStoreDataFeatureMapVisible	Visitor which can save a visible piece of data; subsequently the data can be stored to a file
CLayerStoreDataIdentAll	Visitor which can save a full set of Identifications; subsequently the data can be stored to a file
CLayerStoreDataIdentVisible	Visitor which can save a visible piece of data; subsequently the data can be stored to a file
CLayerStoreDataPeakMapAll	Visitor which can save a full experiment; subsequently the data can be stored to a file
CLayerStoreDataPeakMapVisible	Visitor which can save a visible piece of data; subsequently the data can be stored to a file
CLevelContextInference	Shared OpenSwath analysis context inference for peptide, protein, and gene rows
CLevelContextInferenceConfig	Configuration for peptide-, protein-, and gene-level context inference
CLevelContextInputRow	Compact level-context input row independent of file format
CLevelContextResultRow	Final level-context result row
►CLevMarqFitter1D	Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization
CGenericFunctor
CLinearResamplerAlign	Linear Resampling of raw data with alignment
CListEditor	Editor for editing int, double and string lists (including output and input file lists)
CListFilterDialog	Dialog for creating and changing a DataFilter
►CListUtils	Collection of utility functions for management of vectors
CDoubleTolerancePredicate_	Predicate to check double equality with a given tolerance
CLogConfigHandler	The LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream
CLogWindow	A log window (QTextEdit) with convenience functions
CLowessSmoothing	LOWESS (locally weighted scatterplot smoothing)
►CLPWrapper	A wrapper class for linear programming (LP) solvers
CSolverParam	Struct that holds the parameters of the LP solver
CMapAlignmentAlgorithmIdentification	A map alignment algorithm based on peptide identifications from MS2 spectra
CMapAlignmentAlgorithmKD	An efficient reference-free feature map alignment algorithm for unlabeled data
CMapAlignmentAlgorithmPoseClustering	A map alignment algorithm based on pose clustering
CMapAlignmentAlgorithmTreeGuided	A map alignment algorithm based on peptide identifications from MS2 spectra
CMapAlignmentEvaluationAlgorithm	Base class for all Caap evaluation algorithms
CMapAlignmentEvaluationAlgorithmPrecision	Caap evaluation algorithm to obtain a precision value
CMapAlignmentEvaluationAlgorithmRecall	Caap evaluation algorithm to obtain a recall value
CMapAlignmentTransformer	This class collects functions for applying retention time transformations to data structures
CMapConversion	Static helpers that convert between the three OpenMS container types (PeakMap, FeatureMap, ConsensusMap)
CMapUtilities	Utilities for Feature and ConsensusMap
CMascotGenericFile	Read/write Mascot generic files (MGF)
CMascotRemoteQuery	Class which handles the communication between OpenMS and the Mascot server
CMascotXMLFile	Used to load Mascot XML files
CMassAnalyzer	Description of a mass analyzer (part of a MS Instrument)
CMassAnalyzerVisualizer	Class that displays all meta information for MassAnalyzer objects
CMassDecomposition	Class represents a decomposition of a mass into amino acids
CMassDecompositionAlgorithm	Mass decomposition algorithm, given a mass it suggests possible compositions
CMassExplainer	Computes empirical formulas for given mass differences using a set of allowed elements
CMassFeatureTrace	Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by SpectralDeconvolution In other words, per spectrum deconvolved masses are converted into deconvolved features Currently only works for MS1 spectra. (Top-down DIA is not yet used much). Every time an MS1 spectrum is deconvolved, the relevant information is stored in this class. This class also comes with tsv, TopFD feature file formats
CMassTrace	A container type that gathers peaks similar in m/z and moving along retention time
CMasstraceCorrelator	Correlates individual masstraces found in mass spectrometric maps
►CMassTraceDetection	A mass trace extraction method that gathers peaks similar in m/z and moving along retention time
CApex
CPeakCandidate	Encapsulates peak finding logic for both up and down directions
CTraceExtensionState	Encapsulates trace extension state
CMatchedIterator	For each element in the reference container the closest peak in the target will be searched. If no match is found within the tolerance window, the peak will be skipped over
CMatrix	A 2D matrix class with efficient buffer access for NumPy interoperability
CMaxLikeliFitter1D	Abstract base class for all 1D-model fitters using maximum likelihood optimization
CMetaboliteFeatureDeconvolution	An algorithm to decharge small molecule features (i.e. as found by FeatureFinder)
CMetaboliteSpectralMatching	Metabolomics spectral-library search by hyperscore
►CMetaboTargetedAssay	This class provides methods for the extraction of targeted assays for metabolomics
CCompoundSpectrumPair	CompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum
CCompoundTargetDecoyPair	CompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum (target, decoy)
CTargetDecoyGroup	TargetDecoyGroup stores the mz, rt and file number in correspondence to the index of a MetaboTargetedAssay vector
►CMetaboTargetedTargetDecoy	Resolve overlapping fragments and missing decoys for experimental specific decoy generation in targeted/pseudo targeted metabolomics
CMetaboTargetDecoyMassMapping	MetaboTargetDecoyMassMapping introduces a mapping of target and decoy masses and their respective compound reference using an identifier
CMetaDataBrowser	A meta data visualization widget
CMetaInfo	A Type-Name-Value tuple class
CMetaInfoDescription	Description of the meta data arrays of MSSpectrum
CMetaInfoDescriptionVisualizer	Class that displays all meta information for MetaInfoDescription objects
CMetaInfoInterface	Interface for classes that can store arbitrary meta information (Type-Name-Value tuples)
CMetaInfoInterfaceUtils	Utilities operating on containers inheriting from MetaInfoInterface
CMetaInfoRegistry	Registry which assigns unique integer indices to strings
CMetaInfoVisualizer	MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member
CMinimumDistance	Basic data structure for distances between clusters
CMissedCleavages	This class is a metric for the QualityControl TOPP Tool
►CMobilityPeak1D	A 1-dimensional raw data mobility point or peak. The unit (ms, 1/K_0, etc) is implicit
CIntensityLess
CMobilityLess	Comparator by mobility position
CPositionLess	Comparator by position. As this class has dimension 1, this is basically an alias for MobilityLess
►CMobilityPeak2D	A 2-dimensional raw data point or peak
CIMLess	Comparator by IM position
CIntensityLess
CMZLess	Comparator by m/z position
CPositionLess	Comparator by position. Lexicographical comparison (first IM then m/z) is done
►CMobilogram	The representation of a 1D ion mobilogram
CRTLess	Comparator for the RT of the mobilogram
CMobilogramParquetConsumer	Writes Mobilograms (ion-mobility traces) to a Parquet file using a PyProphet-compatible-like schema
CModelDescription	Stores the name and parameters of a model
CModificationDataProvider	Interface for providing ResidueModification data to ModificationsDB
CModificationDefinition
CModificationDefinitionsSet
CModificationsDB	Database which holds all residue modifications from UniMod
CModifiedNASequenceGenerator	Generator of modified nucleic-acid sequences for fixed and variable modification placement
►CModifiedPeptideGenerator	Generate fixed- and variable-modification variants of an AASequence, lock-free
CMapToResidueType	Cached mapping ResidueModification* -> already-instantiated modified Residue*
►CModifiedSincSmoother	Computes a modified sinc smoothing filter for profile data
CLinearRegression	Helper class for weighted linear regression
CModomicsJSONDataProvider	Loads Ribonucleotide data from a Modomics JSON file
►CMonosaccharideDB	Singleton database of monosaccharides for glycan notation
CMonosaccharide	Structure representing a monosaccharide
►CMorpheusScore	An implementation of the Morpheus PSM scoring function Inspired by a C# implementation by C. Wenger released under MIT license
CResult	Score and subscores
CMorphologicalFilter	This class implements baseline filtering operations using methods from mathematical morphology
CMRMAssay	Generate assays from a TargetedExperiment
CMRMBatchFeatureSelector	Batch processing wrapper for MRMFeatureSelector
CMRMChromHandler	Default SRM/MRM chromatogram provider declaration
CMRMDecoy	This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object
CMRMFeature	A multi-chromatogram MRM feature
CMRMFeatureFilter	The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria
►CMRMFeatureFinderScoring	The MRMFeatureFinder finds and scores peaks of transitions that co-elute
COpenSwath_Ind_Scores_Pooled	Pooled variant of OpenSwath_Ind_Scores to allow pre-allocation and reuse
CTransitionGroupCache	Cache of transition-group invariant data to avoid per-feature recomputation
CMRMFeatureOpenMS	An implementation of the OpenSWATH MRM Feature Access interface using OpenMS
►CMRMFeaturePicker	MRMFeaturePicker defines the structures containing parameters to be used in MRMTransitionGroupPicker for components and components groups
CComponentGroupParams	Structure to contain information about a component group with its parameters
CComponentParams	Structure to contain information about a single component with its parameters
CMRMFeaturePickerFile	Loads MRM component and component-group parameter sets from a comma-separated file
►CMRMFeatureQC	The MRMFeatureQC is a class to handle the parameters and options for MRMFeatureFilter
CComponentGroupPairQCs	Quality Controls (QCs) for multiple components (between or within component_groups)
CComponentGroupQCs	Quality Controls (QCs) within a component group
CComponentQCs	Quality Controls (QCs) for individual components
CMRMFeatureQCFile	File adapter for MRMFeatureQC files
►CMRMFeatureSelector	A base class for selection of MRM Features through Linear Programming optimization
CSelectorParameters
CMRMFeatureSelector_test
CMRMFeatureSelectorQMIP	MRMFeatureSelector implementation that selects MRM features via a quadratic-programming formulation over relative retention time
CMRMFeatureSelectorScore	MRMFeatureSelector implementation that selects MRM features via a linear program with score-weighted per-feature variables
CMRMFile	Minimal SRM/MRM file loader returning a single SwathMap wrapping the chromatogram container
CMRMIonSeries	Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy
CMRMMapping	A class to map targeted assays to chromatograms
CMRMRTNormalizer	The MRMRTNormalizer will find retention time peptides in data
CMRMTransitionGroup	The representation of a group of transitions in a targeted proteomics experiment
CMRMTransitionGroupPicker	The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors
CMS2AdductsOfSinglePrecursorAdduct
CMS2File
►CMs2IdentificationRate	This class is a metric for the QualityControl-ToppTool
CIdentificationRateData	Structure for storing results
►CMs2SpectrumStats	QC metric to determine the number of MS2 scans per MS1 scan over RT
CScanEvent
►CMSChromatogram	The representation of a chromatogram
CMZLess	Comparator for the precursor m/z time
CMSChromatogramParquetConsumer	Writes chromatograms to a Parquet file with a PyProphet-compatible schema
CMSDataAggregatingConsumer	Aggregates spectra by retention time
CMSDataCachedConsumer	Transforming and cached writing consumer of MS data
CMSDataChainingConsumer	Consumer class that passes all consumed data through a set of operations
CMSDataSqlConsumer	A data consumer that inserts MS data into a SQLite database
CMSDataStoringConsumer	Consumer class that simply stores the data
CMSDataTransformingConsumer	Transforming consumer of MS data
CMSDataWritingConsumer	Consumer class that writes MS data to disk using the mzML format
►CMSExperiment	In-Memory representation of a mass spectrometry run
CContainerAdd_	Helper class to add either general data points in set2DData or use mass traces from meta values
CContainerAdd_< ContainerValueType, false >
CContainerAdd_< ContainerValueType, true >
CSumIntensityReduction	Calculates the sum of intensities for a range of elements
CMSExperimentArrowExport	Export MSExperiment data to Apache Arrow format
CMSImagingExperiment	In-memory model for a 2D imaging mass spectrometry dataset
►CMSImagingGeometry	Pixel grid metadata and (x, y) -> spectrum_index lookup for MSI data
CPixel	A pixel in the imaging grid, linked to one spectrum in the experiment
CMSImagingRegion	A spatial region within an MSI dataset, in global pixel coordinates
CMsInspectFile
►CMSNumpressCoder	Class to encode and decode data encoded with MSNumpress
CNumpressConfig	Configuration class for MSNumpress
CMSPFile	File adapter for MSP files (NIST spectra library)
CMSPGenericFile	Load MSP text file and save it into an MSExperiment
CMSPGenericFile_friend
►CMSSpectrum	The representation of a 1D spectrum
CChunk	Used to remember what subsets in a spectrum are sorted already to allow faster sorting of the spectrum
CChunks	Container for organizing and managing multiple chunks in a spectrum
CIMLess	Comparator for the ion mobility
CRTLess	Comparator for the retention time
►CMSstatsFile	File adapter for MSstats files
CAggregatedConsensusInfo
CMSstatsLine_
CMSstatsTMTLine_
CMultiGradient	A gradient of multiple colors and arbitrary distances between colors
CMultiGradientSelector	A widget witch allows constructing gradients of multiple colors
►CMultiplexClustering	Clusters results from multiplex filtering
CMultiplexDistance	Scaled Euclidean distance for clustering
►CMultiplexDeltaMasses	Data structure for mass shift pattern
CDeltaMass	Mass shift with corresponding label set
►CMultiplexDeltaMassesGenerator	Generates complete list of all possible mass shifts due to isotopic labelling
CLabel	Complete label information
CMultiplexFilteredMSExperiment	Data structure storing all peaks (and optionally their raw data points) of an experiment corresponding to one specific peak pattern
CMultiplexFilteredPeak	Data structure storing a single peak that passed all filters
CMultiplexFiltering	Base class for filtering centroided and profile data for peak patterns
CMultiplexFilteringCentroided	Filters centroided data for peak patterns
CMultiplexFilteringProfile	Filters centroided and profile data for peak patterns
CMultiplexIsotopicPeakPattern	Data structure for pattern of isotopic peaks
CMultiplexSatelliteCentroided	Data structure storing a single satellite peak
CMultiplexSatelliteProfile	Data structure storing a single satellite data point
CMzCalibration	QC metric calculating (un)calibrated m/z error
CMzDataFile	File adapter for MzData files
CMzIdentMLFile	File adapter for MzIdentML files
►CMzMLFile	File adapter for MzML files
CSpecInfo
CMzMLSpectrumDecoder	A class to decode input strings that contain an mzML chromatogram or spectrum tag
CMzMLSwathFileConsumer	On-disk mzML implementation of FullSwathFileConsumer
CMzPAF	Parser and writer for mzPAF (Peak Annotation Format) notation
CMzPAFAnnotation	A single mzPAF peak annotation
CMzPAFMassDelta	Mass delta in an mzPAF annotation
CMzPAFNeutralLoss	Neutral loss in an mzPAF annotation
CMzPAFParseError	Parse error for mzPAF notation
CMzPAFPeakAnnotations	Multiple mzPAF annotations for a single peak
CMzQCFile	File adapter for mzQC files used to load and store mzQC files
►CMzTab	Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/
CCMMzTabStream
CIDMzTabStream
CMzTabAssayMetaData
CMzTabBase
CMzTabBoolean
CMzTabContactMetaData
CMzTabCVMetaData
CMzTabDouble
CMzTabDoubleList
CMzTabFile	File adapter for MzTab files
CMzTabInstrumentMetaData
CMzTabInteger
CMzTabIntegerList
CMzTabM	Data model of MzTab-M files Please see the MzTab-M specification at https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc#use-cases-for-mztab
CMzTabMAssayMetaData	MztabM Assay Metadata
CMzTabMDatabaseMetaData	MztabM Database Metadata
CMzTabMetaData	All meta data of a mzTab file. Please refer to specification for documentation
CMzTabMFile	File adapter for MzTab-M files
CMzTabMMetaData	MztabM Metadata
CMzTabMMSRunMetaData	MztabM MSRun Metadata
CMzTabModification	Data model of MzTab files
CMzTabModificationList
CMzTabModificationMetaData
CMzTabMSmallMoleculeEvidenceSectionRow	SME Small molecule evidence section (mztab-m)
CMzTabMSmallMoleculeFeatureSectionRow	SMF Small molecule feature section (mztab-m)
CMzTabMSmallMoleculeSectionRow	SML Small molecule section (mztab-m)
CMzTabMSRunMetaData
CMzTabMStudyVariableMetaData	MztabM StudyVariable Metadata
►CMzTabNucleicAcidSectionRow	NUC - Nucleic acid section (table-based)
CRowCompare	Comparison operator for sorting rows
►CMzTabOligonucleotideSectionRow	OLI - Oligonucleotide section (table-based)
CRowCompare	Comparison operator for sorting rows
►CMzTabOSMSectionRow	OSM - OSM (oligonucleotide-spectrum match) section (table-based)
CRowCompare	Comparison operator for sorting rows
CMzTabParameter
CMzTabParameterList
►CMzTabPeptideSectionRow	PEP - Peptide section (Table based)
CRowCompare	Comparison operator for sorting rows
►CMzTabProteinSectionRow	PRT - Protein section (Table based)
CRowCompare	Comparison operator for sorting rows
►CMzTabPSMSectionRow	PSM - PSM section (Table based)
CRowCompare	Comparison operator for sorting rows
CMzTabSampleMetaData
CMzTabSmallMoleculeSectionRow	SML Small molecule section (table based)
CMzTabSoftwareMetaData
CMzTabSpectraRef
CMzTabString
CMzTabStringList
CMzTabStudyVariableMetaData
►CMZTrafoModel	Create and apply models of a mass recalibration function
CRTLess	Comparator by position. As this class has dimension 1, this is basically an alias for MZLess
CMzXMLFile	File adapter for MzXML 3.1 files
►CNASequence	Representation of a nucleic acid sequence
CConstIterator	ConstIterator of NASequence class
CIterator	Iterator of NASequence class
CNeedlemanWunsch	Global-alignment similarity score for two amino-acid sequences using the Needleman-Wunsch algorithm
►CNeighborSeq	Subset-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
CNeighborStats	Statistics of how many neighbors were found per reference peptide
CNetwork	Convenience wrapper around NetworkGetRequest for one-shot HTTP/HTTPS downloads
CNetworkGetRequest	Synchronous HTTP GET request backed by libcurl
CNLargest	NLargest removes all but the n largest peaks
CNonNegativeLeastSquaresSolver	Wrapper around the Lawson-Hanson non-negative least squares (NNLS) Fortran routine
CNoopMSDataConsumer	Consumer class that performs no operation
CNoopMSDataWritingConsumer	Consumer class that perform no operation
CNormalizer	Normalizes the peak intensities spectrum-wise
CNucleicAcidSpectrumGenerator	Generates theoretical spectra for nucleic acid sequences
CNuXLAnnotateAndLocate	Post-scoring step of the OpenNuXL pipeline: annotates fragment-ion peaks of each candidate hit and localises the NA cross-link to a residue
CNuXLAnnotatedHit
CNuXLConstants	Index positions of the per-peak IntegerDataArrays used by the OpenNuXL pipeline
CNuXLDeisotoper	Deisotoping of nucleotide cross-link mass spectra
CNuXLFDR	Class-separated FDR calculation for nucleic-acid cross-links (NuXL)
CNuXLFragmentAdductDefinition
►CNuXLFragmentAnnotationHelper	Convenience functions to construct appealing fragment annotation strings and store them as PeptideHit::PeakAnnotation
CFragmentAnnotationDetail_	Single fragment annotation
CNuXLFragmentIonGenerator	Augments a peptide-cross-link fragment spectrum with NuXL-specific ions that TheoreticalSpectrumGenerator does not produce
CNuXLMarkerIonExtractor
►CNuXLModificationMassesResult	Result of NuXLModificationsGenerator::initModificationMassesNA — empirical formulas with their monoisotopic mass and the disambiguating nucleotide-composition lookup
CMyStringLengthCompare	Comparator that orders strings primarily by length (shortest first) and lexicographically within the same length
CNuXLModificationsGenerator	Enumerator of precursor-adduct masses for NuXL cross-link searches
CNuXLParameterParsing
CNuXLProteinReport	Protein report
CNuXLReport	Create PSM report
CNuXLReportRow	Struct to hold a single report line
CNuXLReportRowHeader	Create header line
COBODataProvider	Loads ResidueModification data from an OBO ontology file (PSI-MOD or XLMOD)
COMSFile	This class supports reading and writing of OMS files
COMSSACSVFile
COMSSAXMLFile	Used to load OMSSAXML files
COnDiscImzMLExperiment	Random-access, on-disc reader for imzML mass spectrometry imaging datasets
COnDiscMSExperiment	Representation of a mass spectrometry experiment on disk
CONNXPredictorBase
COpenPepXLAlgorithm	Search for peptide pairs linked with a labeled cross-linker
►COpenSearchModificationAnalysis	Utility class for analyzing modification patterns in open search results
CDeltaMassEntry	Statistics for a single delta mass bin in the histogram
CDeltaMassStatistics	Container for delta mass statistics table
CFuzzyDoubleComparator	Comparator for approximate comparison of double values
CModificationPattern	Stores details of a modification pattern found in the data
CModificationSummary	Data structure for modification summary output
COpenSearchAnalysisResult	Combined result of open search modification analysis
CPTMEntry	Statistics for a mapped PTM
CPTMStatistics	Container for PTM statistics table
COpenSwath_Ind_Scores	A structure to hold the individual scores computed for unique ion signatures (UIS) scores for the Inference of Peptidoforms (IPF) workflow
COpenSwath_Scores	A structure to hold the different scores computed by OpenSWATH
COpenSwath_Scores_Usage	A structure to store which scores should be used by the OpenSWATH Algorithm
COpenSwathDataAccessHelper	Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces
COpenSwathExportFilterConfig	Shared filter configuration for OpenSWATH export readers
COpenSwathExportRow	Filtered feature-level row used by results and matrix exports
COpenSwathFeatureScoreRow	Feature-level scored row for Parquet export
COpenSwathFeatureScoreTable	Feature-level Parquet export table with dynamically discovered FEATURE_MS1 / FEATURE_MS2 columns
COpenSwathGeneInference	OpenSwath gene-level context inference
COpenSwathHelper	A helper class that is used by several OpenSWATH tools
COpenSwathMatrixExportConfig	Configuration for matrix exports
COpenSwathMatrixExporter	Build and write OpenSWATH quantification matrices
►COpenSwathOSWParquetReader	Reader for OpenSwath OSW Parquet output
CPeakGroupFeatureScoresResult
CRow	Single extracted row combining feature + precursor + run metadata
CTransitionFeaturesResult	Result container for transition-level features
CUnscoredResult	Result container for an unscored table
COpenSwathOSWParquetWriter
►COpenSwathOSWWriter	Class to write out an OpenSwath OSW SQLite output (PyProphet input)
COSWData	Buffered OSW table rows ready for insertion through prepared statements
►COSWValue	Typed OSW cell value used for direct SQLite binding
CStorage
COpenSwathParquetExportConfig	Configuration for scored feature Parquet exports
COpenSwathParquetExporter	Write scored OpenSWATH feature and transition tables to Parquet
COpenSwathPeptideInference	OpenSwath peptide-level context inference
►COpenSwathPeptidoformInference	OpenSwath inference of peptidoforms (IPF)
CBayesianModelRow	Compact Bayesian model row used by the public helper methods
CPosteriorRow	Posterior probability row returned by applyBM
►COpenSwathPercolatorScoring	In-process Percolator scoring for OpenSWATH OSW and OSWPQ results
CScoreSummary	Small execution summary returned by score()
COpenSwathProteinInference	OpenSwath protein-level context inference
COpenSwathQuantMatrix	Dense matrix representation used by matrix exports
COpenSwathResultsExportConfig	Configuration for user-facing feature results exports
COpenSwathResultsExporter	Write filtered OpenSWATH feature results to TSV or Parquet
COpenSwathScoring
COpenSwathTransitionScoreRow	Transition-level scored row for optional Parquet export
COpenSwathTransitionScoreTable	Transition-level Parquet export table with dynamically discovered FEATURE_TRANSITION columns
COpenSwathWorkflow	Execute all steps in an OpenSwath analysis
COpenSwathWorkflowBase
►COpenSwathWorkflowScheduler	Plans memory-bounded OpenSwathWorkflow work waves and exposes a small concurrency-limiter pair
CConcurrencyEstimate	Derived scheduler limits computed by estimateConcurrency for one extraction/scoring run
CConcurrencyLimiter	Counting semaphore for paths that still stream one SWATH per worker
COptions	Memory and concurrency knobs used by wave planning and batch sizing
CScopedSlot	RAII slot guard for ConcurrencyLimiter — acquires on construction, releases on destruction
CWave	A wave: a group of SWATH indices (into the original swath_maps vector) that may be resident at the same time. Populated by planWaves
►COPXLDataStructs	Namespace-style container holding the data types shared across the OpenPepXL cross-linking pipeline
CAASeqWithMass	The AASeqWithMass struct represents a normal peptide with its precomputed mass
CAASeqWithMassComparator	The AASeqWithMassComparator is a comparator for AASeqWithMass objects
CCLSMScoreComparator	Comparator to sort CrossLinkSpectrumMatches by the main score
CCrossLinkSpectrumMatch	The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum in OpenPepXL
CPreprocessedPairSpectra	The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spectra to each other
CProteinProteinCrossLink	The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL
CXLPrecursor	The XLPrecursor struct represents a cross-link candidate in the process of filtering candidates by precursor masses in OpenPepXL
CXLPrecursorComparator	The XLPrecursorComparator is a comparator for XLPrecursors, that allows direct comparison of the XLPrecursor precursor mass with double numbers
►COPXLHelper	Functions needed by OpenPepXL to reduce duplicated code
CPeptideIDScoreComparator	A comparator for PeptideIdentifications that compares the scores in the first PeptideHit
COPXLSpectrumProcessingAlgorithms	Spectrum preprocessing and theoretical-vs-experimental peak alignment helpers used by the OpenPepXL cross-link search engines
COSWData	Holds all or partial information from an OSW file
COSWFeaturePrecursorSchema	Schema for OpenSWATH feature-level precursor intensity table
COSWFeatureSchema	Schema for OpenSWATH feature scoring results table
COSWFeatureTransitionSchema	Schema for OpenSWATH per-transition feature scoring results table
►COSWFile	This class serves for reading in and writing OpenSWATH OSW files
CPercolatorFeature
COSWHierarchy	Hierarchy levels of the OSWData tree
COSWIndexTrace	Index path into the OSWData tree from the root down to a specific node
COSWPeakGroup	A peak group (also called feature) is defined on a small RT range (leftWidth to rightWidth) in a group of extracted transitions (chromatograms)
COSWPeptidePrecursor	A peptide with a charge state
COSWPrecursorSchema	Schema for OpenSWATH precursor (peptide query) table
COSWProtein	A Protein is the highest entity and contains one or more peptides which were found/traced
COSWRunSchema	Schema for OpenSWATH run metadata table
COSWTransition	High-level meta-data of one fragment-ion transition referenced by an OSWPeakGroup
COSWTransitionSchema	Schema for OpenSWATH transition (fragment ion) table
COutputDirectory	A simple widget with a line-edit and a browse button to choose filenames
CPainter1DBase	A base class for painting all items from a data layer (as supported by class derived from here) onto a 1D Canvas
CPainter1DChrom	Painter1D for chromatograms
CPainter1DIonMobility	Painter1D for mobilograms
CPainter1DPeak	Painter1D for spectra
CPainter2DBase	A base class for painting all items from a data layer (as supported by class derived from here) onto a 2D Canvas
CPainter2DChrom	Painter2D for chromatograms
CPainter2DConsensus	Painter2D for ConsensusFeatures
CPainter2DFeature	Painter2D for Features
CPainter2DIdent	Painter2D for Identifications
CPainter2DIonMobility	Painter2D for ion mobilograms
CPainter2DPeak	Painter2D for spectra
CPainterBase	An empty base class with some static convenience functions
►CParam	Management and storage of parameters / INI files
CParamEntry	Parameter entry used to store the actual information inside of a Param entry
►CParamIterator	Forward const iterator for the Param class
CTraceInfo	Struct that captures information on entered / left nodes for ParamIterator
CParamNode	Node inside a Param object which is used to build the internal tree
CParamCTDFile	Serializes a Param class in paramCTD file format. Note: only storing is currently possible
CParamCWLFile	Exports .cwl files
CParamEditor	A GUI for editing or viewing a Param object
CParameterInformation	Struct that captures all information of a command line parameter
CParamJSONFile	Load from JSON (in a Common Workflow Language (CWL) compatible way) into the Param class
CParamValue	Class to hold strings, numeric values, vectors of strings and vectors of numeric values using the stl types
CParamXMLFile	The file pendant of the Param class used to load and store the param datastructure as paramXML (i.e. INI files)
CParquetFile	Shared utilities for reading, writing, and packaging Parquet-based file formats
CParquetFilter	Typed filter builder for parquet-backed datasets
CParquetFilterBuilder	Fluent builder for ParquetFilter objects
CParquetWriteConfig	Configuration for Parquet file writing
►CPeak1D	A 1-dimensional raw data point or peak
CIntensityLess
CMZLess	Comparator by m/z position
CPositionLess	Comparator by position. As this class has dimension 1, this is basically an alias for MZLess
►CPeak2D	A 2-dimensional raw data point or peak
CIntensityLess
CMZLess	Comparator by m/z position
CPositionLess	Comparator by position. Lexicographical comparison (first RT then m/z) is done
CRTLess	Comparator by RT position
CPeakAlignment	Make a PeakAlignment of two PeakSpectra
CPeakCandidate	A small structure to hold peak candidates
CPeakFileOptions	Options for loading files containing peak data
CPeakGroup	Class 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
CPeakGroupScoring	Scoring 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
CPeakIndex	Index of a peak or feature
►CPeakIntegrator	Compute the area, background and shape metrics of a peak
CPeakArea
CPeakBackground
CPeakShapeMetrics
►CPeakMapExtractor	Extract raw mz/RT/IM peak clouds for targeted OpenSWATH coordinates
CExtractedPeakMap	One extracted targeted peak map
CPeakPickerChromatogram	The PeakPickerChromatogram finds peaks a single chromatogram
►CPeakPickerHiRes	This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width
CPeakBoundary	Structure for peak boundaries
CPeakPickerIM	Peak picking algorithm for ion mobility data
CPeakPickerIterative	This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data)
►CPeakPickerMobilogram	The PeakPickerMobilogram finds peaks a single mobilogram
CPeakPositions	Struct to hold peak positions
CPeakSpectrumCompareFunctor	Base class for compare functors of spectra, that return a similarity value for two spectra
CPeakTypeEstimator	Estimates if the data of a spectrum is raw data or peak data
CPeakWidthEstimator	Rough estimation of the peak width at m/z
CPEFFCustomKeyDef	Represents a custom key definition from the PEFF header
CPEFFDatabaseMetadata	Metadata from a PEFF database header section
CPEFFDisulfideBond	Represents a disulfide bond annotation in PEFF
CPEFFEntry	Represents a single entry in a PEFF file with all annotations
CPEFFFile	This class serves for reading and writing PEFF (PSI Extended FASTA Format) files
CPEFFModification	Represents a PEFF modification annotation
CPEFFProcessedRegion	Represents a PEFF processed region (signal peptide, transit peptide, etc.)
CPEFFVariantComplex	Represents a complex PEFF variant (insertion, deletion, or substitution of multiple amino acids)
CPEFFVariantSimple	Represents a simple PEFF variant (single amino acid substitution)
CPepNovoInfile
CPepNovoOutfile	Representation of a PepNovo output file
CPeptDeepCCSInference	Inference engine for PeptDeep collisional cross section prediction
CPeptDeepMS2Inference	Inference engine for PeptDeep MS2 Fragment Intensity prediction
CPeptDeepRTInference
►CPeptideAndProteinQuant	Helper class for peptide and protein quantification based on feature data annotated with IDs
CFileLabelHash
CPeptideData	Quantitative and associated data for a peptide
CProteinData	Quantitative and associated data for a protein
CStatistics	Statistics for processing summary
CPeptideEvidence	Representation of a peptide evidence
►CPeptideHit	Represents a single spectrum match (candidate) for a specific tandem mass spectrum (MS/MS)
CPeakAnnotation	Contains annotations of a peak
CPepXMLAnalysisResult	Analysis Result (containing search engine / prophet results)
CRankLess	Lesser predicate for scores of hits
CScoreLess	Lesser predicate for scores of hits
CScoreMore	Greater predicate for scores of hits
CSequenceChargeEqual	Equality functor for PeptideHit based on sequence and charge
CSequenceChargeHash	Hash functor for PeptideHit based on sequence and charge
CSequenceLessComparator	Lesser predicate for (modified) sequence of hits
CPeptideHitVisualizer	Class that displays all meta information for PeptideHit objects
CPeptideIdentification	Represents the set of candidates (SpectrumMatches) identified for a single precursor spectrum
CPeptideIdentificationList	Container for peptide identifications from multiple spectra
CPeptideIdentificationVisualizer	Class that displays all meta information for PeptideIdentification objects
CPeptideIndexing	Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds target/decoy information
CPeptideMass	QC metric annotating the OBSERVED neutral mass of a peptide from the precursor m/z (precursor_mz - proton_mass)*charge, NOT the theoretical sequence mass
CPeptideProteinResolution	Resolves shared peptides based on protein scores
CPeptidoformInferenceConfig	Configuration for peptidoform inference
►CPepXMLFile	Used to load and store PepXML files
CAminoAcidModification
CPepXMLFileMascot	Used to load Mascot PepXML files
CPercolator	In-process Percolator: semi-supervised target/decoy rescoring with q-values + PEPs
►CPercolatorFeatureSetHelper	Percolator feature set and integration helper
Clq_PeptideEvidence	For accession dependent sorting of PeptideEvidences
Clq_ProteinHit	For accession dependent sorting of ProteinHits
CPercolatorInfile	Class for storing Percolator tab-delimited input files
CPercolatorModel	Trained Percolator model: averaged SVM weights in raw feature space
CPercolatorOutfile	Class for reading Percolator tab-delimited output files
CPickerPoolShared
CPipEchoAlgorithm	Match-between-runs feature grouping via the PIP-ECHO algorithm
CPlainMSDataWritingConsumer	Consumer class that writes MS data to disk using the mzML format
CPlot1DCanvas	Canvas for visualization of one or several spectra
CPlot1DGoToDialog	Simple goto/set visible area dialog for exact placement of the viewing window
CPlot1DWidget	Widget for visualization of several spectra
CPlot2DCanvas	Canvas for 2D-visualization of peak map, feature map and consensus map data
CPlot2DGoToDialog	GoTo dialog used to zoom to a m/z and retention time range or to a feature
CPlot2DWidget	Widget for 2D-visualization of peak map and feature map data
CPlot3DCanvas	Canvas for 3D-visualization of peak map data
CPlot3DOpenGLCanvas	OpenGL Canvas for 3D-visualization of map data
CPlot3DWidget	Widget for 3D-visualization of map data
CPlotCanvas	Base class for visualization canvas classes
CPlotWidget	Base class for spectrum widgets
CPoseClusteringAffineSuperimposer	A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation
CPoseClusteringShiftSuperimposer	A superimposer that uses a voting scheme, also known as pose clustering, to find a good shift transformation
CPpmTrait
CPrecisionWrapper	Wrapper class to implement output with appropriate precision. See precisionWrapper()
CPrecursor	Precursor meta information
CPrecursorCorrection	This class provides methods for precursor correction
CPrecursorMassComparator	Strict-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
►CPrecursorPurity	Precursor purity or noise estimation
CPurityScores
CPrecursorVisualizer	Class that displays all meta information for Precursor objects
CProbablePhosphoSites
CProduct	Product meta information
CProductVisualizer	Class that displays all meta information for Product objects
►CProForma	ProForma v2 peptidoform notation parser and data structures
CAdductIon	Adduct ion specification for charge state
CAmbiguousRegion	Ambiguous amino acid region
CConversionIssue	Description of a conversion issue from Peptidoform to AASequence
CCrossLinkGroup	Cross-link group connecting sites across chains
CCvAccession	Controlled vocabulary accession for a modification
CFormulaTag	Chemical formula with optional charge
CGlobalModification	Global modification applied to specific locations
CGlycanComposition	Glycan composition specification
CInfoTag	Info tag for arbitrary text annotations
CIsotopeReplacement	Isotope replacement for stable isotope labeling
CLabel	Label for cross-links, branches, or ambiguous grouping
CLabileModification	Labile modification that may be lost during fragmentation
CMassDelta	Mass delta modification with optional source hint
CModification	A modification with one or more alternative tags
CModifiedRange	Modified sequence range with shared modifications
CNamedMod	Named modification with optional CV prefix hint
CParseError	Structured parse error with context for ProForma parsing
CPeptidoform	A single peptidoform (one peptide chain)
CPeptidoformIon	A peptidoform ion (one or more chains with optional charge)
CPositionConstraint	Position constraint specifying allowed residues for a modification
CSequenceElement	A single amino acid with its modifications
CUnlocalisedMod	Unlocalised modification with optional occurrence count
►CProgressLogger	Base class for all classes that want to report their progress
CProgressLoggerImpl	This class represents an actual implementation of a logger
►CProSEAlgorithm	Fragment-index-based peptide database search algorithm (experimental)
CAnnotatedHit_	Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space
CCalibrationResult_	Result of a calibration pass
CDecoyStrategy_	Resolved decoy handling for one concrete input database
CMultiFileSearchResult	Multi-file search result bundle
CRunStatistics	Per-run identification statistics for the end-of-search report
CSearchContext	Prepared per-database state shared across multiple spectrum files
CSearchResult	Comprehensive search result including modification analysis
CSharedSearchStats	Configuration, database and fragment-index facts shared across all input files of one ProSE invocation
CProteaseDB	Database for enzymes that digest proteins (proteases)
CProteaseDigestion	Class for the enzymatic digestion of proteins represented as AASequence or String
CProteinGroupArrowExport	Export protein group data to Apache Arrow format following QPX pg schema
CProteinGroupSchema	Schema for protein group (indistinguishable group) results table
►CProteinHit	Representation of a protein hit
CProteinHitAccessionHash	Hash of a ProteinHit based on its accession only!
CProteinHitPtrAccessionHash
CScoreLess	Lesser predicate for scores of hits
CScoreMore	Greater predicate for scores of hits
CProteinHitVisualizer	Class that displays all meta information for ProteinHit objects
►CProteinIdentification	Representation of a protein identification run
CProteinGroup	Bundles multiple (e.g. indistinguishable) proteins in a group
CSearchParameters	Search parameters of the DB search
CProteinIdentificationArrowIO	Import and export ProteinIdentification data to/from Apache Arrow format
CProteinIdentificationVisualizer	Class that displays all meta information for ProteinIdentification objects
►CProteinModificationSummary	Map a protein position to all observed modifications and associated statistics
CStatistics	Basic modification statistic
CProteinSchema	Schema for protein identification results table
CProtXMLFile	Used to load (storing not supported, yet) ProtXML files
CPScore	Implementation of the PScore PSM scoring algorithm
CPSMArrowIO	Read and write OpenMS identification data as a parquet bundle (.idparquet)
►CPSMExplainedIonCurrent
CStatistics	Structure for storing results: average and variance over all PSMs
CPSMSchema	Schema for peptide-spectrum match (PSM) results table
CPTMXMLFile	Used to load and store PTMXML files
CPythonInfo	Detect Python and retrieve information
CQApplicationTOPP	Extension to the QApplication for running TOPPs GUI tools
►CQCBase	This class serves as an abstract base class for all QC classes
CSpectraMap	Map to find a spectrum via its NativeID
►CQcMLFile	File adapter for QcML files used to load and store QcML files
CAttachment	Representation of an attachment
CQualityParameter	Representation of a quality parameter
CQPXFeatureSchema	Schema for QPX feature view (quantms Parquet eXchange format)
CQPXFile	Export PSM (Peptide Spectrum Match) data to Apache Arrow format following QPX PSM schema
CQPXPgSchema	Schema for QPX protein group export (quantms Parquet eXchange format, pg table)
CQPXPSMSchema	Schema for QPX PSM export (quantms Parquet eXchange format, PSM table)
►CQTCluster	A representation of a QT cluster used for feature grouping
CBulkData	Class to store the bulk internal data (neighbors, annotations, etc.)
CElement
CNeighbor
CQTClusterFinder	A variant of QT clustering for the detection of feature groups
CQvalue	Qvalue : contains functions to calculate Qvalues from deconvolution quality score (Qscore) defined in PeakGroupScoring
CRAIICleanup	Exception-safe way of executing arbitrary code at the end of a scope
CRange	Internal structure to store a lower and upper bound of an m/z range
CRangeBase	Base class for a simple range with minimum and maximum
CRangeIntensity
CRangeManager	Handles the management of a multidimensional range, e.g. RangeMZ and RangeIntensity for spectra
CRangeManagerContainer
CRangeMobility
CRangeMZ
CRangeRT
CRangeStats	Struct representing the statistics about a set of values
CRangeStatsType	Origin and name of a statistic
CRankScaler	Scales each peak by ranking the peaks per spectrum and assigning intensity according to rank
►CReactionMonitoringTransition	This class stores a SRM/MRM transition
CNameLess	Comparator by name
CProductMZLess	Comparator by Product ion MZ
CRecentFilesMenu	Manages recent files opened by the user and provides a QMenu to go with it
CRegularSwathFileConsumer	In-memory implementation of FullSwathFileConsumer
CRescoreInput	Input to domain-agnostic Percolator::rescore
CRescoreOutput	Output from Percolator::rescore. Aligned 1:1 with RescoreInput::features
CResidue	Representation of an amino acid residue
CResidueDB	OpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called
CResidueModification	Representation of a modification on an amino acid residue
CRibonucleotide	Representation of a ribonucleotide (modified or unmodified)
CRibonucleotideDataProvider	Interface for providing Ribonucleotide data to RibonucleotideDB
CRibonucleotideDB	Database of ribonucleotides (modified and unmodified)
CRibonucleotideEntry	Holds a Ribonucleotide together with optional ambiguity codes
CRibonucleotideTSVDataProvider	Loads Ribonucleotide data from a tab-separated values (TSV) file
CRichPeak2D	A 2-dimensional raw data point or peak with meta information
CRNaseDB	Database for enzymes that digest RNA (RNases)
CRNaseDigestion	Class for the enzymatic digestion of RNAs
CRTAlignment	Take the original retention time before map alignment and use the alignment's trafoXML for calculation of the new alignment retention times
CRWrapper	R-Wrapper Class
CSample	Meta information about the sample
CSampleVisualizer	Class that displays all meta information of sample objects
CSaveImageDialog	Dialog for saving an image
CSavitzkyGolayFilter	Computes the Savitzky-Golay filter coefficients using QR decomposition
CScanWindow	Scan window description
CScanWindowVisualizer	Class that displays all meta information for ScanWindow objects
►CScores	Utility class for score type handling in identification and quantification workflows
CMaps_	Holds the static score type lookup maps (thread-safe via C++11 function-local static)
CScoreToTgtDecLabelPairs
CSearchEngineBase	Base class for TOPP search-engine adapters
CSearchParamsSchema	Schema for search engine parameters and settings table
CSeedListGenerator	Generate seed lists for feature detection
CSequenceCoverage	Compute sequence coverage of a protein by peptide sequences
CSequestInfile
CSequestOutfile	Representation of a Sequest output file
CSignalProvider	Signal mechanism (by deriving from QObject) for classes which are not allowed to have signals themselves
►CSignalToNoiseEstimator	This class represents the abstract base class of a signal to noise estimator
CGaussianEstimate	Protected struct to store parameters my, sigma for a Gaussian distribution
CSignalToNoiseEstimatorMeanIterative	Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities
CSignalToNoiseEstimatorMedian	Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based)
►CSignalToNoiseEstimatorMedianRapid	Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based)
CNoiseEstimator	Class to compute the noise value at a given position
CSignalToNoiseOpenMS	An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS
CSimpleOpenMSSpectraFactory	A factory method that returns two ISpectrumAccess implementations
►CSimpleSearchEngineAlgorithm	Minimal in-memory peptide-spectrum search engine
CAnnotatedHit_	Compact internal record for one scored peptide candidate against one spectrum
►CSimpleSVM	Simple interface to support vector machines for classification and regression (via LIBSVM)
CPrediction	SVM/SVR prediction result
►CSimpleTSGXLMS	Generates theoretical spectra for cross-linked peptides
CLossIndex
CSimplePeak	A simple struct to represent peaks with mz and charge and sort them easily
CSimplePeakComparator	Comparator to sort SimplePeaks by mz
CSingleLinkage	SingleLinkage ClusterMethod
CSiriusExportAlgorithm	Algorithm class behind the SiriusExport tool: writes a SIRIUS .ms input file from MS data and (optionally) a featureXML
►CSiriusFragmentAnnotation
CSiriusTargetDecoySpectra	SiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from SIRIUS)
►CSiriusMSFile	Writes a SIRIUS .ms file from an MSExperiment, optionally enriched with feature/adduct/formula annotations
CAccessionInfo	Source-file accession metadata of the input mzML, captured for the mzTab-M MS_RUN section
CCompoundInfo	Per-compound metadata accumulated while writing the .ms file
CSoftware	Description of the software used for processing
CSoftwareVisualizer	Class that displays all meta information for Software objects
CSourceFile	Description of a file location, used to store the origin of (meta) data
CSourceFileVisualizer	Class that displays all meta information for SourceFile objects
CSpecArrayFile	File adapter for SpecArray (.pepList) files
►CSpectraIDViewTab	Tabular visualization / selection of identified spectra
CSelfResizingTableView_
CSpectralDeconvolution	FLASHDeconv algorithm: ultrafast mass deconvolution algorithm for top down mass spectrometry dataset From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps: i) decharging and select candidate masses - speed up via binning ii) collecting isotopes from the candidate masses and deisotope - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups)
CSpectralMatch	One library-search match record: the observed spectrum, the matching DB spectrum, the score, and the metabolite metadata copied from the hit
CSpectralMatchScoreComparator	Strict-weak ordering on SpectralMatch by hyperscore (descending — top-scoring match comes first when sorted)
CSpectraLongSchema	Schema for spectra in long (one row per peak) format
►CSpectraMerger	Offers spectra merging and averaging algorithms to increase the quality of a spectrum
CSpectraDistance_
CSpectraSemiWideSchema	Schema for spectra in semi-wide (one row per spectrum, list columns for peaks) format
CSpectraSTSimilarityScore	Similarity score of SpectraST
CSpectraTreeTab	Hierarchical visualization and selection of spectra
CSpectrumAccessOpenMS	An implementation of the OpenSWATH Spectrum Access interface using OpenMS
CSpectrumAccessOpenMSCached	OpenSwath::ISpectrumAccess implementation backed by an on-disk OpenMS::CachedmzML cache
CSpectrumAccessOpenMSInMemory	OpenSwath::ISpectrumAccess implementation that holds the complete spectrum / chromatogram payload in memory
CSpectrumAccessQuadMZTransforming	A transforming m/z wrapper around spectrum access using a quadratic equation
CSpectrumAccessSqMass	OpenSwath::ISpectrumAccess implementation backed by an sqMass (SQLite) spectrum store
CSpectrumAccessTransforming	An abstract base class implementing a transforming wrapper around spectrum access
CSpectrumAddition	The SpectrumAddition is used to add up individual spectra
CSpectrumAlignment	Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) alignment if absolute tolerances are given. Scoring function is the m/z distance between peaks. Intensity does not play a role!
CSpectrumAlignmentDialog	Lets the user select two spectra and set the parameters for the spectrum alignment
CSpectrumAlignmentScore	Similarity score via spectra alignment
CSpectrumAnnotator	Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options
CSpectrumCheapDPCorr	SpectrumCheapDPCorr calculates an optimal alignment on stick spectra
CSpectrumCount
CSpectrumLookup	Helper class for looking up spectra based on different attributes
►CSpectrumMetaDataLookup	Helper class for looking up spectrum meta data
CSpectrumMetaData	Meta data of a spectrum
CSpectrumNativeIDParser	Parser for extracting scan numbers from spectrum native IDs
CSpectrumPrecursorComparator	SpectrumPrecursorComparator compares just the parent mass of two spectra
CSpectrumRangeManager	Advanced range manager for MS spectra with separate ranges for each MS level
CSpectrumSettings	Representation of 1D spectrum settings
CSpectrumSettingsVisualizer	Class that displays all meta information for SpectrumSettings objects
►CSplineInterpolatedPeaks	Data structure for spline interpolation of MS1 spectra and chromatograms
CNavigator	Iterator class for access of spline packages
CSplinePackage	Fundamental data structure for SplineInterpolatedPeaks
CSqliteConnector	File adapter for Sqlite files
►CSqMassFile	Read and write mass-spectrometry data in the on-disk sqMass (SQLite) format
CSqMassConfig	Compression / metadata options used when reading or writing an sqMass file
CSqrtScaler	Scales the intensity of peaks to the sqrt
CStablePairFinder	This class implements a pair finding algorithm for consensus features
CStatsCounter	Simple counting struct, for non-numerical occurrences of meta-values
CSteinScottImproveScore	Similarity score based of Stein & Scott
►CStopWatch	This class is used to determine the current process' CPU (user and/or kernel) and wall time
CTimeDiff_
CStreamHandler	Provides a central class to register globally used output streams. Currently supported streams are
CStringListUtils	Utilities operating on lists of Strings
CStringUtilsHelper
CSummary	Summary of fitting results
CSVOutStream	Stream class for writing to comma/tab/...-separated values files
CSwathFile	File adapter for Swath files
CSwathMapMassCorrection	A class containing correction functions for Swath MS maps
CSwathWindowLoader
►CSysInfo	Some functions to get system information
CMemUsage	A convenience class to report either absolute or delta (between two timepoints) RAM usage
CTableView	A better QTable for TOPPView, which supports exporting to TSV and conveniently adding data to cells and headers
CTagger	Calculate sequence tags from m/z values
CTargetedDataFileLoader
►CTargetedExperiment	A description of a targeted experiment containing precursor and production ions
CSummaryStatistics
►CTargetedSpectraExtractor	This class filters, annotates, picks, and scores spectra (e.g., taken from a DDA experiment) based on a target list
CBinnedSpectrumComparator	Comparator implementation that scores query spectra against the library using BinnedSpectralContrastAngle on pre-binned spectra
CComparator	Abstract base interface for spectral-library scoring strategies consumed by matchSpectrum
CMatch
CTextFile
►CTheoreticalSpectrumGenerationDialog	Dialog which allows to enter an AA or NA sequence and generates a theoretical spectrum for it
CCheckBox	Struct for all information about a check box of an ion
CTheoreticalSpectrumGenerator	Generates theoretical spectra for peptides with various options
►CTheoreticalSpectrumGeneratorXLMS
CLossIndex
CThresholdMower	Removes all peaks below an intensity threshold
►CTIC	Total Ion Current (TIC) as a QC metric
CResult	Computed Total Ion Current trace plus stability counters
CTMTEighteenPlexQuantitationMethod	TMT 18plex quantitation to be used with the IsobaricQuantitation
CTMTElevenPlexQuantitationMethod	TMT 11plex quantitation to be used with the IsobaricQuantitation
CTMTSixPlexQuantitationMethod	TMT 6plex quantitation to be used with the IsobaricQuantitation
CTMTSixteenPlexQuantitationMethod	TMT 16plex quantitation to be used with the IsobaricQuantitation
CTMTTenPlexQuantitationMethod	TMT 10plex quantitation to be used with the IsobaricQuantitation
CTMTThirtyFivePlexQuantitationMethod	TMT 35plex quantitation to be used for the IsobaricQuantitation. Parameters of this class are: Name Type Default Restrictions Description channel_126_description string   Description for the content of the 126 channel. channel_127N_description string   Description for the content of the 127N channel. channel_127C_description string   Description for the content of the 127C channel. channel_127D_description string   Description for the content of the 127D channel. channel_128N_description string   Description for the content of the 128N channel. channel_128C_description string   Description for the content of the 128C channel. channel_128ND_description string   Description for the content of the 128ND channel. channel_128CD_description string   Description for the content of the 128CD channel. channel_129N_description string   Description for the content of the 129N channel. channel_129C_description string   Description for the content of the 129C channel. channel_129ND_description string   Description for the content of the 129ND channel. channel_129CD_description string   Description for the content of the 129CD channel. channel_130N_description string   Description for the content of the 130N channel. channel_130C_description string   Description for the content of the 130C channel. channel_130ND_description string   Description for the content of the 130ND channel. channel_130CD_description string   Description for the content of the 130CD channel. channel_131N_description string   Description for the content of the 131N channel. channel_131C_description string   Description for the content of the 131C channel. channel_131ND_description string   Description for the content of the 131ND channel. channel_131CD_description string   Description for the content of the 131CD channel. channel_132N_description string   Description for the content of the 132N channel. channel_132C_description string   Description for the content of the 132C channel. channel_132ND_description string   Description for the content of the 132ND channel. channel_132CD_description string   Description for the content of the 132CD channel. channel_133N_description string   Description for the content of the 133N channel. channel_133C_description string   Description for the content of the 133C channel. channel_133ND_description string   Description for the content of the 133ND channel. channel_133CD_description string   Description for the content of the 133CD channel. channel_134N_description string   Description for the content of the 134N channel. channel_134C_description string   Description for the content of the 134C channel. channel_134ND_description string   Description for the content of the 134ND channel. channel_134CD_description string   Description for the content of the 134CD channel. channel_135N_description string   Description for the content of the 135N channel. channel_135ND_description string   Description for the content of the 135ND channel. channel_135CD_description string   Description for the content of the 135CD channel. reference_channel string 126 126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134C, 134ND, 134CD, 135N, 135ND, 135CD The reference channel (126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134C, 134ND, 134CD, 135N, 135ND, 135CD). correction_matrix string list [NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA]   Ignored for TMT 35-plex (identity matrix is always used). Isotope correction is not yet supported for this method. Note: If a section name is documented, the documentation is displayed as tooltip. Advanced parameter names are italic.
CTMTThirtyTwoPlexQuantitationMethod	TMT 32plex quantitation to be used for the IsobaricQuantitation. Parameters of this class are: Name Type Default Restrictions Description channel_126_description string   Description for the content of the 126 channel. channel_127N_description string   Description for the content of the 127N channel. channel_127C_description string   Description for the content of the 127C channel. channel_127D_description string   Description for the content of the 127D channel. channel_128N_description string   Description for the content of the 128N channel. channel_128C_description string   Description for the content of the 128C channel. channel_128ND_description string   Description for the content of the 128ND channel. channel_128CD_description string   Description for the content of the 128CD channel. channel_129N_description string   Description for the content of the 129N channel. channel_129C_description string   Description for the content of the 129C channel. channel_129ND_description string   Description for the content of the 129ND channel. channel_129CD_description string   Description for the content of the 129CD channel. channel_130N_description string   Description for the content of the 130N channel. channel_130C_description string   Description for the content of the 130C channel. channel_130ND_description string   Description for the content of the 130ND channel. channel_130CD_description string   Description for the content of the 130CD channel. channel_131N_description string   Description for the content of the 131N channel. channel_131C_description string   Description for the content of the 131C channel. channel_131ND_description string   Description for the content of the 131ND channel. channel_131CD_description string   Description for the content of the 131CD channel. channel_132N_description string   Description for the content of the 132N channel. channel_132C_description string   Description for the content of the 132C channel. channel_132ND_description string   Description for the content of the 132ND channel. channel_132CD_description string   Description for the content of the 132CD channel. channel_133N_description string   Description for the content of the 133N channel. channel_133C_description string   Description for the content of the 133C channel. channel_133ND_description string   Description for the content of the 133ND channel. channel_133CD_description string   Description for the content of the 133CD channel. channel_134N_description string   Description for the content of the 134N channel. channel_134ND_description string   Description for the content of the 134ND channel. channel_134CD_description string   Description for the content of the 134CD channel. channel_135ND_description string   Description for the content of the 135ND channel. reference_channel string 126 126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134ND, 134CD, 135ND The reference channel (126, 127N, 127C, 127D, 128N, 128C, 128ND, 128CD, 129N, 129C, 129ND, 129CD, 130N, 130C, 130ND, 130CD, 131N, 131C, 131ND, 131CD, 132N, 132C, 132ND, 132CD, 133N, 133C, 133ND, 133CD, 134N, 134ND, 134CD, 135ND). correction_matrix string list [NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA, NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA/NA]   Ignored for TMT 32-plex (identity matrix is always used). Isotope correction is not yet supported for this method. Note: If a section name is documented, the documentation is displayed as tooltip. Advanced parameter names are italic.
CToolDescriptionFile	File adapter for ToolDescriptor files
CToolHandler
CToolInfo	A struct to pass information about the tool as one parameter
CToolsDialog	TOPP tool selection dialog
CTopDownIsobaricQuantification	Isobaric quantification for Top down proteomics. The report ion ratios from multiple MS2 are merged when their precursor masses belong to the same deconvolved features (MassFeature instances)
CTOPPASBase	Main window of the TOPPAS tool
CTOPPASEdge	An edge representing a data flow in TOPPAS
CTOPPASInputFileDialog	Dialog which allows to specify an input file
CTOPPASInputFileListVertex	A vertex representing an input file list
CTOPPASInputFilesDialog	Dialog which allows to specify a list of input files
CTOPPASIOMappingDialog	Dialog which allows to configure the input/output parameter mapping of an edge
CTOPPASMergerVertex	A special vertex that allows to merge several inputs
CTOPPASOutputFileListVertex	A vertex representing an output file list
CTOPPASOutputFilesDialog	Dialog which allows to specify the directory for the output files
CTOPPASOutputFolderVertex	A vertex representing an output folder
CTOPPASOutputVertex	A vertex representing an output, either folder or files(s)
CTOPPASResource	Represents a data resource for TOPPAS workflows
CTOPPASResources	A dictionary mapping string keys to lists of TOPPASResource objects
►CTOPPASScene
CTOPPProcess	Stores the information for a TOPP process
CTOPPASSplitterVertex	A special vertex that allows to split a list of inputs
CTOPPASToolConfigDialog	TOPP tool configuration dialog
►CTOPPASToolVertex	A vertex representing a TOPP tool
CIOInfo	Stores the information for input/output files/lists
CTOPPASTreeView	Tree view implementation for the list of TOPP tools
►CTOPPASVertex	The base class of the different vertex classes
CTOPPASFilenames
CVertexRoundPackage	Info for one edge and round, to be passed to next node
CTOPPASVertexNameDialog	Dialog which allows to change the name of an input/output vertex
CTOPPASWidget	Widget visualizing and allowing to edit TOPP pipelines
CTOPPBase	Base class for TOPP applications
CTOPPExternalToolBase	Base class for TOPP tools that invoke an external executable
►CTOPPOpenSwathBase	Shared TOPPBase scaffolding for OpenSWATH-family CLI tools (currently OpenSwathWorkflow)
CCalibrationResult	Per-run outputs of the RT / m/z / IM calibration step
CTOPPViewBase	Main window of TOPPView tool
►CTOPPViewMenu	The file menu items for TOPPView
CActionRequirement_
CTOPPViewOpenDialog	Dataset opening options for TOPPView
►CTraceFitter	Abstract base class for fitting an RT-shape model to one or more mass traces
CGenericFunctor	Generic LM functor with a raw-pointer interface, used to keep Eigen out of the public API
CModelData	Helper bundle passed to functors so they can read both the traces and the weighting flag
CTraMLFile	File adapter for HUPO PSI TraML files
►CTransformationDescription	Generic description of a coordinate transformation
CTransformationStatistics	Summary statistics before/after applying the transformation. For deviations before/after transformation, the percentiles 100, 99, 95, 90, 75, 50, 25 are returned
►CTransformationModel	Base class for transformation models
CDataPoint	Coordinate pair (with optional annotation)
CTransformationModelBSpline	B-spline (non-linear) model for transformations
►CTransformationModelInterpolated	Interpolation model for transformations
CInterpolator	The class defines a generic interpolation technique used in the TransformationModelInterpolated
CTransformationModelLinear	Linear model for transformations
CTransformationModelLowess	Lowess (non-linear) model for transformations
CTransformationXMLFile	Used to load and store TransformationXML files
CTransitionGroupOpenMS	An implementation of the OpenSWATH Transition Group Access interface using OpenMS
►CTransitionListEvidenceFilter	Prefilter transition-library precursors by quick raw-data evidence
CPrecursorEvidence	Compact evidence summary for one target precursor candidate
CResult	Result of filtering one run against one transition experiment
CTransitionParquetFile	Read OpenSwath Parquet library input (.oswpq) into LightTargetedExperiment
►CTransitionPQPFile	This class supports reading and writing of PQP files
CPQPSqlQueryInfo	Holds information about a PQP SQL query and optional column availability
►CTransitionTSVFile
CTSVTransition	Internal structure to represent a transition
CTreeView	A better QTreeWidget for TOPPView, which supports header context menu and conveniently adding/getting headers names
►CTriqlerFile	File adapter for Triqler files
CAggregatedConsensusInfo
CTriqlerLine_
CTVControllerBase	Base behavior for different visualizaton modules in TOPPView
CTVDIATreeTabController	Behavior of TOPPView in spectra view mode
CTVIdentificationViewController	Behavior of TOPPView in identification mode
CTVSpectraViewController	Behavior of TOPPView in spectra view mode
CTVToolDiscovery	Scans for tools and generates a param for each asynchronously
CUnimodXMLDataProvider	Loads ResidueModification data from a Unimod XML file
CUnimodXMLFile	Used to load XML files from unimod.org files
CUniProtEntry	A single <entry> from a UniProtKB XML file, in a parser-neutral form
CUniProtFeature	A single <feature> element from a UniProtKB XML entry
CUniProtXMLFile	Reads UniProtKB XML protein databases (.xml or transparently .xml.gz)
CUniqueIdGenerator	A generator for unique ids
CUniqueIdIndexer	A base class for containers with elements derived from UniqueIdInterface. This adds functionality to convert a unique id into an index into the container
CUniqueIdInterface	A base class defining a common interface for all classes having a unique id
CUnnormalizedComparator	Exception thrown if clustering is attempted without a normalized compare functor
CUpdateCheck	Helper Functions to perform an update query to the OpenMS REST server
CUSI	Utility class for handling Universal Spectrum Identifiers (USI)
CValueTrait	Trait for MatchedIterator to find pairs with a certain distance, which is computed directly on the value_type of the container
CVecLowPrecision
►CVersionInfo	Version information class
CVersionDetails	Parsed semver-style version: major.minor.patch with an optional pre-release identifier
CWindowMower	Retains the highest peaks in a sliding or jumping window
►CWNetMatcher	Pairwise point-set matching using Wasserstein optimal transport
CMatchResult	Result of a pairwise matching
CXFDRAlgorithm	Calculates false discovery rate estimates on crosslink identifications
►CXICParquetFile	Reader for OpenSWATH chromatogram Parquet files (.xic)
CXICAnalyte	Analyte metadata container
CXICChromatogram	Lightweight chromatogram container for XIC parquet rows
CXICRunInfo	Unique run information (run_id, source_file)
CXICSchema	Schema for extracted ion chromatogram (XIC) data table
►CXIMParquetFile	Reader for OpenSWATH mobilogram Parquet files (.xim)
CXIMAnalyte	Analyte metadata container
CXIMMobilogram	Lightweight mobilogram container for XIM parquet rows
CXIMRunInfo	Unique run information (run_id, source_file)
CXIMSchema	Schema for extracted ion mobilogram (XIM) data table
CXIPMParquetConsumer	Writes targeted mz/RT/IM peak maps to a Parquet file (.xipm)
►CXIPMParquetFile	Reader for extracted ion peak-map Parquet files (.xipm)
CXIPMPeakMap
CXIPMRunInfo
CXIPMSchema	Schema for extracted ion peak-map (XIPM) data table
CXMassFile
CXMLValidator	Validator for XML files
CXQuestResultXMLFile	Used to load and store xQuest result files
CXQuestScores	An implementation of the scores for cross-link identification from the xQuest algorithm (O. Rinner et al., 2008, "Identification of cross-linked peptides from large sequence databases")
CXTandemInfile	XTandem input file
CXTandemXMLFile	Used to load XTandemXML files
CZhangSimilarityScore	Similarity score of Zhang
CZipArchiveFile	Small libzip-based helpers for working with ZIP archives
CZipIfstream	Streaming reader for the single non-directory entry of a ZIP archive
CZipInputStream	Implements the BinInputStream class of the xerces-c library in order to read ZIP compressed XML files
CZipRandomAccessFile	Factory to obtain an Arrow RandomAccessFile for a named entry inside a zip archive (or a direct file when the archive path is a directory)
CZlibCompression	Compresses and uncompresses arbitrary byte buffers using zlib
RIsFCMap
RLessThanComparable
RIsPeptideOrProteinIdentification
RIsFeatureOrConsensusMap
RIsNotIdentificationVector	Concept to exclude std::vector of identification types (used to disambiguate template overloads)
►NOpenSwath
►NScoring	Scoring functions used by MRMScoring
Cpair_hash	Simple hash function for Scoring::pos2D
CXCorrArrayType
CCSVWriter
CDataMatrix
CIDataFrameWriter
CIFeature
CIMRMFeature
CISignalToNoise
CISpectrumAccess	The interface of a mass spectrometry experiment
CITransitionGroup
CLightCompound
CLightModification
CLightProtein
CLightTargetedExperiment
CLightTransition
Cmean_and_stddev	Functor to compute the mean and stddev of sequence using the std::foreach algorithm
CMockFeature	Mock object implementing IFeature
CMockMRMFeature	Mock object implementing IMRMFeature
CMockSignalToNoise	Mock object implementing ISignalToNoise
CMockTransitionGroup	Mock object implementing ITransitionGroup
CMRMScoring	This class implements different scores for peaks found in SRM/MRM
COSBinaryDataArray	The datastructures used by the OpenSwath interfaces
COSChromatogram	A single chromatogram
COSChromatogramMeta	Identifying information for a chromatogram
COSSpectrum	The structure that captures the generation of a peak list (including the underlying acquisitions)
►COSSpectrumMeta	Identifying information for a spectrum
CRTLess	Comparator for the retention time
CPeptide
CProtein
CSwathMap	Data structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2
CSwathQC	Quality Control function for OpenSwath
CTargetedExperiment
CTransitionFlags	Packed boolean flags for transitions Reduces memory from 4 bytes (4 separate bools) to 1 byte
CTransitionHelper
NOrt
NSQLite
►Nstd	STL namespace
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
NUi