| ►NEigen | |
| CSparseVector | |
| ►Neol_bspline | |
| CBSpline | |
| ►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 | |
| ►NOpenMS | Main OpenMS namespace |
| ►NArrowIOHelpers | Public helpers for writing and concatenating Arrow tables to Parquet files |
| ►CParquetColumn | One column for withColumns(), built without Arrow types |
| CScore | An entry of a SCORE_LIST row: the struct of the QPX additional_scores (QPXPSMSchema::additionalScoresType()) |
| CStructField | |
| CStructValue | |
| CParquetTableStream | A Parquet file written table by table: the merged QPX psm file of a multi-file search, appended run by run while the next run is searched |
| CQPXRunFileNameKeys | MetaInfo indices qpxPsmRunFileName() consults, resolved once |
| ►NArrowSchemaValidation | Utilities for validating Arrow table schemas against expected definitions |
| CValidationResult | Result of schema validation containing validity flag and error messages |
| ►NDataArrays | |
| CFloatDataArray | Float data array class |
| CIntegerDataArray | Integer data array class |
| CStringDataArray | Std::string data array class |
| ►NDetail | |
| CMetaKeyGetter | |
| ►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 |
| ►NIdentificationDataInternal | |
| CAdductCompare | Comparator for adducts |
| CAppliedProcessingStep | |
| CDBSearchParam | Parameters specific to a database search step |
| ►CIDDataContainer | A collection of identification records, unique and ordered by the key formed from the members KeyMembers |
| CCompare | |
| CIdentifiedCompound | |
| CIdentifiedMolecule | Variant type holding Peptide/Compound/Oligo references and convenience functions |
| CIdentifiedSequence | Representation of an identified sequence (peptide or oligonucleotide) |
| ►CIDSequencedContainer | Records kept in the order they were added, unique by the member KeyMember |
| CConstOrderedView | Lookup of records by key |
| Cnth_index | |
| COrderedView | |
| 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, rescoring) |
| 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 | Initialization procedures |
| ►NClassTest | Namespace for class tests |
| CPrecisionWrapped | Stream wrapper printing a floating point value with full precision |
| ►NPASEFHillCentroider | |
| CCentroid | One centroided peak produced by hill detection |
| CParams | |
| 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 |
| CFidHandler | Read-only fid File handler for XMass Analysis |
| CFractionGroupAbundanceData | Parsed parallel arrays carrying protein quantities at (fraction_group, label) grain |
| ►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 | XML event handler for imzML 1.1.0 files, extending OpenMS MzMLHandler |
| CArrayMeta | |
| CCvEntry | A cvParam captured inside a referenceableParamGroup |
| CSpecIMS | |
| CImzMLWriter | Writer for imzML 1.1.0 files (.imzML + companion .ibd) |
| CIndexedMzMLHandler | A low-level class to read an indexedmzML file |
| CIntensityIteratorWrapper | An iterator wrapper to access peak intensities instead of the peak itself |
| CLinearResampling | Shared linear resampling implementation without parameter or progress handling |
| CLooper | |
| CLooper< grid_size, grid_size, EvalResult, Tuple, TupleTypes... > | |
| CLooper< param_index, grid_size, EvalResult, Tuple, FirstTupleType, TupleTypes... > | |
| 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 |
| CParamBuffers_ | Reused attribute buffers for cvParam/userParam elements (avoids allocating per element) |
| 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 |
| COpenMSOSInfo | Snapshot of the runtime operating system: name, version, and pointer-width architecture |
| CParamXMLHandler | XML Handler for Param files |
| CPTMXMLHandler | Handler that is used for parsing PTMXML data |
| CQuantChannel | One label of a quantification unit and the sample it resolves to in the design |
| CQuantificationUnits | |
| CQuantUnit | One QPX quantification unit: exactly one OpenMS experimental-design fraction group |
| 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 |
| CSpectrumIdentification | |
| CSqliteConnectorFriend | |
| CStringManager | Strict UTF-8/UTF-16 conversion and ASCII helpers for XML handlers |
| CThermoPrecursor | One precursor of an MSn scan as reconstructed by ThermoRawFileMetadata::precursors() |
| ►CThermoRawFileMetadata | Resolve the precursor hierarchy from bridge metadata without fetching peaks. Keeps isolation targets distinct from selected ions, and retains SPS selections and supplemental reactions. The filter fallback follows ThermoRawFileParser |
| CState | What is retained per seen scan to resolve later scans' parents |
| ►CThermoRawScanReader | Scan-by-scan conversion of a Thermo RAW file into OpenMS spectra (private) |
| CAccessor | Converts scans independently of each other (random access) |
| CScanInfo | Scan header values needed to select scans before converting them |
| CScanRecord | Everything of a scan that depends on the scans before it (see header()) |
| CThermoRawScanSelection | Scan selection by ThermoRawFile::Options, shared by load(), transform() and OnDiscThermoRawExperiment |
| CThermoReaction | One reaction (isolation plus activation step) of a Thermo MSn scan event |
| CThermoScan | The per-scan metadata needed to reconstruct the precursor hierarchy |
| CThermoTrailerEntry | One "trailer extra" label/value pair of a Thermo scan |
| CThermoTrailerIndex | Per-file trailer label lookup |
| CToolDescription | |
| CToolDescriptionInternal | What the TOPP tool registry knows about one tool |
| 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 |
| ►CXMLAttributes | Non-owning attribute view for an XML start-element callback |
| ►CNativeStore | Reusable UTF-8 attribute storage of an XML parser adapter |
| CEntry | |
| CXMLFile | Base class for loading and storing XML files via libxml2, 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 |
| ►NLogger | Log streams |
| CLogSinkGuard | RAII guard that temporarily removes an attached stream from a LogStream and re-inserts it on scope exit |
| ►CLogStream | Log Stream Class |
| CGuardedRemoval | A destination that LogSinkGuard removed from a global stream (see removeForGuard_()), restored with its prefix and id |
| ►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 |
| CLogVoidify | Turns a whole message into a void expression, which OPENMS_LOG_DEBUG skips when debug output is disabled |
| ►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 | Estimates posterior error probabilities (PEPs) of peptide-spectrum matches from search engine scores |
| CQuadraticRegression | Estimates model parameters for a quadratic equation |
| CRandomShuffler | Portable random shuffle with a reproducible, platform-independent random sequence |
| 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 |
| ►NMS1LabelState | The label state of an identification in MS1-labeled (SILAC, Dimethyl, ...) data |
| CKeys | The registry indices of the three keys, resolved once for a loop over many hits |
| ►NQPXIdentity | Opaque QPX row identities (feature_id, psm_id, pg_id) |
| CFloat32 | A float32 composite component |
| CNull | A composite component that is JSON null (a null column value) |
| ►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 |
| ►NUniPEFFEntries | The annotations of the PEFF entries that UniPEFF writes for a UniProtKB entry: its canonical entry and the entries of its reconstructed isoforms |
| CDisulfidePairItem | |
| CEntryAnnotations | |
| CIsoformEntry | One reconstructed isoform, ready for emission as its own PEFF entry |
| CIsoformScopedTracker | |
| CModResItem | |
| CPreparedEntry | |
| CProcessedItem | |
| CPtmEntry | |
| CVariantComplexItem | |
| CVariantSimpleItem | |
| CAA | |
| CAAIndex | Representation of selected AAIndex properties |
| ►CAALevelLocalization | |
| CLocalizedXL | |
| ►CAASequence | |
| 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 |
| 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 |
| 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 |
| ►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 |
| CBasicProteinInferenceAlgorithm | Simple protein inference by aggregation of per-peptide PSM scores |
| CBayesianProteinInferenceAlgorithm | Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental) |
| CBedRModFile | File adapter for bedRMod v2 files |
| 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 |
| CPeakRef | One peak's hill assignment, recorded by linkScanToHills_ (the hills are built from these afterwards) |
| CPeptideFeature | Aggregated properties of a detected peptide feature |
| CScanPrep | Part of linking one scan that depends on that scan alone (filter, intensity order, m/z and IM bins) |
| 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 ( |
| CBzip2InputStream | Byte stream for reading 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 | |
| CChromatogramIndex | Positions of chromatograms by native ID (see OpenSwathWorkflow::scoreAllChromatograms_()) |
| ►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 |
| ►CClassFDR | FDR within classes of PSMs (e.g. modified vs. unmodified, isoform-specific vs. canonical) |
| CClassSummary | Per-class summary |
| 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 |
| CCellIndexHash | Hash of a cell index |
| CClusterProxyKD | Proxy for a (potential) cluster |
| CCmpHypothesesByScore | |
| CCmpMassTraceByMZ | |
| CCoarseIsotopePatternGenerator | Isotope pattern generator for coarse isotope distributions |
| ►CCoIsolationDetector | Finds precursors co-isolated with the selected one in the isolation window of an MS2 spectrum |
| CCoIsolated | Co-isolated precursor |
| ►CColorizer | Color and style the fonts shown on cout/cerr (or other streams) |
| CColorWithUndo_ | |
| 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 | Internal source selecting bzip2, ZIP or gzip decompression by file magic |
| 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 | |
| ►CConsensusElutionWidth | Re-quantifies linked features at one elution width per precursor |
| CStats | |
| ►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) |
| ►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 |
| ►CConsensusMapNormalizerAlgorithmRTLocal | Normalizes the maps of a consensus map by a per-map offset that may vary with retention time |
| CSettings | Settings of the normalization (all of them at least 1) |
| 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 |
| ►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 |
| ►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 |
| CDataProcessingUtils | Queries on data-processing provenance records |
| 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 |
| CDecompressingInputStream | Decompresses gzip or bzip2 data read from another InputStream, e.g. a remote object |
| 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 |
| ►CDIAQCMetrics | Quality metrics for data-independent acquisition (DIA) runs, per run and per isolation window |
| CGroupStatistics | |
| COptions | Options |
| CRunMetrics | Metrics of one run, including its isolation windows |
| CSpectrumRecord | The per-spectrum data the metrics need |
| CWindowMetrics | Metrics of one isolation window |
| CDIAScoring | Scoring of an spectrum at the peak apex of an chromatographic elution peak |
| 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 |
| 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 |
| CElementLess_ | Orders the elements of a formula independently of where the Element objects are in memory |
| ►CEntrapmentEvaluation | Measures the false discovery proportion (FDP) of identifications with an entrapment database |
| CResult | Result for one class at one q-value threshold and level |
| ►CEnzymaticDigestion | Class for the enzymatic digestion of sequences |
| CSimpleCleavageRule | A cleavage rule of the form "(?<=[KRX])" or "(?<=[KRX])(?!P)", as most enzymes of Enzymes.xml spell theirs |
| 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 | One row of the MS file section: one quantitative channel of one MS file |
| CSampleSection | The sample section: one named row per sample, one column per factor |
| CExperimentalDesignFile | Load an experimental design from a TSV file |
| CExperimentalSettings | Description of the experimental settings |
| 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 |
| CFAIMSHelper | Helper functions for FAIMS data |
| CFAIMSSwathMapGroup | One FAIMS compensation-voltage group represented as ordinary OpenSWATH maps |
| ►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 |
| 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 | |
| CFeatureUniqueIds | Checks that every feature of a map has a valid unique id that no other feature of the map shares |
| 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) |
| 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 |
| CFileNameUtils | Filename-only format recognition and extension manipulation |
| ►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 |
| 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 |
| CCandidateBlock_ | One (precursor charge, isotope error) block of a queryPeaks() call |
| CEntryLength | |
| CEntryWord | Peptide-mass mode: the two halves of a packed prefix entry, held in the parallel arrays entry_words_ and entry_lengths_ (5 bytes per entry; see the design note at entry_words_). Both leave their member uninitialised on purpose, as Fragment does: build() resizes the arrays and writes every element in parallel |
| CFragment | One entry in the fragment index |
| CHit | |
| CIonOffsets | Precomputed ion-type mass offsets (from Residue::getInternalTo*Ion formulas) |
| CModShift_ | |
| CModSlot | A candidate modification slot for a specific peptide |
| ►CPeptide | Compact descriptor of a peptide instance held by the FragmentIndex |
| CSpan | |
| CPeptidoformRendering_ | Rendering classes of the configured modifications, for samePeptidoform_() (peptide:deduplicate) |
| CRemovedOccurrence | A protein occurrence of an indexed peptidoform that peptide:deduplicate removed from the index |
| 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 |
| ►CFragmentIonLikelihoodModel | Per-run likelihood model of fragment ion presence, intensity rank and mass error, learned from confident PSMs |
| CFeatures | Features of one PSM |
| CIon | One theoretical ion after matching |
| CPeakLists | Compact peak lists of the spectra of one run: per peak only its m/z and its intensity-rank bin |
| ►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 | |
| ►CGlycanStructure | A rooted glycan tree, with the reducing-end monosaccharide at node zero |
| CNode | A monosaccharide and its linkage towards the reducing end |
| 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 |
| 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 | |
| CGzipIfstream | Decompresses files which are compressed in the gzip format (*.gzip) |
| CGzipInputStream | Byte stream for reading 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 |
| CHit | |
| CHPLC | Representation of a HPLC experiment |
| CHTTPInputSource | Source for reading XML files from HTTP, HTTPS and FTP URLs, with libcurl |
| 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 |
| CUnresolvedIdentifications | What reduceToOnePerSpectrum() found and did. All counts are over the input list |
| ►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 |
| ►CIDFreeMassErrorEstimator | Identification-free precursor and fragment mass-precision estimator |
| CDiagnostics | Estimator support/accounting counters |
| CFragmentFingerprint | |
| CGaussianUniformFit | |
| CParameters | Tunable estimator thresholds. Defaults match the validated prideQC implementation |
| CPrecursorCluster | |
| CResult | Current precision estimates, optional tolerance suggestions and diagnostics |
| CRobustError | Robust summary of pairwise repeated-measurement differences |
| CToleranceSuggestion | Precision-derived search-tolerance suggestion for one unit system |
| ►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 |
| CIMDataArrayUtils | Interpret ion-mobility array metadata independently of frame conversion |
| CIMDataConverter | This class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models |
| CIMSExperimentRandomAccess | Random access to the spectra and chromatograms of an MS run that stays on disk |
| 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 |
| CAuxArray | Index entry for one auxiliary (non-m/z, non-intensity) external array |
| CImzMLSpectrumRules | Per-spectrum rules shared by every imzML access path (in-memory, streaming, metadata-only, index-only and OnDiscImzMLExperiment), so they cannot drift apart |
| 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 |
| 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 |
| CInputStream | Internal byte stream shared by the XML compression adapters |
| 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 |
| ►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) |
| 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) |
| 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 | Utility class for computing the isoelectric point (pI) and net charge of peptides |
| 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) |
| 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 |
| ►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 |
| CLowessSmoothing | LOWESS (locally weighted scatterplot smoothing) |
| ►CLPWrapper | A wrapper class for the linear programming (LP) solver |
| 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 FeatureMap and 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) |
| 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 | |
| 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 |
| CMetaInfo | A Type-Name-Value tuple class |
| CMetaInfoDescription | Description of the meta data arrays of MSSpectrum |
| 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 |
| 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 | |
| CModificationDefinitionIO | Collect, serialise and re-register the definitions of tool-defined modifications |
| 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 |
| CMS1LabeledFAIMS | Keep FAIMS acquisitions separate while retaining physical run/channel columns |
| ►CMS1LabeledRatioQuantifier | Channel ratios of MS1-labeled (SILAC, Dimethyl, ...) data, aggregated as medians of ratios |
| CChannelRatio | One channel ratio of one peptide or protein group, at (fraction group, channel) grain |
| CMS1LabeledSpectra | Load MS1 peaks and scan metadata for the MS1 labeling workflow |
| 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 |
| CEncodedChromatograms | Rows prepared by encodeChromatogram(), to be appended with consumeEncodedChromatograms() |
| 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_ | |
| ►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 |
| CBlacklistEntry | Entry of blacklist_ (spectrum index and peak index in exp_centroided_) and a value read from or written to it |
| CBlacklistOwner | Who blacklisted a peak: the first and the last filtered peak that reserved it (the same if only one did) |
| CBlacklistOwnerRecord | Owners of a peak of blacklist_ that more than one filtered peak reserved (indices in filtered_peaks_) |
| CBlacklistWriter | Filtered peak that blacklisted a peak, and the mass trace of its pattern it reserved the peak for |
| CDeuteriumLabel | Deuterium label (setDeuteriumLabels()), or the deuterium labels of a peptide |
| CMultiplexFilteringCentroided | Filters centroided data for peak patterns |
| CMultiplexFilteringProfile | Filters centroided and profile data for peak patterns |
| CMultiplexIsotopicPeakPattern | Data structure for pattern of isotopic peaks |
| ►CMultiplexResolverAlgorithm | Completes peptide multiplets and resolves quant/ID conflicts within them |
| COwnerCheckCounts_ | What the owner-aware blacklist check found in resolve(), for its log |
| 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 |
| CMzPeakFile | MzPeak file reader and writer (HUPO-PSI mzPeak: Parquet tables in a ZIP archive or a directory) |
| 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 | |
| CNuXLFragmentAdductRegistry | |
| ►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 |
| CNuXLIndexedAdductList | Fragment adducts of one cross-linked nucleotide with their registry ids and ranks |
| ►CNuXLIonLikelihood | Self-trained fragment ion likelihood for protein-nucleic acid cross-links (after ProSE's ion priors) |
| CEvidence | Matched ions of a hit and of its noise hypothesis |
| CFeatures | Features of one hit |
| COutcomes | Matched ions of one hypothesis (hit or its reversed sequence) |
| CNuXLLogFactorialTable | Logfactorial with the exact same summation sequence as the loop it replaces |
| 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 |
| CPrecursorAdduct | Sum formula and precursor adduct (nucleotide composition) returned by findPrecursorAdduct |
| CNuXLModificationsGenerator | Enumerator of precursor-adduct masses for NuXL cross-link searches |
| CNuXLParameterParsing | |
| CNuXLPrecursorIndex | Sorted precursor masses (same order as the multimap they are created from) with a bucket index |
| CNuXLProteinReport | Protein report |
| CNuXLReport | Create PSM report |
| CNuXLReportRow | Struct to hold a single report line |
| CNuXLReportRowHeader | Create header line |
| ►CNuXLRescoring | Helpers of NuXL:rescoring: the delta score, the training hits of the self-trained ion likelihood, the native score |
| CScoreGap | Best score of the hits of a spectrum and the best score of a different (unmodified) peptide sequence |
| ►CNuXLScoringScratch | Per-thread buffers (no heap allocations per candidate) and memoized match odds |
| CFirstPassEntry | |
| ►CNuXLSiteLocalization | Localizes a cross-link by the chemistry of the cross-linker, within the residues the fragment ions support |
| CProteinTermini | Protein N- and C-terminal peptides of a digest, sorted, to look them up with isProteinNTerminal and isProteinCTerminal |
| CSite | Result of localizing one cross-link |
| CNuXLSpectrumIndex | Search-time lookup structures for the OpenNuXL database search |
| 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 | Owns the ONNX Runtime session of one model file, for the predictors built on it |
| 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 |
| ►COpenSwathLibraryIDNormalizer | Establish and validate canonical precursor/transition identifiers for OpenSWATH libraries |
| CSourceIDMapping | Source-to-canonical precursor provenance captured during library loading |
| ►COpenSwathLibraryPreparation | Shared spectral-library preparation helper for OpenSWATH-family workflows |
| CAssayGeneratorParameters | |
| CDecoyGeneratorParameters | |
| CLibraryStats | |
| CPredictedLibraryParameters | |
| 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 |
| ►COSWParquetFile | Read and update OpenSWATH results in an OSWPQ directory or archive |
| CInferenceResults | Results for one inference level/context, including an explicitly empty result |
| 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 |
| ►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 |
| 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) |
| CParquetDiffResult | Outcome of a table comparison |
| CParquetDiffSettings | Settings for ParquetTableComparator |
| 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 |
| CParquetTableComparator | Primary-key-aware, order-insensitive, tolerant comparison of Parquet tables |
| 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 |
| CPeptDeepLibraryPrecursor | Input precursor for native PeptDeep spectral-library prediction |
| ►CPeptDeepLibraryPredictor | Convert peptide precursors into an OpenSWATH assay batch using native PeptDeep ONNX models |
| CConfig | |
| CPeptDeepMS2Inference | Inference engine for PeptDeep MS2 Fragment Intensity prediction |
| ►CPeptDeepRescoring | Annotates PSMs with rescoring features derived from PeptDeep predictions |
| CPSMRows | |
| CRow | Row of the flat PSM work list built by annotate() |
| CPeptDeepRTInference | Predicts peptide retention times with the PeptDeep RT model (peptdeep_rt_dynamic.onnx) |
| ►CPeptideAndProteinQuant | Helper class for peptide and protein quantification based on feature data annotated with IDs |
| CDesignCell | Experimental-design coordinates of one (basename, label) cell |
| 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 |
| CPeptideIdentification | Represents the set of candidates (SpectrumMatches) identified for a single precursor spectrum |
| CPeptideIdentificationList | Container for peptide identifications from multiple spectra |
| 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 |
| CCappedTrainingInfo | The out-of-fold capped training of the last rescore() (subset_mode 'out_of_fold', 'out_of_fold_avg' or 'learning_curve', active) |
| ►CPercolatorFeatureSetHelper | Percolator feature set and integration helper |
| 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 |
| ►CPercolatorReset | Percolator-RESET: semi-supervised rescoring with FDR control at the peptide (stem) level |
| CAuditFeature | |
| CInput | Rows: one per PSM (all hits of all spectra), in any order |
| COptions | |
| COutput | |
| CStem | One considered or dropped stem |
| 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 |
| 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 | |
| CProbablePhosphoSites | |
| CProduct | Product meta information |
| ►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 |
| CCandidatePoolStats_ | Running summary of the complete candidate pool of one spectrum |
| CCoIsolatedPSM_ | The PSM of a precursor co-isolated with the selected one (chimeric:enabled), until its residual spectrum is built |
| CDecoyStrategy_ | Resolved decoy handling for one concrete input database |
| CDeisotopingSettings_ | MS2 deisotoping rule of preprocessSpectra_() |
| CLocalFragmentEvidence_ | Local fragment evidence of one candidate (annotate:local_fragment_evidence) |
| CMergedResult | The pooled evaluation of a multi-file search (the ProSE tool's -out_merged) |
| CMultiFileSearchResult | Multi-file search result bundle |
| ►CMzRecalibration_ | An m/z error model of a run (calibration:recalibrate), fitted to the calibration PSMs and subtracted from the spectra before the main search |
| CAtRT | |
| CChunk | |
| CPercolatorRescoring | Outcome of the Percolator rescoring of one search run (see rescoreWithPercolator() and the parameter 'rescore') |
| CPercolatorTraining | Options of Percolator's training for the rescoring (the parameters 'rescoring:...'; the defaults are ProSE's training: all PSMs, 10 iterations) |
| CProteinMapping_ | The protein occurrences of the sequences of a search's hits (peptide:protein_mapping = index) |
| CReuseRun_ | Rescore_reuse: a run that trains models: its index in the search (the random halves depend on it) and its PSMs |
| 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 |
| CSpectraCounts_ | |
| 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 |
| ►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 |
| ►CProteinModificationSummary | Map a protein position to all observed modifications and associated statistics |
| CStatistics | Basic modification statistic |
| CProteinReport | |
| CProteinRunReferences | Checks that every peptide identification references an existing protein identification run |
| 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 |
| ►CQCBase | This class serves as an abstract base class for all QC classes |
| CSpectraMap | Map to find a spectrum via its NativeID |
| ►CQPXCollectionExport | Whole-collection preflight for the QPX Parquet export (-out_qpx) |
| CTransaction | Scope guard that leaves no partial QPX collection behind |
| ►CQPXDatasetExport | The parts of a QPX dataset that a search engine adds to the views of QPXFile |
| CMzView | |
| CPeakFilter | The peak filter of the mz view: the top most intense peaks per window Th (top 0: all peaks), and the annotated ones (keptPeaks()) |
| CProvenanceStep | A step of the processing (a row of the provenance view, provenanceView()) |
| CRun | A run of the dataset (a row of the run view, runView()) |
| CRunSample | A sample of a run (the run view's samples) |
| CSample | A sample of the dataset (a row of the sample view, sampleView()) |
| CView | A view of the dataset for writeDataset() |
| 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) |
| ►CQPXValueValidation | Stateful value and primary-key validator for QPX Arrow tables |
| CResult | Result of validating one table or streaming batch |
| ►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 | |
| 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 |
| ►CRegionLevelLocalization | |
| CUnlocalizedXL | |
| CRegularExpression | Compiled Perl-compatible regular expression, including named capture groups |
| CRegularSwathFileConsumer | In-memory implementation of FullSwathFileConsumer |
| CRescoreInput | Input to domain-agnostic Percolator::rescore |
| CRescoreOutput | Output from Percolator::rescore. Aligned 1:1 with the rows of the RescoreInput (RescoreInput::rowCount()) |
| 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 |
| CRNADeisotoper | |
| CRNADirectedDeconvolution | NASE-specific selection of precursor hypotheses and competing envelope evidence |
| ►CRNAPrecursorCorrector | Correct MS2 precursor m/z from FLASH RNA envelopes in the parent MS1 scan |
| CResult | |
| CRNaseDB | Database for enzymes that digest RNA (RNases) |
| ►CRNaseDigestion | Class for the enzymatic digestion of RNAs |
| CCleavageSensitiveModGroups | Cleavage-sensitive modification groups split by cleavage direction |
| CDigestionProduct | Detailed digestion product including sequence and parent coordinates |
| 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 |
| CS3InputSource | Source for reading XML files from Amazon S3 (s3://bucket/key), with Arrow's S3 filesystem |
| CSample | Meta information about the sample |
| CSavitzkyGolayFilter | Computes the Savitzky-Golay filter coefficients using QR decomposition |
| CScanWindow | Scan window description |
| ►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 |
| ►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) |
| CStatistics | What an estimation determined besides the S/N values |
| ►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 |
| CSignalToNoiseEstimatorMedianSettings | The parameters of SignalToNoiseEstimatorMedian as plain values; the defaults are those of its parameters |
| 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 |
| ►CSiriusFragmentAnnotation | |
| CSiriusTargetDecoySpectra | SiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from SIRIUS) |
| ►CSiriusMSFile | Writes a SIRIUS |
| 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 |
| CSoftware | Description of the software used for processing |
| CSourceFile | Description of a file location, used to store the origin of (meta) data |
| CSpecArrayFile | File adapter for SpecArray (.pepList) files |
| ►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) |
| CBitsets | Value-semantic holder for the implementation's bitsets |
| CCandidateSelectionContext | Read-only construction settings; spectrum peaks and candidate bins remain private |
| 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 |
| ►CSpectrumAccessOnDisc | OpenSwath::ISpectrumAccess on an on-disc experiment (e.g. OnDiscThermoRawExperiment or OnDiscMSExperiment) |
| CView | |
| 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! |
| 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 |
| ►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 |
| 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 |
| CSystemSettings | Per-user OpenMS configuration: the OpenMS.ini system parameters and the home, temporary and database directories derived from them |
| 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 | |
| CTempDir | A uniquely named temporary directory, removed when the object is destroyed |
| ►CTempFiles | Temporary files that live until the process exits |
| CRegistry_ | Holds the allocated filenames and deletes the files at program exit |
| CTextFile | |
| ►CTheoreticalGlycanSpectrumGenerator | Generate positive-mode glycan and singly glycosylated peptide fragments |
| CFragment | One interpretation of a fragment, including its charge and attachment |
| COptions | Generation settings; all size and charge ranges are inclusive |
| CPeptideRetention | Independent choices of glycan material retained by a backbone 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 /0.31/9.09 /0.02/0.32, NA/NA /NA/0.78 /NA/9.41 /NA/0.33, NA/NA /0.93/NA /0.35/8.63 /0.01/0.27, NA/0.00 /0.82/0.65 /NA/8.13 /NA/0.26, 0.00/NA /1.47/NA /0.34/6.91 /0.00/0.15, 0.00/0.00 /1.46/1.28 /NA/6.86 /NA/0.15, 0.13/NA /2.59/NA /0.32/6.07 /0.1/0.09, 0.13/0.00 /2.41/0.27 /NA/5.58 /NA/0.10, 0.04/NA /3.10/NA /0.42/4.82 /0.02/0.06, 0.03/0.00 /2.78/0.63 /NA/4.57 /NA/0.12, 0.08/NA /3.90/NA /0.47/3.57 /0.00/0.04, 0.15/0.01 /3.58/0.72 /NA/1.80 /NA/0.00, 0.11/NA /4.55/NA /0.43/1.86 /0.00/0.00, 0.07/0.01 /3.14/0.73 /NA/3.40 /NA/0.03, 0.22/NA /4.96/NA /0.34/1.03 /0.00/NA, 0.30/0.03 /5.49/0.62 /NA/1.14 /NA/NA, 0.14/NA /5.81/NA /0.31/NA /NA/NA, 0.19/0.02 /5.42/0.36 /NA/NA /NA/NA] |
| Correction matrix for the non-deuterated TMTpro channels in percent, taken from the Thermo TMTpro datasheet (identical to the TMT 16-/18-plex correction matrix). Replace these with the values from your reagent lot's Certificate of Analysis for accurate quantitation;Please provide 18 entries (rows), one per non-deuterated channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N), separated by comma, where each entry contains 8 values in the following format: <-2C13>/<-N15-C13>/<-C13>/<-N15>/<+N15>/<+C13>/<+N15+C13>/<+2C13> e.g. one row may look like this: 'NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26'. You may use whitespaces at your leisure to ease reading. |
| correction_matrix_deuterated |
string list | [NA/NA/NA/NA/0.82/NA/NA/0.30/8.71/0.33/0.00/0.00/0.26/0.00, NA/NA/0.00/NA/1.13/NA/0.59/NA/8.61/0.24/NA/NA/0.28/0.00, 0.00/NA/NA/NA/1.47/0.70/NA/0.30/7.55/0.27/0.00/0.00/0.21/0.00, 0.00/NA/0.00/0.00/1.97/0.91/0.61/NA/7.58/0.35/NA/NA/0.19/0.00, 0.00/0.00/NA/NA/1.39/1.37/NA/0.31/6.02/0.50/0.00/0.00/0.08/0.00, 0.00/0.08/0.00/0.00/1.77/1.50/0.59/NA/6.10/0.54/NA/NA/0.09/0.00, 0.00/0.10/NA/NA/1.44/2.18/NA/0.33/5.49/0.40/0.00/0.00/0.06/0.00, 0.01/0.19/0.00/0.00/1.47/2.23/0.61/NA/5.48/0.41/NA/NA/0.05/0.00, 0.02/0.02/NA/NA/2.52/2.61/NA/0.98/4.14/1.15/0.01/0.00/0.02/0.01, 0.02/0.02/0.00/0.00/3.52/1.70/0.60/NA/4.19/0.85/NA/NA/0.01/0.00, 0.00/0.03/NA/NA/1.00/3.35/NA/1.00/3.07/0.94/0.00/0.00/0.00/0.00, 0.00/0.01/0.00/0.00/0.89/2.48/0.63/NA/3.14/0.51/NA/NA/0.00/0.00, 0.01/0.01/NA/NA/1.86/3.73/NA/0.31/1.63/0.79/0.00/0.00/0.00/0.00, 0.02/0.10/0.00/0.00/1.66/3.76/0.22/NA/1.73/0.31/NA/NA/0.00/0.00, 0.03/0.23/NA/NA/1.53/4.94/NA/0.31/0.95/0.31/0.00/0.00/NA/0.00, 0.04/0.23/0.00/0.00/1.54/4.85/0.21/NA/1.03/0.32/NA/NA/NA/0.00, 0.07/0.07/NA/NA/1.90/6.75/NA/0.31/NA/0.22/NA/0.00/NA/NA] |
| Correction matrix for the deuterated TMTpro channels in percent, derived from the Thermo TMTpro deuterated reagent set Certificate of Analysis (products A40000817 and A40000818). Replace these with the values from your reagent lot's Certificate of Analysis for accurate quantitation;Please provide 17 entries (rows), one per deuterated channel (127D, 128ND, 128CD, 129ND, 129CD, 130ND, 130CD, 131ND, 131CD, 132ND, 132CD, 133ND, 133CD, 134ND, 134CD, 135ND, 135CD), separated by comma, where each entry contains 14 values in the following format: <-C13-H2>/<-2C13>/<-N15-H2>/<-C13-N15>/<-H2>/<-C13>/<-N15>/<+N15>/<+C13>/<+H2>/<+N15+C13>/<+N15+H2>/<+2C13>/<+C13+H2> e.g. one row may look like this: 'NA/NA/NA/NA /0.82/NA/NA /0.30/8.71/0.33 /0.00/0.00/0.26/0.00'. You may use whitespaces at your leisure to ease reading. |
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 / 0.31/9.09 / 0.02/0.32, NA/NA / NA/0.78 / NA/9.41 / NA/0.33, NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27, NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26, 0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15, 0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15, 0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09, 0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10, 0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06, 0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12, 0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04, 0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00, 0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00, 0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03, 0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA, 0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA] |
| Correction matrix for the non-deuterated TMTpro channels in percent, taken from the Thermo TMTpro datasheet (identical to the TMT 16-/18-plex correction matrix). Replace these with the values from your reagent lot's Certificate of Analysis for accurate quantitation;Please provide 16 entries (rows), one per non-deuterated channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N), separated by comma, where each entry contains 8 values in the following format: <-2C13>/<-N15-C13>/<-C13>/<-N15>/<+N15>/<+C13>/<+N15+C13>/<+2C13> e.g. one row may look like this: 'NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26'. You may use whitespaces at your leisure to ease reading. |
| correction_matrix_deuterated |
string list | [NA/NA/NA/NA/0.82/NA/NA/0.30/8.71/0.33/0.00/0.00/0.26/0.00, NA/NA/0.00/NA/1.13/NA/0.59/NA/8.61/0.24/NA/NA/0.28/0.00, 0.00/NA/NA/NA/1.47/0.70/NA/0.30/7.55/0.27/0.00/0.00/0.21/0.00, 0.00/NA/0.00/0.00/1.97/0.91/0.61/NA/7.58/0.35/NA/NA/0.19/0.00, 0.00/0.00/NA/NA/1.39/1.37/NA/0.31/6.02/0.50/0.00/0.00/0.08/0.00, 0.00/0.08/0.00/0.00/1.77/1.50/0.59/NA/6.10/0.54/NA/NA/0.09/0.00, 0.00/0.10/NA/NA/1.44/2.18/NA/0.33/5.49/0.40/0.00/0.00/0.06/0.00, 0.01/0.19/0.00/0.00/1.47/2.23/0.61/NA/5.48/0.41/NA/NA/0.05/0.00, 0.02/0.02/NA/NA/2.52/2.61/NA/0.98/4.14/1.15/0.01/0.00/0.02/0.01, 0.02/0.02/0.00/0.00/3.52/1.70/0.60/NA/4.19/0.85/NA/NA/0.01/0.00, 0.00/0.03/NA/NA/1.00/3.35/NA/1.00/3.07/0.94/0.00/0.00/0.00/0.00, 0.00/0.01/0.00/0.00/0.89/2.48/0.63/NA/3.14/0.51/NA/NA/0.00/0.00, 0.01/0.01/NA/NA/1.86/3.73/NA/0.31/1.63/0.79/0.00/0.00/0.00/0.00, 0.02/0.10/0.00/0.00/1.66/3.76/0.22/NA/1.73/0.31/NA/NA/0.00/0.00, 0.03/0.23/NA/NA/1.53/4.94/NA/0.31/0.95/0.31/0.00/0.00/NA/0.00, 0.04/0.23/0.00/0.00/1.54/4.85/0.21/NA/1.03/0.32/NA/NA/NA/0.00] |
| Correction matrix for the deuterated TMTpro channels in percent, derived from the Thermo TMTpro deuterated reagent set Certificate of Analysis (product A40000817). Replace these with the values from your reagent lot's Certificate of Analysis for accurate quantitation;Please provide 16 entries (rows), one per deuterated channel (127D, 128ND, 128CD, 129ND, 129CD, 130ND, 130CD, 131ND, 131CD, 132ND, 132CD, 133ND, 133CD, 134ND, 134CD, 135ND), separated by comma, where each entry contains 14 values in the following format: <-C13-H2>/<-2C13>/<-N15-H2>/<-C13-N15>/<-H2>/<-C13>/<-N15>/<+N15>/<+C13>/<+H2>/<+N15+C13>/<+N15+H2>/<+2C13>/<+C13+H2> e.g. one row may look like this: 'NA/NA/NA/NA /0.82/NA/NA /0.30/8.71/0.33 /0.00/0.00/0.26/0.00'. You may use whitespaces at your leisure to ease reading. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
|
| CToolHandler | Registry of TOPP tools and their TOPPAS categories |
| CToolInfo | Tool metadata shared by parameter-file serializers |
| 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) |
| 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 |
| ►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 |
| CTransformationModelDefaults | Shared transformation-model parameters for alignment algorithms and tools |
| ►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 |
| 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 |
| CUniProtIsoform | One <isoform> definition from <comment type="alternative products"> |
| 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 | Byte stream for reading 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 |
| CZstdCompression | Compresses and uncompresses byte buffers using Zstandard (zstd), optionally combined with the byte-shuffling and dictionary transforms defined for mzML |
| ►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 | |
| ►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 |
| CImmoniumIonsInPeptide | |
| CIterator | |
| CMQEvidence | Builds a MaxQuant Evidence.txt |
| ►CMQExporterHelper | Helper class for common functions and NON trivial values needed for exporting MaxQuant outputs |
| CMQCommonOutputs | |
| CMQMsms | Builds a MaxQuant msms.txt |
| ►CNucleicAcidSearchEngine | |
| CAnnotatedHit | |
| CHasInvalidLength | |
| CPrecursorInfo | |
| CNuXLLinearRescore | |
| CNuXLRTPrediction | |
| CRefVariant | |
| CTOPPFLASHDeconv | |
| CTOPPGNPSExport | |
1.9.8 