| ►NEigen | |
| CMatrix | |
| CSparseVector | |
| ►Neol_bspline | |
| CBSpline | |
| NH5 | |
| NIsoSpec | |
| ►NKDTree | |
| C_Node_base | |
| C_Node | |
| C_Node_compare | |
| C_Bracket_accessor | |
| Calways_true | |
| Csquared_difference | |
| Csquared_difference_counted | |
| ►C_Alloc_base | |
| CNoLeakAlloc | |
| C_Iterator | |
| C_Base_iterator | |
| C_Region | |
| CKDTree | |
| ►Nms | |
| ►Nnumpress | |
| NMSNumpress | |
| ►NOpenMS | Main OpenMS namespace |
| ►NConstants | Mathematical and physical constants namespace |
| NUserParam | |
| ►NDataArrays | |
| CFloatDataArray | Float data array class |
| CIntegerDataArray | Integer data array class |
| CStringDataArray | String data array class |
| Ndetail | |
| ►NDetail | |
| CMetaKeyGetter | |
| NDIAHelpers | |
| ►NException | Exception namespace |
| CUnregisteredParameter | An unregistered parameter was accessed |
| CWrongParameterType | A parameter was accessed with the wrong type |
| CRequiredParameterNotGiven | A required parameter was not given |
| CBaseException | Exception base class |
| CPrecondition | Precondition failed exception |
| CPostcondition | Postcondition failed exception |
| CMissingInformation | Not all required information provided |
| CIndexUnderflow | Int underflow exception |
| CSizeUnderflow | UInt underflow exception |
| CIndexOverflow | Int overflow exception |
| CFailedAPICall | A call to an external library (other than OpenMS) went wrong |
| CInvalidRange | Invalid range exception |
| CInvalidSize | Invalid UInt exception |
| COutOfRange | Out of range exception |
| CInvalidValue | Invalid value exception |
| CInvalidParameter | Exception indicating that an invalid parameter was handed over to an algorithm |
| CConversionError | Invalid conversion exception |
| CIllegalSelfOperation | Illegal self operation exception |
| CNullPointer | Null pointer argument is invalid exception |
| CInvalidIterator | Invalid iterator exception |
| CIncompatibleIterators | Incompatible iterator exception |
| CNotImplemented | Not implemented exception |
| CIllegalTreeOperation | Illegal tree operation exception |
| COutOfMemory | Out of memory exception |
| CBufferOverflow | Buffer overflow exception |
| CDivisionByZero | Division by zero error exception |
| COutOfGrid | Out of grid exception |
| CFileNotFound | File not found exception |
| CFileNotReadable | File not readable exception |
| CFileNotWritable | File not writable exception |
| CFileNameTooLong | Filename is too long to be writable/readable by the filesystem |
| CIOException | General IOException |
| CSqlOperationFailed | SqlOperation failed exception |
| CFileEmpty | File is empty |
| CIllegalPosition | Invalid 3-dimensional position exception |
| CParseError | Parse Error exception |
| CUnableToCreateFile | Unable to create file exception |
| CIllegalArgument | A method or algorithm argument contains illegal values |
| CInternalToolError | A tool or algorithm which was called internally raised an exception |
| CElementNotFound | Element could not be found exception |
| CUnableToFit | Exception used if an error occurred while fitting a model to a given dataset |
| CUnableToCalibrate | Exception used if an error occurred while calibrating a dataset |
| CDepletedIDPool | Exception used if no more unique document ID's can be drawn from ID pool |
| CGlobalExceptionHandler | OpenMS global exception handler |
| NFastLowessSmoothing | LOWESS (locally weighted scatterplot smoothing) |
| ►NGUIHelpers | |
| COverlapDetector | A heuristic: Given a set of levels (rows), try to add items at to topmost row which does not overlap an already placed item in this row (according to its x-coordinate) |
| CGUILock | RAII class to disable the GUI and set a busy cursor and go back to the original state when this class is destroyed |
| ►CColorBrewer | |
| CDistinct | |
| NHelpers | |
| ►NIdentificationDataInternal | |
| CAppliedProcessingStep | |
| CDBSearchParam | Parameters specific to a database search step |
| CIdentifiedCompound | |
| CIdentifiedMolecule | Variant type holding Peptide/Compound/Oligo references and convenience functions |
| CIdentifiedSequence | Representation of an identified sequence (peptide or oligonucleotide) |
| CInputFile | Information about input files that were processed |
| CIteratorWrapper | Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi_index_containers |
| CObservation | Representation of an observation, e.g. a spectrum or feature, in an input data file |
| CAdductCompare | Comparator for adducts |
| CObservationMatch | Representation of a search hit (e.g. peptide-spectrum match) |
| CObservationMatchGroup | : Group of related (co-identified) input matches |
| CParentGroup | : Group of ambiguously identified parent sequences (e.g. protein group) |
| CParentGroupSet | Set of groups of ambiguously identified parent sequences (e.g. results of running a protein inference algorithm) |
| CParentMatch | Meta data for the association between an identified molecule (e.g. peptide) and a parent sequence (e.g. protein) |
| CParentSequence | Representation of a parent sequence that is identified only indirectly (e.g. a protein) |
| CProcessingSoftware | Information about software used for data processing |
| CProcessingStep | Data processing step that is applied to the data (e.g. database search, PEP calculation, filtering, ConsensusID) |
| CScoredProcessingResult | Base class for ID data with scores and processing steps (and meta info) |
| CScoreType | Information about a score type |
| ►Nims | |
| ►CIMSAlphabet | Holds an indexed list of bio-chemical elements |
| 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 | Handles decomposing of non-integer values/masses over a set of non-integer weights with an error allowed |
| CWeights | Represents a set of weights (double values and scaled with a certain precision their integer counterparts) with a quick access |
| ►NInterfaces | |
| CBinaryDataArray | The datastructures used by the OpenSwath interfaces |
| CChromatogramMeta | Identifying information for a chromatogram |
| CChromatogram | A single chromatogram |
| CSpectrumMeta | Identifying information for a spectrum |
| CSpectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
| CIMSDataConsumer | The interface of a consumer of spectra and chromatograms |
| CISpectraReader | The interface of read-access to a list of spectra |
| CIChromatogramsReader | The interface of read-access to a list of chromatograms |
| CISpectraWriter | |
| CIChromatogramsWriter | |
| ►NInternal | Namespace used to hide implementation details from users |
| NClassTest | Namespace for class tests |
| NSqliteHelper | |
| ►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. If not known or not defined, returns (-1.0, false) |
| 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 |
| CMessagePasserFactory | |
| ►CRNPxlFragmentAnnotationHelper | Convenience functions to construct appealing fragment annotation strings and store them as PeptideHit::PeakAnnotation |
| CFragmentAnnotationDetail_ | Single fragment annotation |
| CDIntervalBase | A base class for D-dimensional interval |
| CFileMapping | Maps input/output files to filenames for the external program |
| CMappingParam | Filename mappings for all input/output files |
| CToolDescriptionInternal | ToolDescription Class |
| CToolExternalDetails | |
| CToolDescription | |
| CIntensityIteratorWrapper | An iterator wrapper to access peak intensities instead of the peak itself |
| CAcqusHandler | Read-only acqus File handler for XMass Analysis |
| 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 |
| CFeatureXMLHandler | This class provides Input/Output functionality for feature maps |
| CFidHandler | Read-only fid File handler for XMass Analysis |
| CIndexedMzMLHandler | A low-level class to read an indexedmzML file |
| CMascotXMLHandler | Handler that is used for parsing MascotXML data |
| CMzDataHandler | |
| ►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 |
| ►CMzMLHandler | Handler for mzML file format |
| CChromatogramData | Data necessary to generate a single chromatogram |
| CSpectrumData | Data necessary to generate a single spectrum |
| ►CMzMLHandlerHelper | Helper for mzML file format |
| CBinaryData | Representation for binary data in mzML |
| CMzMLSqliteHandler | Sqlite handler for storing spectra and chromatograms in sqMass format |
| CMzMLSqliteSwathHandler | Sqlite handler for SWATH data sets |
| CMzQuantMLHandler | XML handler for MzQuantMLFile |
| ►CMzXMLHandler | |
| CSpectrumData | Data necessary to generate a single spectrum |
| CParamXMLHandler | XML Handler for Param files |
| CPTMXMLHandler | Handler that is used for parsing PTMXML data |
| CToolDescriptionHandler | XML handler for ToolDescriptionFile |
| CTraMLHandler | XML handler for TraMLFile |
| CUnimodXMLHandler | Handler that is used for parsing XTandemXML data |
| Cshared_xerces_ptr | |
| Cunique_xerces_ptr | |
| CStringManager | |
| ►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 |
| COMSFileLoad | Helper class for loading .oms files (SQLite format) |
| COMSFileStore | Helper class for storing .oms files (SQLite format) |
| CMzDataValidator | Semantically validates MzXML files |
| CMzIdentMLValidator | Semantically validates MzXML files |
| CMzMLValidator | Semantically validates MzXML files |
| CMzQuantMLValidator | Semantically validates MzQuantML files |
| ►CSemanticValidator | Semantically validates XML files using CVMappings and a ControlledVocabulary |
| CCVTerm | Representation of a parsed CV term |
| CTraMLValidator | Semantically validates MzXML files |
| CXMLFile | Base class for loading/storing XML files that have a handler derived from XMLHandler |
| ►CAreaIterator | Forward iterator for an area of peaks in an experiment |
| CParam | |
| COpenMSOSInfo | |
| COpenMSBuildInfo | Struct with some static methods to get informations on the build configuration |
| CFLASHDeconvTabWidget | A multi-tabbed widget for the FLASHDeconvWizard offering setting of parameters, input-file specification and running FLASHDeconv and more |
| CPlot1DPrefDialog | Preferences dialog for Plot1DWidget |
| CPlot2DPrefDialog | Preferences dialog for Plot2DWidget |
| CPlot3DPrefDialog | Preferences dialog for Plot3DWidget |
| CPythonModuleRequirement | |
| CPythonSelector | |
| CSwathTabWidget | A multi-tabbed widget for the SwathWizard offering setting of parameters, input-file specification and running Swath and more |
| CTOPPViewPrefDialog | Preferences dialog for TOPPView |
| CWizardGUILock | RAII class to switch to certain TabWidget, disable the GUI and go back to the orignal Tab when this class is destroyed |
| CArgs | Custom arguments to allow for looping calls |
| CCommand | |
| CFilterList | A widget which shows a list of DataFilter items |
| CInputFileList | A widget shows a list of input files (i.e. existing files on a mounted drive), which allows adding/removing files and supports drag'n'drop from the window manager |
| CListTable | |
| CListEditorDelegate | Internal delegate class |
| CFilterableList | A widget which shows a list of text items, which can be filtered |
| COpenMSLineEdit | Custom QLineEdit which emits a signal when losing focus (such that we can commit its data) |
| CParamEditorDelegate | Internal delegate class for QTreeWidget |
| CParamTree | QTreeWidget that emits a signal whenever a new row is selected |
| ►NLogger | Log streams |
| ►CLogStreamBuf | Stream buffer used by LogStream |
| CLogCacheStruct | Holds a counter of occurrences and an index for the occurrence sequence of the corresponding log message |
| CStreamStruct | Holds a stream that is connected to the LogStream. It also includes the minimum and maximum level at which the LogStream redirects messages to this stream |
| CLogStreamNotifier | |
| CLogStream | Log Stream Class |
| ►NMath | Math namespace |
| 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 |
| 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 |
| CRandomShuffler | |
| CRANSACParam | A simple struct to carry all the parameters required for a RANSAC run |
| 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 |
| CAsymmetricStatistics | Internal class for asymmetric distributions |
| CAveragePosition | Maintain an average position by summing up positions with weights |
| CBasicStatistics | Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation |
| ►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 |
| 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, \( Y(c,x) = c_0 + c_1 x \) |
| CPosteriorErrorProbabilityModel | Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture |
| CQuadraticRegression | |
| ►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> |
| NNNLS | |
| ►NOptimizationFunctions | |
| CPenaltyFactorsIntensity | Class for the penalty factors used during the optimization |
| CPenaltyFactors | Class for the penalty factors used during the optimization |
| ►NSimTypes | |
| CSimProtein | Plain data object holding sequence and abundance information on a single protein |
| CSimRandomNumberGenerator | Wrapper class for random number generators used by the simulation classes |
| NSiriusVersion | |
| ►NStringConversions | |
| CBK_PrecPolicy | |
| NStringUtils | |
| ►NTargetedExperimentHelper | This class stores helper structures that are used in multiple classes of the TargetedExperiment (e.g. ReactionMonitoringTransition and IncludeExcludeTarget) |
| CConfiguration | |
| CCV | |
| CProtein | |
| CRetentionTime | This class stores a retention time structure that is used in TargetedExperiment (representing a TraML file) |
| CPeptideCompound | Base class to represent either a peptide or a compound |
| CCompound | Represents a compound (small molecule) |
| ►CPeptide | Represents a peptide (amino acid sequence) |
| CModification | |
| CContact | |
| CPublication | |
| CInstrument | |
| CPrediction | |
| CInterpretation | Product ion interpretation |
| CTraMLProduct | Represents a product ion |
| NTest | |
| CFeatureDeconvolution | An algorithm to decharge features (i.e. as found by FeatureFinder) |
| CILPDCWrapper | |
| CMetaboliteFeatureDeconvolution | An algorithm to decharge small molecule features (i.e. as found by FeatureFinder) |
| CCompNovoIdentification | Run with CompNovoIdentification |
| ►CCompNovoIdentificationBase | Run with CompNovoIdentificationBase |
| CPermut | Simple class to store permutations and a score |
| CCompNovoIdentificationCID | Run with CompNovoIdentificationCID |
| CCompNovoIonScoring | Run with CompNovoIonScoring |
| ►CCompNovoIonScoringBase | Run with CompNovoIonScoringBase |
| CIonScore | |
| CCompNovoIonScoringCID | Run with CompNovoIonScoringCID |
| CDeNovoAlgorithm | Base class for ion scoring implementation for de novo algorithms |
| CDeNovoIdentification | Base class for de novo identification |
| ►CDeNovoIonScoring | Base class for ion scoring implementation for de novo algorithms |
| CIonScore | IonScore |
| CDeNovoPostScoring | Base class for ion scoring implementation for de novo algorithms |
| CAccurateMassSearchResult | |
| ►CAccurateMassSearchEngine | An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB) |
| CCompareEntryAndMass_ | |
| CMappingEntry_ | |
| CHit | |
| CAA | |
| CIndex | |
| ►CACNode | |
| CDepthHits | Internal struct to steal one bit from depth to use as hit indicator |
| CACSpawn | Spin-off search path through the trie, which can deal with ambiguous AAs and mismatches |
| CACTrieState | |
| CACTrie | An Aho Corasick trie (a set of nodes with suffix links mainly) |
| CProbablePhosphoSites | |
| 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) |
| CBasicProteinInferenceAlgorithm | Algorithm class that implements simple protein inference by aggregation of peptide scores. It has multiple parameter options like the aggregation method, when to distinguish peptidoforms, and if you want to use shared peptides ("use_shared_peptides"). First, the best PSM per spectrum is used, then only the best PSM per peptidoform is aggregated. Peptidoforms can optionally be distinguished via the treat_X_separate parameters: |
| CBayesianProteinInferenceAlgorithm | Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental) |
| ►CConsensusIDAlgorithm | Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs) |
| CHitInfo | |
| CConsensusIDAlgorithmAverage | Calculates a consensus from multiple ID runs by averaging the search scores |
| CConsensusIDAlgorithmBest | Calculates a consensus from multiple ID runs by taking the best search score |
| CConsensusIDAlgorithmIdentity | Abstract base class for ConsensusID algorithms that compare only identical sequences |
| CConsensusIDAlgorithmPEPIons | Calculates a consensus from multiple ID runs based on PEPs and shared ions |
| CConsensusIDAlgorithmPEPMatrix | Calculates a consensus from multiple ID runs based on PEPs and sequence similarities |
| CConsensusIDAlgorithmRanks | Calculates a consensus from multiple ID runs based on the ranks of the search hits |
| CConsensusIDAlgorithmSimilarity | Abstract base class for ConsensusID algorithms that take peptide similarity into account |
| CConsensusIDAlgorithmWorst | Calculates a consensus from multiple ID runs by taking the worst search score (conservative approach) |
| CConsensusMapMergerAlgorithm | Merges identification data in ConsensusMaps |
| ►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 |
| CFIAMSDataProcessor | Data processing for FIA-MS data |
| CFIAMSScheduler | |
| CHMMState | Hidden Markov Model State class for the Hidden Markov Model |
| CHiddenMarkovModel | Hidden Markov Model implementation of PILIS |
| CIDConflictResolverAlgorithm | Resolves ambiguous annotations of features with peptide identifications |
| ►CIDDecoyProbability | IDDecoyProbability calculates probabilities using decoy approach |
| CTransformation_ | Struct to be used to store a transformation (used for fitting) |
| ►CIDMapper | Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications |
| CSpectraIdentificationState | Result of a partitioning by identification state with mapPrecursorsToIdentifications() |
| CIDMergerAlgorithm | Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but concatenates PSMs. Checks search engine consistency of all inserted runs. It differs from the IDMerger tool, in that it is an algorithm class and it allows inserting multiple peptide hits per peptide sequence (not only the first occurrence) |
| ►CIDRipper | Ripping protein/peptide identification according their file origin |
| 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 |
| CScoreToTgtDecLabelPairs | |
| ►CIDScoreGetterSetter | A class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps |
| CIsHitType | |
| CIsIDType | |
| CIDScoreSwitcherAlgorithm | |
| CIonIdentityMolecularNetworking | |
| CPrecursorMassComparator | |
| CSpectralMatch | |
| CSpectralMatchScoreComparator | |
| CMetaboliteSpectralMatching | |
| CPeptideIndexing | Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds target/decoy information |
| CConnectedComponent | |
| CPeptideProteinResolution | Resolves shared peptides based on protein scores |
| ►CPercolatorFeatureSetHelper | Percolator feature set and integration helper |
| Clq_PeptideEvidence | For accession dependent sorting of PeptideEvidences |
| Clq_ProteinHit | For accession dependent sorting of ProteinHits |
| ►CPrecursorPurity | Precursor purity or noise estimation |
| CPurityScores | |
| CProtonDistributionModel | A proton distribution model to calculate the proton distribution over charged peptides |
| ►CSimpleSearchEngineAlgorithm | |
| CAnnotatedHit_ | Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space |
| ►CSiriusAdapterAlgorithm | |
| CFingerid | |
| CParameterModifier | |
| CParameterSection | |
| CPassatutto | |
| CPreprocessing | |
| CProject | |
| CSirius | |
| CSiriusTemporaryFileSystemObjects | Struct for temporary folder structure |
| ►CSiriusMSFile | |
| CAccessionInfo | < class to store information about accessions |
| CCompoundInfo | |
| CBaseGroupFinder | The base class of all element group finding algorithms |
| CBaseSuperimposer | The base class of all superimposer algorithms |
| CConsensusMapNormalizerAlgorithmMedian | Algorithms of ConsensusMapNormalizer |
| CConsensusMapNormalizerAlgorithmQuantile | Algorithms of ConsensusMapNormalizer |
| CConsensusMapNormalizerAlgorithmThreshold | Algorithms of ConsensusMapNormalizer |
| ►CFeatureDistance | A functor class for the calculation of distances between features or consensus features |
| CDistanceParams_ | Structure for storing distance parameters |
| CFeatureGroupingAlgorithm | Base class for all feature grouping algorithms |
| CClusterProxyKD | Proxy for a (potential) cluster |
| 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 |
| ►CFeatureMapping | |
| CFeatureMappingInfo | Stores information required for preprocessing |
| CFeatureToMs2Indices | Stores preprocessed feature mapping information |
| CLabeledPairFinder | The LabeledPairFinder allows the matching of labeled features (features with a fixed distance) |
| 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 |
| ►CMapAlignmentAlgorithmSpectrumAlignment | A map alignment algorithm based on spectrum similarity (dynamic programming) |
| CCompare | Inner class necessary for using the sort algorithm |
| 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 |
| 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 |
| CQTClusterFinder | A variant of QT clustering for the detection of feature groups |
| CSimplePairFinder | This class implements a simple point pair finding algorithm |
| CStablePairFinder | This class implements a pair finding algorithm for consensus features |
| ►CTransformationDescription | Generic description of a coordinate transformation |
| CTransformationStatistics | Summary statistics before/after applying the transformation. For deviations before/after transformation, the percentiles 100, 99, 95, 90, 75, 50, 25 are returned |
| ►CTransformationModel | Base class for transformation models |
| CDataPoint | Coordinate pair (with optional annotation) |
| CTransformationModelBSpline | B-spline (non-linear) model for transformations |
| ►CTransformationModelInterpolated | Interpolation model for transformations |
| CInterpolator | The class defines a generic interpolation technique used in the TransformationModelInterpolated |
| CTransformationModelLinear | Linear model for transformations |
| CTransformationModelLowess | Lowess (non-linear) model for transformations |
| CMRMFragmentSelection | This class can select appropriate fragment ions of an MS/MS spectrum of a peptide |
| ►CReactionMonitoringTransition | This class stores a SRM/MRM transition |
| CNameLess | Comparator by name |
| CProductMZLess | Comparator by Product ion MZ |
| CChromatogramExtractor | The ChromatogramExtractor extracts chromatograms from a spectra file |
| ►CChromatogramExtractorAlgorithm | The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data |
| CExtractionCoordinates | |
| ►CConfidenceScoring | |
| CGLM_ | Binomial GLM |
| CRTNorm_ | Helper for RT normalization (range 0-100) |
| COpenSwathDataAccessHelper | Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces |
| CFeatureOpenMS | An implementation of the OpenSWATH Feature Access interface using OpenMS |
| CMRMFeatureOpenMS | An implementation of the OpenSWATH MRM Feature Access interface using OpenMS |
| CTransitionGroupOpenMS | An implementation of the OpenSWATH Transition Group Access interface using OpenMS |
| CSignalToNoiseOpenMS | An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS |
| CSimpleOpenMSSpectraFactory | A factory method that returns two ISpectrumAccess implementations |
| CSpectrumAccessOpenMS | An implementation of the OpenSWATH Spectrum Access interface using OpenMS |
| CSpectrumAccessOpenMSCached | An implementation of the Spectrum Access interface using on-disk caching |
| CSpectrumAccessOpenMSInMemory | An implementation of the OpenSWATH Spectrum Access interface completely in memory |
| CSpectrumAccessQuadMZTransforming | A transforming m/z wrapper around spectrum access using a quadratic equation |
| CSpectrumAccessSqMass | An implementation of the Spectrum Access interface using SQL files |
| CSpectrumAccessTransforming | An abstract base class implementing a transforming wrapper around spectrum access |
| CDiaPrescore | Scoring of an spectrum given library intensities of a transition group |
| CDIAScoring | Scoring of an spectrum at the peak apex of an chromatographic elution peak |
| CIonMobilityScoring | A class that calls the ion mobility scoring routines |
| CMasstraceCorrelator | Correlates individual masstraces found in mass spectrometric maps |
| CMRMAssay | Generate assays from a TargetedExperiment |
| CMRMBatchFeatureSelector | |
| CMRMDecoy | This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object |
| CMRMFeatureFilter | The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria |
| CMRMFeatureFinderScoring | The MRMFeatureFinder finds and scores peaks of transitions that co-elute |
| ►CMRMFeaturePicker | _MRMFeaturePicker_ defines the structures containing parameters to be used in [MRMTransitionGroupPicker](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 |
| ►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 |
| ►CMRMFeatureSelector | |
| CSelectorParameters | |
| CMRMFeatureSelectorQMIP | |
| CMRMFeatureSelectorScore | |
| CMRMFeatureSelector_test | |
| CMRMIonSeries | Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy |
| CMRMRTNormalizer | The MRMRTNormalizer will find retention time peptides in data |
| CMRMTransitionGroupPicker | The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors |
| COpenSwathHelper | A helper class that is used by several OpenSWATH tools |
| COpenSwathOSWWriter | Class to write out an OpenSwath OSW SQLite output (PyProphet input) |
| COpenSwath_Scores_Usage | A structure to store which scores should be used by the OpenSWATH Algorithm |
| COpenSwath_Scores | A structure to hold the different scores computed by OpenSWATH |
| COpenSwath_Ind_Scores | |
| COpenSwathScoring | A class that calls the scoring routines |
| COpenSwathTSVWriter | Class to write out an OpenSwath TSV output (mProphet input) |
| CChromExtractParams | ChromatogramExtractor parameters |
| COpenSwathWorkflowBase | |
| COpenSwathCalibrationWorkflow | Execute all steps for retention time and m/z calibration of SWATH-MS data |
| COpenSwathWorkflow | Execute all steps in an OpenSwath analysis |
| COpenSwathWorkflowSonar | Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data) |
| ►CPeakIntegrator | Compute the area, background and shape metrics of a peak |
| CPeakArea | |
| CPeakBackground | |
| CPeakShapeMetrics | |
| CPeakPickerMRM | The PeakPickerMRM finds peaks a single chromatogram |
| CSONARScoring | Scoring of an spectrum using SONAR data |
| CSpectrumAddition | The SpectrumAddition is used to add up individual spectra |
| CSwathMapMassCorrection | A class containing correction functions for Swath MS maps |
| CSwathWindowLoader | Class to read a file describing the Swath Windows |
| ►CTargetedSpectraExtractor | This class filters, annotates, picks, and scores spectra (e.g., taken from a DDA experiment) based on a target list |
| CBinnedSpectrumComparator | |
| CComparator | |
| CMatch | |
| CTransitionPQPFile | This class supports reading and writing of PQP files |
| ►CTransitionTSVFile | This class supports reading and writing of OpenSWATH transition lists |
| CTSVTransition | Internal structure to represent a transition |
| ►CLocalLinearMap | Trained Local Linear Map (LLM) model for peak intensity prediction |
| CLLMParam | Define parameters needed by the Local Linear Map (LLM) model |
| CPeakIntensityPredictor | Predict peak heights of peptides based on Local Linear Map model |
| 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 |
| ►CIsobaricChannelExtractor | Extracts individual channels from MS/MS spectra for isobaric labeling experiments |
| CPuritySate_ | Small struct to capture the current state of the purity computation |
| CIsobaricIsotopeCorrector | Performs isotope impurity correction on the intensities extracted from an isobaric labeling experiment |
| CIsobaricNormalizer | Performs median normalization on the extracted ratios of isobaric labeling experiment |
| 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) |
| CMatrix | A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access |
| ►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 |
| 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)) |
| ►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 |
| CKDTreeFeatureMaps | Stores a set of features, together with a 2D tree for fast search |
| CKDTreeFeatureNode | A node of the kD-tree with pointer to corresponding data and index |
| ►CPeptideAndProteinQuant | Helper class for peptide and protein quantification based on feature data annotated with IDs |
| CPeptideData | Quantitative and associated data for a peptide |
| CProteinData | Quantitative and associated data for a protein |
| CStatistics | Statistics for processing summary |
| CProteinInference | [experimental class] given a peptide quantitation, infer corresponding protein quantities |
| ►CProteinResolver | Helper class for peptide and protein quantification based on feature data annotated with IDs |
| CISDGroup | |
| CMSDGroup | Representation of an msd group. Contains peptides, proteins and a pointer to its ISD group |
| CPeptideEntry | Peptide. First in silico. If experimental is set to true it is MS/MS derived |
| CProteinEntry | Protein from FASTA file |
| CResolverResult | |
| CQuantitativeExperimentalDesign | Merge files according to experimental design |
| 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 |
| ►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 |
| ►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 |
| CPScore | Implementation of the PScore PSM scoring algorithm |
| CRNPxlMarkerIonExtractor | |
| CRNPxlModificationMassesResult | |
| CRNPxlModificationsGenerator | |
| CRNPxlReportRow | Struct to hold a single report line |
| CRNPxlReportRowHeader | Create header line |
| CRNPxlReport | Create report |
| CNeedlemanWunsch | This class contains functions that are used to calculate the global alignment score of two amino acid sequences. This class uses the Needleman-Wunsch algorithm. For match and mismatch it uses a similarity scoring matrix |
| ►CSimpleSVM | Simple interface to support vector machines for classification and regression (via LIBSVM) |
| CPrediction | SVM/SVR prediction result |
| CSVMData | Data structure used in SVMWrapper |
| CSVMWrapper | Serves as a wrapper for the libsvm |
| CIncludeExcludeTarget | This class stores a SRM/MRM transition |
| ►CInclusionExclusionList | Provides functionality for writing inclusion or exclusion lists |
| CIEWindow | |
| CWindowDistance_ | Determine distance between two spectra |
| ►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 |
| CMRMMapping | A class to map targeted assays to chromatograms |
| ►COfflinePrecursorIonSelection | Implements different algorithms for precursor ion selection |
| CPairComparatorSecondElement | |
| ►CPrecursorIonSelection | This class implements different precursor ion selection strategies |
| CSeqTotalScoreMore | Compare by score |
| CTotalScoreMore | Compare by score |
| CPrecursorIonSelectionPreprocessing | This class implements the database preprocessing needing for precursor ion selection |
| ►CPSLPFormulation | Implements ILP formulation of precursor selection problems |
| CIndexLess | |
| CIndexTriple | Struct that holds the indices of the precursors in the feature map and the ilp formulation |
| CScanLess | |
| CVariableIndexLess | |
| CPSProteinInference | This class implements protein inference for the precursor ion selection strategies |
| ►CTargetedExperiment | A description of a targeted experiment containing precursor and production ions |
| CSummaryStatistics | |
| CDeconvolvedSpectrum | A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroups 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 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 |
| 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 deisotope - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups) |
| ►CFLASHDeconvHelperStructs | Wrapper struct for all the structs needed by the FLASHDeconv Three structures are defined: PrecalculatedAveragine, TopPicItem, and LogMzPeak 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) TopPicItem - represent TopPic identification. Currently used for Qscore training. TopPic is the top-down proteomics identification tool (https://www.toppic.org/). iii) LogMzPeak - Log transformed peak from original peak. Contains information such as charge, isotope index, and uncharged mass |
| 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 | Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine calculation |
| CMassFeatureTrace | Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by FLASHDeconvAlgorithm 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. Tracing is performed at the end of FLASHDeconv run. This class also comes with tsv, TopFD, ProMex format output functions |
| 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 by Qscore calculation. DeconvolvedSpectrum consists of PeakGroups |
| CQscore | Qscore : quality score for PeakGroup. This class is being updated. For now, simply it calculate the Qscore using a fixed weight vector. The weight vector has been determined by logistic regression. But afterwards, the training part for the Qscore should be added in here. Or other technique such as deep learning would be used. This class also contains tsv output function. The tsv file contains features of PeakGroups which are used for training |
| CQvalue | Qvalue : contains functions to calculate Qvalues from deconvolution quality score |
| COpenPepXLAlgorithm | Search for peptide pairs linked with a labeled cross-linker |
| COpenPepXLLFAlgorithm | Search for cross-linked peptide pairs in tandem MS spectra |
| ►COPXLDataStructs | |
| 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 and OpenPepXLLF to reduce duplicated code |
| CPeptideIDScoreComparator | A comparator for PeptideIdentifications that compares the scores in the first PeptideHit |
| COPXLSpectrumProcessingAlgorithms | |
| CXFDRAlgorithm | Calculates false discovery rate estimates on crosslink identifications |
| 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") |
| CConsoleUtils | |
| CINIUpdater | |
| CTOPPOpenSwathBase | |
| CParameterInformation | Struct that captures all information of a command line parameter |
| CSearchEngineBase | Base class for Search Engine Adapters |
| CToolHandler | |
| CCitation | Stores Citations for individual TOPP tools |
| CTOPPBase | Base class for TOPP applications |
| CAAIndex | Representation of selected AAIndex properties |
| ►CAASequence | Representation of a peptide/protein sequence |
| CConstIterator | ConstIterator for AASequence |
| CIterator | Iterator class for AASequence |
| CAdductInfo | |
| CCrossLinksDB | |
| CDecoyGenerator | Methods to generate isobaric decoy sequences for DDA target-decoy searches |
| CDigestionEnzyme | Base class for digestion enzymes |
| CDigestionEnzymeDB | Digestion enzyme database (base class) |
| CDigestionEnzymeProtein | Representation of a digestion enzyme for proteins (protease) |
| CDigestionEnzymeRNA | Representation of a digestion enzyme for RNA (RNase) |
| CElement | Representation of an element |
| CElementDB | Singleton that stores elements and isotopes |
| CEmpiricalFormula | Representation of an empirical formula |
| CEnzymaticDigestion | Class for the enzymatic digestion of sequences |
| ►CEnzymaticDigestionLogModel | Class for the Log L model of enzymatic digestion of proteins |
| CBindingSite_ | |
| CCleavageModel_ | |
| CCoarseIsotopePatternGenerator | Isotope pattern generator for coarse isotope distributions |
| CFineIsotopePatternGenerator | Isotope pattern generator for fine isotope distributions |
| CIsoSpecGeneratorWrapper | Interface for the IsoSpec algorithm - a generator of infinitely-resolved theoretical spectra |
| CIsoSpecWrapper | A convenience class for the IsoSpec algorithm - easier to use than the IsoSpecGeneratorWrapper classes |
| 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) |
| CIsoSpecThresholdGeneratorWrapper | Provides a threshold-based generator of isotopologues: generates all isotopologues more probable than a given probability threshold |
| CIsoSpecOrderedGeneratorWrapper | Generate the stream of configurations, ordered from most likely to least likely |
| 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) |
| CIsoSpecThresholdWrapper | A non-generator version of IsoSpecThresholdGeneratorWrapper |
| CIsotopeDistribution | |
| CIsotopePatternGenerator | Provides an interface for different isotope pattern generator methods |
| CMassDecomposition | Class represents a decomposition of a mass into amino acids |
| CMassDecompositionAlgorithm | Mass decomposition algorithm, given a mass it suggests possible compositions |
| CModificationDefinition | Representation of modification definition |
| CModificationDefinitionsSet | Representation of a set of modification definitions |
| CModificationsDB | Database which holds all residue modifications from UniMod |
| CModifiedNASequenceGenerator | |
| ►CModifiedPeptideGenerator | |
| CMapToResidueType | |
| ►CNASequence | Representation of a nucleic acid sequence |
| CConstIterator | ConstIterator of NASequence class |
| CIterator | Iterator of NASequence class |
| CNucleicAcidSpectrumGenerator | Generates theoretical spectra for nucleic acid sequences |
| CProteaseDB | Database for enzymes that digest proteins (proteases) |
| CProteaseDigestion | Class for the enzymatic digestion of proteins represented as AASequence or String |
| 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) |
| CRibonucleotideDB | Database of ribonucleotides (modified and unmodified) |
| CRNaseDB | Database for enzymes that digest RNA (RNases) |
| CRNaseDigestion | Class for the enzymatic digestion of RNAs |
| ►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 |
| CSpectrumAnnotator | Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options |
| ►CSvmTheoreticalSpectrumGenerator | Simulates MS2 spectra with support vector machines |
| CDescriptorSet | A set of descriptors for a single training row |
| CIonType | Nested class |
| CSvmModelParameterSet | Simple container storing the model parameters required for simulation |
| CSvmTheoreticalSpectrumGeneratorSet | Loads SvmTheoreticalSpectrumGenerator instances for different charges |
| CSvmTheoreticalSpectrumGeneratorTrainer | Train SVM models that are used by SvmTheoreticalSpectrumGenerator |
| CTagger | Calculate sequence tags from m/z values |
| CTheoreticalSpectrumGenerator | Generates theoretical spectra for peptides with various options |
| ►CTheoreticalSpectrumGeneratorXLMS | Generates theoretical spectra for cross-linked peptides |
| CLossIndex | |
| CWeightWrapper | Encapsulated weight queries to simplify mono vs average weight computation |
| CAverageLinkage | AverageLinkage ClusterMethod |
| 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 |
| CUnnormalizedComparator | Exception thrown if clustering is attempted without a normalized compare functor |
| CClusteringGrid | Data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering |
| CCompleteLinkage | CompleteLinkage ClusterMethod |
| CEuclideanSimilarity | CompareFunctor for 2Dpoints |
| CGridBasedCluster | Basic data structure for clustering |
| CMinimumDistance | Basic data structure for distances between clusters |
| CGridBasedClustering | 2D hierarchical clustering implementation optimized for large data sets containing many small clusters i.e. dimensions of clusters << dimension of entire dataset |
| ►CHashGrid | Container for (2-dimensional coordinate, value) pairs |
| CConstIterator | Constant element iterator for the hash grid |
| CIterator | Element iterator for the hash grid |
| CSingleLinkage | SingleLinkage ClusterMethod |
| 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 |
| CPeakAlignment | Make a PeakAlignment of two PeakSpectra |
| CPeakSpectrumCompareFunctor | Base class for compare functors of spectra, that return a similarity value for two spectra |
| CSpectraSTSimilarityScore | Similarity score of SpectraST |
| 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 |
| CSpectrumCheapDPCorr | SpectrumCheapDPCorr calculates an optimal alignment on stick spectra |
| CSpectrumPrecursorComparator | SpectrumPrecursorComparator compares just the parent mass of two spectra |
| CSteinScottImproveScore | Similarity score based of Stein & Scott |
| CZhangSimilarityScore | Similarity score of Zhang |
| ►CColorizer | Color and style the fonts shown on cout/cerr (or other streams) |
| CColorWithUndo_ | |
| CFactory | Returns FactoryProduct* based on the name of the desired concrete FactoryProduct |
| CFactoryBase | Base class for Factory<T> |
| ►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 |
| CLogConfigHandler | The LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream |
| CPrecisionWrapper | Wrapper class to implement output with appropriate precision. See precisionWrapper() |
| ►CProgressLogger | Base class for all classes that want to report their progress |
| CProgressLoggerImpl | This class represents an actual implementation of a logger |
| CRAIICleanup | Exception-safe way of executing arbitrary code at the end of a scope |
| CSingletonRegistry | Holds pointers to unique instance of a singleton factory |
| CStreamHandler | Provides a central class to register globally used output streams. Currently supported streams are |
| 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 |
| ►CVersionInfo | Version information class |
| CVersionDetails | |
| CAdduct | |
| CBinaryTreeNode | Elements of a binary tree used to represent a hierarchical clustering process |
| CCalibrationData | A helper class, holding all calibration points |
| 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+, ..) |
| CCompomer | Holds information on an edge connecting two features from a (putative) charge ladder |
| ►CConstRefVector | This vector holds pointer to the elements of another container |
| CConstRefVectorConstIterator | ConstIterator for the ConstRefVector |
| CConstRefVectorIterator | Mutable iterator for the ConstRefVector |
| CConvexHull2D | A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling |
| 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 |
| CDataValue | Class to hold strings, numeric values, lists of strings and lists of numeric values |
| CDate | Date Class |
| CDateTime | DateTime Class |
| CDBoundingBox | A D-dimensional bounding box |
| CDefaultParamHandler | A base class for all classes handling default parameters |
| CDistanceMatrix | A two-dimensional distance matrix, similar to OpenMS::Matrix |
| CDPosition | Representation of a coordinate in D-dimensional space |
| CDRange | A D-dimensional half-open interval |
| CExposedVector | Makes a vector<VectorElement> available in the derived class and exposed commonly used vector member functions at class level |
| 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 |
| ►CDecoyHelper | Helper class for calculations on decoy proteins |
| CDecoyStatistics | Struct for intermediate results needed for calculations on decoy proteins |
| CResult | |
| CFlagSet | Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64 |
| CGridFeature | Representation of a feature in a hash grid |
| ►CIsotopeCluster | Stores information about an isotopic cluster (i.e. potential peptide charge variants) |
| CChargedIndexSet | Index set with associated charge estimate |
| ►CListUtils | Collection of utility functions for management of vectors |
| CDoubleTolerancePredicate_ | Predicate to check double equality with a given tolerance |
| CVecLowPrecision | |
| ►CLPWrapper | |
| CSolverParam | Struct that holds the parameters of the LP solver |
| CMassExplainer | Computes empirical formulas for given mass differences using a set of allowed elements |
| 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 |
| CValueTrait | Trait for MatchedIterator to find pairs with a certain distance, which is computed directly on the value_type of the container |
| CPpmTrait | |
| CDaTrait | |
| COSWHierarchy | Hierarchy levels of the OSWData tree |
| COSWIndexTrace | |
| COSWTransition | High-level meta data of a transition |
| COSWPeakGroup | |
| COSWPeptidePrecursor | A peptide with a charge state |
| COSWProtein | A Protein is the highest entity and contains one or more peptides which were found/traced |
| COSWData | Holds all or partial information from an OSW file |
| ►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 |
| CParamValue | Class to hold strings, numeric values, vectors of strings and vectors of numeric values using the stl types |
| ►CQTCluster | A representation of a QT cluster used for feature grouping |
| CBulkData | Class to store the bulk internal data (neighbors, annotations, etc.) |
| CElement | |
| CNeighbor | |
| CString | A more convenient string class |
| CStringListUtils | Utilities operating on lists of Strings |
| ►CStringUtilsHelper | |
| Creal_policies_NANfixed_ | |
| CStringView | StringView provides a non-owning view on an existing string |
| CMapUtilities | Utilities for Feature and ConsensusMap |
| CMorphologicalFilter | This class implements baseline filtering operations using methods from mathematical morphology |
| ►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 |
| ►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 |
| CPrecursorCorrection | This class provides methods for precursor correction |
| CTOFCalibration | This class implements an external calibration for TOF data using external calibrant spectra |
| ►CDataFilters | DataFilter array providing some convenience functions |
| CDataFilter | Representation of a peak/feature filter combining FilterType, FilterOperation and a value (either double or String) |
| CDeisotoper | |
| CElutionPeakDetection | Extracts chromatographic peaks from a mass trace |
| CFeatureHypothesis | Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis) |
| CCmpMassTraceByMZ | |
| CCmpHypothesesByScore | |
| CRange | Internal structure to store a lower and upper bound of an m/z range |
| 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 |
| CFeatureOverlapFilter | |
| CIsotopeDistributionCache | Pre-calculate isotope distributions for interesting mass ranges |
| ►CMassTraceDetection | A mass trace extraction method that gathers peaks similar in m/z and moving along retention time |
| CApex | |
| ►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 |
| ►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 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? |
| CHasMatchingAccession | Given a list of protein accessions, do any occur in the annotation(s) of this hit? |
| CHasMatchingAccessionUnordered | 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? |
| CHasMaxRank | Is the rank of this hit below or at the given cut-off? |
| CHasMetaValue | Is a meta value with given key and value set on this hit? |
| CHasNoHits | Is the list of hits of this peptide/protein ID empty? |
| CPeptideDigestionFilter | Filter Peptide Hit by its digestion product |
| ►CSignalToNoiseEstimator | This class represents the abstract base class of a signal to noise estimator |
| CGaussianEstimate | Protected struct to store parameters my, sigma for a Gaussian distribution |
| CSignalToNoiseEstimatorMeanIterative | Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities |
| CSignalToNoiseEstimatorMedian | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) |
| ►CSignalToNoiseEstimatorMedianRapid | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based) |
| CNoiseEstimator | Class to compute the noise value at a given position |
| 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 |
| CLowessSmoothing | LOWESS (locally weighted scatterplot smoothing) |
| CSavitzkyGolayFilter | Computes the Savitzky-Golay filter coefficients using QR decomposition |
| CBernNorm | BernNorm scales the peaks by ranking them and then scaling them according to rank |
| CComplementFilter | Total intensity of peak pairs that could result from complementing fragments of charge state 1 |
| CComplementMarker | ComplementMarker marks peak pairs which could represent y - b ion pairs |
| CFilterFunctor | A FilterFunctor extracts some spectrum characteristics for quality assessment |
| CGoodDiffFilter | GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss |
| CIntensityBalanceFilter | IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions |
| CIsotopeDiffFilter | IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks |
| CIsotopeMarker | IsotopeMarker marks peak pairs which could represent an ion and its isotope |
| CLinearResampler | Linear Resampling of raw data |
| CLinearResamplerAlign | Linear Resampling of raw data with alignment |
| CMarkerMower | MarkerMower uses PeakMarker to find peaks, those that are not marked get removed |
| CNeutralLossDiffFilter | NeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained by a neutral loss |
| CNeutralLossMarker | NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water, ammonia) |
| CNLargest | NLargest removes all but the n largest peaks |
| CNormalizer | Normalizes the peak intensities spectrum-wise |
| CParentPeakMower | ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions |
| CPeakMarker | PeakMarker marks peaks that seem to fulfill some criterion |
| CScaler | Scaler scales the peak by ranking the peaks and assigning intensity according to rank |
| ►CSpectraMerger | Merges blocks of MS or MS2 spectra |
| CSpectraDistance_ | |
| CSqrtMower | Scales the intensity of peaks to the sqrt |
| CThresholdMower | ThresholdMower removes all peaks below a threshold |
| CTICFilter | TICFilter calculates TIC |
| CWindowMower | WindowMower augments the highest peaks in a sliding or jumping window |
| CAbsoluteQuantitationMethodFile | File adapter for AbsoluteQuantitationMethod files |
| CAbsoluteQuantitationStandardsFile | Load files containing runConcentration data |
| ►CBase64 | Class to encode and decode Base64 |
| CReinterpreter32_ | Internal class needed for type-punning |
| CReinterpreter64_ | Internal class needed for type-punning |
| CBzip2Ifstream | Decompresses files which are compressed in the bzip2 format (*.bz2) |
| CBzip2InputStream | Implements the BinInputStream class of the xerces-c library in order to read bzip2 compressed XML files |
| CCachedmzML | An class that uses on-disk caching to read and write spectra and chromatograms |
| CChromeleonFile | Load Chromeleon HPLC text file and save it into a `MSExperiment` |
| CCompressedInputSource | This class is based on xercesc::LocalFileInputSource |
| CConsensusXMLFile | This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation |
| ►CControlledVocabulary | Representation of a controlled vocabulary |
| CCVTerm | Representation of a CV term |
| CCsvFile | This class handles csv files. Currently only loading is implemented |
| CCVMappingFile | Used to load CvMapping files |
| ►CCsiFingerIdMzTabWriter | |
| CCsiAdapterHit | Internal structure used in SiriusAdapter that is used for the conversion of the Csi:FingerID output to an mzTab |
| CCsiAdapterIdentification | |
| CCsiAdapterRun | |
| 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 |
| CPlainMSDataWritingConsumer | Consumer class that writes MS data to disk using the mzML format |
| CNoopMSDataWritingConsumer | Consumer class that perform no operation |
| CNoopMSDataConsumer | Consumer class that performs no operation |
| ►CSiriusFragmentAnnotation | |
| CSiriusTargetDecoySpectra | SiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from SIRIUS) |
| ►CSiriusMzTabWriter | |
| CSiriusAdapterHit | Internal structure used in SiriusAdapter that is used for the conversion of the sirius output to an mzTab |
| CSiriusAdapterIdentification | |
| CSiriusAdapterRun | |
| CSiriusSpectrumMSInfo | |
| CFullSwathFileConsumer | Abstract base class which can consume spectra coming from SWATH experiment stored in a single file |
| CRegularSwathFileConsumer | In-memory implementation of FullSwathFileConsumer |
| CCachedSwathFileConsumer | On-disk cached implementation of FullSwathFileConsumer |
| CMzMLSwathFileConsumer | On-disk mzML implementation of FullSwathFileConsumer |
| CDTA2DFile | DTA2D File adapter |
| CDTAFile | File adapter for DTA files |
| CEDTAFile | File adapter for Enhanced DTA files |
| CExperimentalDesignFile | Load an experimental design from a TSV file. (see ExperimentalDesign for details on the supported format) |
| ►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 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 |
| CFeatureXMLFile | This class provides Input/Output functionality for feature maps |
| CFileHandler | Facilitates file handling by file type recognition |
| CFileTypes | Centralizes the file types recognized by FileHandler |
| ►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 |
| 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 |
| CGNPSMetaValueFile | |
| CGNPSMGFFile | |
| CGNPSQuantificationFile | |
| CGzipIfstream | Decompresses files which are compressed in the gzip format (*.gzip) |
| CGzipInputStream | Implements the BinInputStream class of the xerces-c library in order to read gzip compressed XML files |
| CIndexedMzMLDecoder | A class to analyze indexedmzML files and extract the offsets of individual tags |
| CMzMLSpectrumDecoder | A class to decode input strings that contain an mzML chromatogram or spectrum tag |
| CHDF5Connector | File adapter for HDF5 files |
| CIBSpectraFile | Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results |
| CIdXMLFile | Used to load and store idXML files |
| CIndentedStream | Class for writing data which spans multiple lines with an indentation for each line (all except the first) |
| CIndexedMzMLFileLoader | A class to load an indexedmzML file |
| CInspectInfile | Inspect input file adapter |
| CInspectOutfile | Representation of an Inspect outfile |
| CKroenikFile | File adapter for Kroenik (HardKloer sibling) files |
| CLibSVMEncoder | Serves for encoding sequences into feature vectors |
| CMascotGenericFile | Read/write Mascot generic files (MGF) |
| CMascotInfile | Mascot input file adapter |
| CMascotRemoteQuery | Class which handles the communication between OpenMS and the Mascot server |
| CMascotXMLFile | Used to load Mascot XML files |
| CMRMFeaturePickerFile | _MRMFeaturePickerFile_ loads components and components groups parameters from a .csv file |
| CMRMFeatureQCFile | File adapter for MRMFeatureQC files |
| CMS2File | MS2 input file adapter |
| CMsInspectFile | File adapter for MsInspect files |
| ►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 | |
| ►CMSstatsFile | File adapter for MSstats files |
| CAggregatedConsensusInfo | |
| CMSstatsLine_ | |
| CMSstatsTMTLine_ | |
| CMzDataFile | File adapter for MzData files |
| CMzIdentMLFile | File adapter for MzIdentML files |
| ►CMzMLFile | File adapter for MzML files |
| CSpecInfo | |
| CMzQCFile | File adapter for mzQC files used to load and store mzQC files |
| CMzQuantMLFile | File adapter for MzQuantML files |
| CMzTabModification | Data model of MzTab files |
| CMzTabModificationList | |
| CMzTabModificationMetaData | |
| CMzTabAssayMetaData | |
| CMzTabMSRunMetaData | |
| CMzTabStudyVariableMetaData | |
| CMzTabMetaData | All meta data of a mzTab file. Please refer to specification for documentation |
| ►CMzTabProteinSectionRow | PRT - Protein section (Table based) |
| CRowCompare | Comparison operator for sorting rows |
| ►CMzTabPeptideSectionRow | PEP - Peptide section (Table based) |
| CRowCompare | Comparison operator for sorting rows |
| ►CMzTabPSMSectionRow | PSM - PSM section (Table based) |
| CRowCompare | Comparison operator for sorting rows |
| CMzTabSmallMoleculeSectionRow | SML Small molecule section (table based) |
| ►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 |
| ►CMzTab | Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/ |
| CCMMzTabStream | |
| CIDMzTabStream | |
| CMzTabDouble | |
| CMzTabDoubleList | |
| CMzTabInteger | |
| CMzTabIntegerList | |
| CMzTabBoolean | |
| CMzTabString | |
| CMzTabParameter | |
| CMzTabParameterList | |
| CMzTabStringList | |
| CMzTabSpectraRef | |
| CMzTabSoftwareMetaData | |
| CMzTabSampleMetaData | |
| CMzTabCVMetaData | |
| CMzTabInstrumentMetaData | |
| CMzTabContactMetaData | |
| CMzTabBase | |
| CMzTabFile | File adapter for MzTab files |
| 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 |
| CMzTabMAssayMetaData | MztabM Assay Metadata |
| CMzTabMMSRunMetaData | MztabM MSRun Metadata |
| CMzTabMStudyVariableMetaData | MztabM StudyVariable Metadata |
| CMzTabMDatabaseMetaData | MztabM Database Metadata |
| CMzTabMMetaData | MztabM Metadata |
| CMzTabMSmallMoleculeSectionRow | SML Small molecule section (mztab-m) |
| CMzTabMSmallMoleculeFeatureSectionRow | SMF Small molecule feature section (mztab-m) |
| CMzTabMSmallMoleculeEvidenceSectionRow | SME Small molecule evidence section (mztab-m) |
| 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 |
| CMzTabMFile | File adapter for MzTab-M files |
| CMzXMLFile | File adapter for MzXML 3.1 files |
| COMSFile | This class supports reading and writing of OMS files |
| COMSSACSVFile | File adapter for OMSSACSV files |
| COMSSAXMLFile | Used to load OMSSAXML files |
| CFeatureFileOptions | Options for loading files containing features |
| CPeakFileOptions | Options for loading files containing peak data |
| ►COSWFile | This class serves for reading in and writing OpenSWATH OSW files |
| CPercolatorFeature | |
| CToolInfo | A struct to pass information about the tool as one parameter |
| CParamCTDFile | Serializes a Param class in paramCTD file format. Note: only storing is currently possible |
| CParamCWLFile | Load from JSON (in a Common Workflow Language (CWL) compatible way) into the Param class |
| CParamXMLFile | The file pendant of the Param class used to load and store the param datastructure as paramXML |
| CPeakTypeEstimator | Estimates if the data of a spectrum is raw data or peak data |
| CPepNovoInfile | PepNovo input file adapter |
| CPepNovoOutfile | Representation of a PepNovo output file |
| ►CPepXMLFile | Used to load and store PepXML files |
| CAminoAcidModification | |
| CPepXMLFileMascot | Used to load Mascot PepXML files |
| CPercolatorInfile | Class for storing Percolator tab-delimited input files |
| CPercolatorOutfile | Class for reading Percolator tab-delimited output files |
| CProtXMLFile | Used to load (storing not supported, yet) ProtXML files |
| CPTMXMLFile | Used to load and store PTMXML files |
| ►CQcMLFile | File adapter for QcML files used to load and store QcML files |
| CAttachment | Representation of an attachment |
| CQualityParameter | Representation of a quality parameter |
| CSequestInfile | Sequest input file adapter |
| CSequestOutfile | Representation of a Sequest output file |
| CSpecArrayFile | File adapter for SpecArray (.pepList) files |
| CSqliteConnector | File adapter for Sqlite files |
| ►CSqMassFile | An class that uses on-disk SQLite database to read and write spectra and chromatograms |
| CSqMassConfig | Configuration class for SqMassFile |
| CSVOutStream | Stream class for writing to comma/tab/...-separated values files |
| CSwathFile | File adapter for Swath files |
| CTextFile | This class provides some basic file handling methods for text files |
| CToolDescriptionFile | File adapter for ToolDescriptor files |
| CTraMLFile | File adapter for HUPO PSI TraML files |
| CTransformationXMLFile | Used to load and store TransformationXML files |
| ►CTriqlerFile | File adapter for Triqler files |
| CAggregatedConsensusInfo | |
| CTriqlerLine_ | |
| CUnimodXMLFile | Used to load XML files from unimod.org files |
| CXMLValidator | Validator for XML files |
| CXMassFile | File adapter for 'XMass Analysis (fid)' files |
| CXQuestResultXMLFile | Used to load and store xQuest result files |
| CXTandemInfile | XTandem input file |
| CXTandemXMLFile | Used to load XTandemXML files |
| CZlibCompression | Compresses and uncompresses data using zlib |
| CFAIMSHelper | Helper functions for FAIMS data |
| CIMDataConverter | This class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models |
| CIMTypes | |
| ►CBaseFeature | A basic LC-MS feature |
| CQualityLess | Compare by quality |
| ►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 |
| CChromatogramTools | Conversion class to convert chromatograms |
| ►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 |
| ►CConsensusMap | A container for consensus elements |
| CColumnHeader | Description of the columns in a consensus map |
| CMapConversion | |
| 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 |
| CDimRT | |
| CDimMZ | |
| CDimINT | |
| CDimIM | |
| 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) |
| CArea | |
| CDPeak | Metafunction to choose among Peak1D respectively Peak2D through a template argument |
| CFeature | An LC-MS feature |
| ►CFeatureHandle | Representation of a Peak2D, RichPeak2D or Feature |
| CFeatureHandleMutable_ | Helper class returned by FeatureHandle::asMutable(), which see |
| CIndexLess | Comparator by map and unique id |
| CAnnotationStatistics | |
| CFeatureMap | A container for features |
| CMassTrace | A container type that gathers peaks similar in m/z and moving along retention time |
| ►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 |
| CMRMFeature | A multi-chromatogram MRM feature |
| CMRMTransitionGroup | The representation of a group of transitions in a targeted proteomics experiment |
| ►CMSChromatogram | The representation of a chromatogram |
| CMZLess | Comparator for the retention time |
| ►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 > | |
| ►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 | |
| CIMLess | Comparator for the ion mobility |
| CRTLess | Comparator for the retention time |
| COnDiscMSExperiment | Representation of a mass spectrometry experiment on disk |
| ►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 |
| CPeakIndex | Index of a peak or feature |
| CRangeBase | Base class for a simple range with minimum and maximum |
| CRangeRT | |
| CRangeMZ | |
| CRangeIntensity | |
| CRangeMobility | |
| CRangeManager | Handles the management of a multidimensional range, e.g. RangeMZ and RangeIntensity for spectra |
| CRangeManagerContainer | |
| CHasMetaValue | Predicate that determines if a class has a certain metavalue |
| CInRTRange | Predicate that determines if a spectrum lies inside/outside a specific retention time range |
| CInMSLevelRange | Predicate that determines if a spectrum lies inside/outside a specific MS level set |
| CHasScanMode | Predicate that determines if a spectrum has a certain scan mode |
| CHasScanPolarity | Predicate that determines if a spectrum has a certain scan polarity |
| CIsEmptySpectrum | Predicate that determines if a spectrum is empty |
| CIsZoomSpectrum | Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum |
| CHasActivationMethod | Predicate that determines if a spectrum was generated using any activation method given in the constructor list |
| CInPrecursorMZRange | Predicate that determines if a spectrum's precursor is within a certain m/z range |
| CHasPrecursorCharge | Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list |
| CInMzRange | Predicate that determines if a peak lies inside/outside a specific m/z range |
| CInIntensityRange | Predicate that determines if a peak lies inside/outside a specific intensity range |
| CIsInCollisionEnergyRange | Predicate that determines if an MSn spectrum was generated with a collision energy in the given range |
| CIsInIsolationWindowSizeRange | Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range |
| CIsInIsolationWindow | Predicate that determines if the isolation window covers ANY of the given m/z values |
| CRichPeak2D | A 2-dimensional raw data point or peak with meta information |
| CBSpline2d | B spline interpolation |
| CCubicSpline2d | Cubic spline interpolation as described in R.L. Burden, J.D. Faires, Numerical Analysis, 4th ed. PWS-Kent, 1989, ISBN 0-53491-585-X, pp. 126-131 |
| CEmgGradientDescent | Compute the area, background and shape metrics of a peak |
| CEmgGradientDescent_friend | |
| CGridSearch | |
| CNonNegativeLeastSquaresSolver | Wrapper for a non-negative least squares (NNLS) solver |
| ►CAbsoluteQuantitationStandards | AbsoluteQuantitationStandards is a class to handle the relationship between runs, components, and their actual concentrations |
| CfeatureConcentration | Structure to hold a single component and its corresponding known concentration |
| CrunConcentration | Structure to map runs to components to known concentrations |
| 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 |
| CChromatogramSettings | Representation of chromatogram settings, e.g. SRM/MRM chromatograms |
| CContactPerson | Contact person information |
| ►CCVTerm | Representation of controlled vocabulary term |
| CUnit | |
| CCVTermList | Representation of controlled vocabulary term list |
| CCVTermListInterface | Interface to the controlled vocabulary term list |
| CDataProcessing | Description of the applied preprocessing steps |
| CDigestion | Meta information about digestion of a sample |
| CDocumentIdentifier | Manage source document information |
| CDocumentIDTagger | Tags OpenMS file containers with a DocumentID |
| ►CExperimentalDesign | Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class |
| CMSFileSectionEntry | |
| CSampleSection | |
| CExperimentalSettings | Description of the experimental settings |
| CGradient | Representation of a HPLC gradient |
| CHPLC | Representation of a HPLC experiment |
| ►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): |
| CIdentification | Represents a object which can store the information of an analysisXML instance |
| CIdentificationHit | Represents a object which can store the information of an analysisXML instance |
| CInstrument | Description of a MS instrument |
| CInstrumentSettings | Description of the settings a MS Instrument was run with |
| CIonDetector | Description of a ion detector (part of a MS Instrument) |
| CIonSource | Description of an ion source (part of a MS Instrument) |
| CMassAnalyzer | Description of a mass analyzer (part of a MS Instrument) |
| 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 |
| CModification | Meta information about chemical modification of a sample |
| ►CMSQuantifications | |
| CAnalysisSummary | |
| CAssay | |
| CPeptideEvidence | Representation of a peptide evidence |
| ►CPeptideHit | Representation of a peptide hit |
| 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 |
| CSequenceLessComparator | Lesser predicate for (modified) sequence of hits |
| CPeptideIdentification | Represents the peptide hits for a spectrum |
| CPrecursor | Precursor meta information |
| CProduct | Product meta information |
| ►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 |
| CMapping | Two way mapping from ms-run-path to protID|pepID-identifier |
| CProteinGroup | Bundles multiple (e.g. indistinguishable) proteins in a group |
| CSearchParameters | Search parameters of the DB search |
| CSample | Meta information about the sample |
| CSampleTreatment | Base class for sample treatments (Digestion, Modification, Tagging, ...) |
| CScanWindow | Scan window description |
| CSoftware | Description of the software used for processing |
| CSourceFile | Description of a file location, used to store the origin of (meta) data |
| CSpectrumIdentification | Represents a object which can store the information of an analysisXML instance |
| 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 |
| CSpectrumSettings | Representation of 1D spectrum settings |
| CTagging | Meta information about tagging of a sample e.g. ICAT labeling |
| ►CContaminants | This class is a metric for the QualityControl TOPP tool |
| CContaminantsSummary | Structure for storing results |
| ►CDBSuitability | This class holds the functionality of calculating the database suitability |
| CSuitabilityData | Struct to store results |
| CDBSuitability_friend | |
| ►CFeatureSummary | |
| CResult | |
| ►CFragmentMassError | |
| CStatistics | Structure for storing results: average and variance of all FragmentMassErrors in ppm |
| CFWHM | QC metric calculating (un)calibrated m/z error |
| ►CIdentificationSummary | |
| CResult | |
| CUniqueID | |
| CMissedCleavages | This class is a metric for the QualityControl TOPP Tool |
| ►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 | |
| CMzCalibration | QC metric calculating (un)calibrated m/z error |
| CPeptideMass | QC metric calculating theoretical mass of a peptide sequence |
| ►CPSMExplainedIonCurrent | |
| CStatistics | Structure for storing results: average and variance over all PSMs |
| ►CQCBase | This class serves as an abstract base class for all QC classes |
| CSpectraMap | Map to find a spectrum via its NativeID |
| CRTAlignment | Take the original retention time before map alignment and use the alignment's trafoXML for calculation of the new alignment retention times |
| CSpectrumCount | |
| ►CTIC | |
| CResult | |
| CDetectabilitySimulation | Simulates peptide detectability |
| CDigestSimulation | Simulates protein digestion |
| ►CEGHFitter1D | Exponential-Gaussian hybrid 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) |
| CEGHFitterFunctor | |
| CEGHModel | Exponential-Gaussian hybrid distribution model for elution profiles |
| CIonizationSimulation | Simulates Protein ionization |
| CBaseLabeler | Abstract base class for all kinds of labeling techniques |
| CICPLLabeler | Simulate ICPL experiments |
| CITRAQLabeler | Simulate iTRAQ experiments |
| CLabelFreeLabeler | Abstract base class for all kinds of labeling techniques |
| CO18Labeler | Simulate O-18 experiments |
| CSILACLabeler | Simulate SILAC experiments |
| CMSSim | Central class for simulation of mass spectrometry experiments |
| ►CRawMSSignalSimulation | Simulates MS signals for a given set of peptides |
| CContaminantInfo | |
| CRawTandemMSSignalSimulation | Simulates tandem MS signals for a given set of peptides |
| CRTSimulation | Simulates/Predicts retention times for peptides or peptide separation |
| CExternalProcess | A wrapper around QProcess to conveniently start an external program and forward its outputs |
| ►CFile | Basic file handling operations |
| CTempDir | Class representing a temporary directory |
| CTemporaryFiles_ | Internal helper class, which holds temporary filenames and deletes these files at program exit |
| CFileWatcher | Watcher that monitors file changes |
| CJavaInfo | Detect Java and retrieve information |
| CNetworkGetRequest | |
| CPythonInfo | Detect Python and retrieve information |
| CRWrapper | R-Wrapper Class |
| ►CStopWatch | This class is used to determine the current process' CPU (user and/or kernel) and wall time |
| CTimeDiff_ | |
| ►CSysInfo | Some functions to get system information |
| CMemUsage | A convenience class to report either absolute or delta (between two timepoints) RAM usage |
| CUpdateCheck | Helper Functions to perform an update query to the OpenMS REST server |
| CBaseModel | Abstract base class for all D-dimensional models |
| CBiGaussFitter1D | BiGaussian distribution fitter (1-dim.) approximated using linear interpolation |
| CBiGaussModel | BiGaussian distribution approximated using linear interpolation |
| ►CEGHTraceFitter | A RT Profile fitter using an Exponential Gaussian Hybrid background model |
| CEGHTraceFunctor | |
| CElutionModelFitter | Helper class for fitting elution models to features |
| ►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 | |
| CEmgModel | Exponentially modified gaussian distribution model for elution profiles |
| CEmgScoring | Scoring of an elution peak using an exponentially modified gaussian distribution model |
| CExtendedIsotopeFitter1D | Extended isotope distribution fitter (1-dim.) approximated using linear interpolation |
| CExtendedIsotopeModel | Extended isotope distribution approximated using linear interpolation |
| CFeatureFinder | The main feature finder class |
| CSummary | Summary of fitting results |
| CFeatureFinderAlgorithm | Abstract base class for FeatureFinder algorithms |
| ►CFeatureFinderAlgorithmIsotopeWavelet | Implements the isotope wavelet feature finder |
| CBoxElement | Internally used data structure for the sweep line algorithm |
| ►CFeatureFinderAlgorithmMetaboIdent | |
| CFeatureCompare | Comparison functor for features |
| CFeatureFilterQuality | Predicate for filtering features by overall quality |
| CFeatureFinderMetaboIdentCompound | Compound in the assay library |
| CMassTraceBounds | Boundaries for a mass trace in a feature |
| CFeatureFinderAlgorithmMRM | FeatureFinderAlgorithm for MRM experiments |
| 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 | |
| CFeatureCompare | Comparison functor for features |
| CFeatureFilterPeptides | Predicate for filtering features by assigned peptides: |
| CFeatureFilterQuality | Predicate for filtering features by overall quality: |
| CPeptideCompare | Comparison functor for (unassigned) peptide IDs |
| CRTRegion | Region in RT in which a peptide elutes: |
| CFeatureFinderMultiplexAlgorithm | |
| CFitter1D | Abstract base class for all 1D-dimensional model fitter |
| 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 | |
| CInterpolationModel | Abstract class for 1D-models that are approximated using linear interpolation |
| CIsotopeFitter1D | Isotope distribution fitter (1-dim.) approximated using linear interpolation |
| CIsotopeModel | Isotope distribution approximated using linear interpolation |
| ►CIsotopeWavelet | Implements the isotope wavelet function |
| Cfi_ | Internal union for fast computation of the power function |
| ►CIsotopeWaveletTransform | A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the FeatureFinderAlgorithmIsotopeWavelet class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform |
| CBoxElement | Internally used data structure |
| CTransSpectrum | Internally (only by GPUs) used data structure . It allows efficient data exchange between CPU and GPU and avoids unnecessary memory moves. The class is tailored on the isotope wavelet transform and is in general not applicable on similar - but different - situations |
| ►CLevMarqFitter1D | Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization |
| CGenericFunctor | |
| CMaxLikeliFitter1D | Abstract base class for all 1D-model fitters using maximum likelihood optimization |
| CModelDescription | Stores the name and parameters of a model |
| ►CMultiplexClustering | Clusters results from multiplex filtering |
| CMultiplexDistance | Scaled Euclidean distance for clustering |
| ►CMultiplexDeltaMasses | Data structure for mass shift pattern |
| CDeltaMass | Mass shift with corresponding label set |
| ►CMultiplexDeltaMassesGenerator | Generates complete list of all possible mass shifts due to isotopic labelling |
| CLabel | Complete label information |
| CMultiplexFilteredMSExperiment | Data structure storing all peaks (and optionally their raw data points) of an experiment corresponding to one specific peak pattern |
| CMultiplexFilteredPeak | Data structure storing a single peak that passed all filters |
| CMultiplexFiltering | Base class for filtering centroided and profile data for peak patterns |
| CMultiplexFilteringCentroided | Filters centroided data for peak patterns |
| CMultiplexFilteringProfile | Filters centroided and profile data for peak patterns |
| CMultiplexIsotopicPeakPattern | Data structure for pattern of isotopic peaks |
| CMultiplexSatelliteCentroided | Data structure storing a single satellite peak |
| CMultiplexSatelliteProfile | Data structure storing a single satellite data point |
| CPeakWidthEstimator | Rough estimation of the peak width at m/z |
| CProductModel | Class for product models i.e. models with D independent dimensions |
| CProductModel< 2 > | The class template is only implemented for D=2 because we use Peak2D here |
| CSeedListGenerator | Generate seed lists for feature detection |
| ►CTraceFitter | Abstract fitter for RT profile fitting |
| CGenericFunctor | |
| CModelData | |
| CContinuousWaveletTransform | This class is the base class of the continuous wavelet transformation |
| CContinuousWaveletTransformNumIntegration | This class computes the continuous wavelet transformation using a marr wavelet |
| ►COptimizePeakDeconvolution | This class provides the deconvolution of peak regions using non-linear optimization |
| CData | Class containing the data needed for optimization |
| ►COptimizePick | This class provides the non-linear optimization of the peak parameters |
| CData | |
| COptPeakFunctor | |
| ►CPeakPickerCWT | This class implements a peak picking algorithm using wavelet techniques |
| CPeakArea_ | Class for the internal peak representation |
| ►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 |
| CPeakCandidate | A small structure to hold peak candidates |
| CPeakPickerIterative | This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data) |
| ►CPeakPickerMaxima | This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width |
| CPeakCandidate | The PeakCandidate describes the output of the peak picker |
| CPeakPickerSH | |
| ►CPeakShape | Internal representation of a peak shape (used by the PeakPickerCWT) |
| CPositionLess | Comparison of mz_positions |
| ►CTwoDOptimization | This class provides the two-dimensional optimization of the picked peak parameters |
| CData | Helper struct (contains the size of an area and a raw data container) |
| CTwoDOptFunctor | |
| CAnnotation1DCaret | An annotation item which paints a set of carets on the canvas |
| CAnnotation1DDistanceItem | An annotation item which represents a measured distance between two peaks |
| CAnnotation1DItem | An abstract class acting as an interface for the different 1D annotation items |
| CAnnotation1DPeakItem | A peak annotation item |
| CAnnotation1DTextItem | An annotation item which represents an arbitrary text on the canvas |
| CAnnotation1DVerticalLineItem | An annotation item which represents a vertical line (or more precisely a line along the gravity axis, i.e. it could also be horizontal) and text label on top |
| CAnnotations1DContainer | Container for annotations to content of Plot1DCanvas |
| CFLASHDeconvWizardBase | Main window of the FLASHDeconvWizard tool |
| CINIFileEditorWindow | Shows the ParamEditor widget in a QMainWindow with a toolbar |
| CQApplicationTOPP | Extension to the QApplication for running TOPPs GUI tools |
| CSwathWizardBase | Main window of the SwathWizard tool |
| CTOPPASBase | Main window of the TOPPAS tool |
| CTOPPViewBase | Main window of TOPPView tool |
| CAxisPainter | Draws a coordinate axis. It has only static methods, that's why the constructor is private |
| CAxisTickCalculator | Calculates ticks for a given value range |
| CAxisWidget | Widget that represents an axis of a graph |
| CColorSelector | A widget for selecting a color |
| CDataTabBase | All tabs need to implement this interface |
| CDataSelectionTabs | A tabbed view, to browse lists of spectra or identifications |
| CDataFilterDialog | Dialog for creating and changing a DataFilter |
| CFeatureEditDialog | Dialog for editing a feature |
| CHistogramDialog | Dialog that show a HistogramWidget |
| CLayerStatisticsDialog | Dialog showing statistics about the data of the current layer |
| CListFilterDialog | Dialog for creating and changing a DataFilter |
| CPlot1DGoToDialog | Simple goto/set visible area dialog for exact placement of the viewing window |
| CPlot2DGoToDialog | GoTo dialog used to zoom to a m/z and retention time range or to a feature |
| CSaveImageDialog | Dialog for saving an image |
| CSpectrumAlignmentDialog | Lets the user select two spectra and set the parameters for the spectrum alignment |
| ►CTheoreticalSpectrumGenerationDialog | Dialog which allows to enter an AA or NA sequence and generates a theoretical spectrum for it |
| CCheckBox | Struct for all information about a check box of an ion |
| CToolsDialog | TOPP tool selection dialog |
| CTOPPASInputFileDialog | Dialog which allows to specify an input file |
| CTOPPASInputFilesDialog | Dialog which allows to specify a list of input files |
| CTOPPASIOMappingDialog | Dialog which allows to configure the input/output parameter mapping of an edge |
| CTOPPASOutputFilesDialog | Dialog which allows to specify the directory for the output files |
| CTOPPASToolConfigDialog | TOPP tool configuration dialog |
| CTOPPASVertexNameDialog | Dialog which allows to change the name of an input/output vertex |
| CTOPPViewOpenDialog | Dataset opening options for TOPPView |
| CDIATreeTab | Hierarchical visualization and selection of spectra |
| CEnhancedTabBar | Convenience tab bar implementation |
| CSignalProvider | Signal mechanism (by deriving from QObject) for classes which are not allowed to have signals themselves |
| CEnhancedTabBarWidgetInterface | Widgets that are placed into an EnhancedTabBar must implement this interface |
| CEnhancedWorkspace | |
| CGUIProgressLoggerImpl | Implements a GUI version of the ProgressLoggerImpl |
| CHistogramWidget | Widget which can visualize a histogram |
| CInputFile | A simple widget with a line-edit and a browse button to choose filenames |
| CIPeptideIds | Abstract base class which defines an interface for PeptideIdentifications |
| CLayerData1DBase | Base class for all 1D layers, a special case of LayerData |
| CLayerData1DChrom | |
| CLayerData1DIonMobility | |
| CLayerData1DPeak | |
| ►CLayerDataDefs | |
| ►CProjectionData | Result of computing a projection on X and Y axis in a 2D Canvas; see LayerDataBase::getProjection() |
| CSummary | |
| CLayerDataBase | Class that stores the data for one layer |
| CLayerAnnotatorBase | |
| CLayerAnnotatorPeptideID | |
| CLayerAnnotatorAMS | |
| CLayerAnnotatorOSW | |
| CLayerDataChrom | Class that stores the data for one layer of type Chromatogram |
| CLayerDataConsensus | Class that stores the data for one layer of type ConsensusMap |
| CLayerDataFeature | Class that stores the data for one layer of type FeatureMap |
| CLayerDataIdent | Class that stores the data for one layer of type PeptideIdentifications |
| CLayerDataIonMobility | Class that stores the data for one layer of type IonMobility |
| CLayerDataPeak | Class that stores the data for one layer of type PeakMap |
| CLayerListView | Pimped QListView for Layers of a Canvas |
| CListEditor | Editor for editing int, double and string lists (including output and input file lists) |
| CLogWindow | A log window (QTextEdit) with convenience functions |
| CMetaDataBrowser | A meta data visualization widget |
| CExternalProcessMBox | A wrapper around ExternalProcess to conveniently show a MessageBox when an error occurs |
| CMultiGradient | A gradient of multiple colors and arbitrary distances between colors |
| CMultiGradientSelector | A widget witch allows constructing gradients of multiple colors |
| COutputDirectory | A simple widget with a line-edit and a browse button to choose filenames |
| CPainter1DBase | A base class for painting all items from a data layer (as supported by class derived from here) onto a 1D Canvas |
| CPainter1DPeak | Painter1D for spectra |
| CPainter1DChrom | Painter1D for chromatograms |
| CPainter1DIonMobility | Painter1D for mobilograms |
| CPainter2DBase | A base class for painting all items from a data layer (as supported by class derived from here) onto a 2D Canvas |
| CPainter2DPeak | Painter2D for spectra |
| CPainter2DChrom | Painter2D for chromatograms |
| CPainter2DIonMobility | Painter2D for ion mobilograms |
| CPainter2DFeature | Painter2D for Features |
| CPainter2DConsensus | Painter2D for ConsensusFeatures |
| CPainter2DIdent | Painter2D for Identifications |
| CPainterBase | An empty base class with some static convenience functions |
| CParamEditor | A GUI for editing or viewing a Param object |
| CGravitator | Manipulates X or Y component of points in the X-Y plane, by assuming one axis (either X or Y axis) has gravity acting upon it |
| CPlot1DCanvas | Canvas for visualization of one or several spectra |
| CPlot1DWidget | Widget for visualization of several spectra |
| CPlot2DCanvas | Canvas for 2D-visualization of peak map, feature map and consensus map data |
| CPlot2DWidget | Widget for 2D-visualization of peak map and feature map data |
| CPlot3DCanvas | Canvas for 3D-visualization of peak map data |
| CPlot3DOpenGLCanvas | OpenGL Canvas for 3D-visualization of map data |
| CPlot3DWidget | Widget for 3D-visualization of map data |
| CLayerStack | |
| CPlotCanvas | Base class for visualization canvas classes |
| CPlotWidget | Base class for spectrum widgets |
| CRecentFilesMenu | Manages recent files opened by the user and provides a QMenu to go with it |
| ►CSpectraIDViewTab | Tabular visualization / selection of identified spectra |
| CSelfResizingTableView_ | |
| CSpectraTreeTab | Hierarchical visualization and selection of spectra |
| CSwathLibraryStats | A multi-tabbed widget for the SwathWizard offering setting of parameters, input-file specification and running Swath and more |
| CTableView | A better QTable for TOPPView, which supports exporting to TSV and conveniently adding data to cells and headers |
| CTOPPASEdge | An edge representing a data flow in TOPPAS |
| CTOPPASInputFileListVertex | A vertex representing an input file list |
| CTOPPASMergerVertex | A special vertex that allows to merge several inputs |
| CTOPPASOutputFileListVertex | A vertex representing an output file list |
| CTOPPASResource | Represents a data resource for TOPPAS workflows |
| CTOPPASResources | A dictionary mapping string keys to lists of TOPPASResource objects |
| CFakeProcess | A FakeProcess class |
| ►CTOPPASScene | A container for all visual items of a TOPPAS workflow |
| CTOPPProcess | Stores the information for a TOPP process |
| CTOPPASSplitterVertex | A special vertex that allows to split a list of inputs |
| ►CTOPPASToolVertex | A vertex representing a TOPP tool |
| CIOInfo | Stores the information for input/output files/lists |
| CTOPPASTreeView | Tree view implementation for the list of TOPP tools |
| ►CTOPPASVertex | The base class of the different vertex classes |
| CTOPPASFilenames | |
| CVertexRoundPackage | Info for one edge and round, to be passed to next node |
| CTOPPASWidget | Widget visualizing and allowing to edit TOPP pipelines |
| ►CTOPPViewMenu | The file menu items for TOPPView |
| CActionRequirement_ | |
| CTreeView | A better QTreeWidget for TOPPView, which supports header context menu and conveniently adding/getting headers names |
| CTVControllerBase | Base behavior for different visualizaton modules in TOPPView |
| CTVDIATreeTabController | Behavior of TOPPView in spectra view mode |
| CTVIdentificationViewController | Behavior of TOPPView in identification mode |
| CTVSpectraViewController | Behavior of TOPPView in spectra view mode |
| CTVToolDiscovery | Scans for tools/utils and generates a param for each asynchronously |
| CRangeStats | Struct representing the statistics about a set of values |
| CStatsCounter | Simple counting struct, for non-numerical occurrences of meta-values |
| CRangeStatsType | Origin and name of a statistic |
| CLayerStatistics | Compute summary statistics (count/min/max/avg) about a container, e.g. intensity, charge, meta values, .. |
| CLayerStatisticsPeakMap | Computes statistics and distributions for a PeakMap |
| CLayerStatisticsFeatureMap | Computes statistics and distributions for a PeakMap |
| CLayerStatisticsConsensusMap | Computes statistics and distributions for a PeakMap |
| CLayerStatisticsIdent | Computes statistics and distributions for a vector<PeptideIdentifications> |
| CLayerStoreData | Base class to store either the currently visible or all data of a canvas |
| CLayerStoreDataPeakMapVisible | Visitor which can save a visible piece of data; subsequently the data can be stored to a file |
| CLayerStoreDataPeakMapAll | Visitor which can save a full experiment; subsequently the data can be stored to a file |
| CLayerStoreDataFeatureMapVisible | Visitor which can save a visible piece of data; subsequently the data can be stored to a file |
| CLayerStoreDataFeatureMapAll | Visitor which can save a full FeatureMap; subsequently the data can be stored to a file |
| CLayerStoreDataConsensusMapVisible | Visitor which can save a visible piece of data; subsequently the data can be stored to a file |
| CLayerStoreDataConsensusMapAll | Visitor which can save a full ConsensusMap; subsequently the data can be stored to a file |
| CLayerStoreDataIdentVisible | Visitor which can save a visible piece of data; subsequently the data can be stored to a file |
| CLayerStoreDataIdentAll | Visitor which can save a full set of Identifications; subsequently the data can be stored to a file |
| CAcquisitionInfoVisualizer | Class that displays all meta information for AcquisitionInfo objects |
| CAcquisitionVisualizer | Class that displays all meta information for Acquisition objects |
| CBaseVisualizer | A base class for all visualizer classes |
| CBaseVisualizerGUI | A base class for all visualizer classes |
| CContactPersonVisualizer | Class that displays all meta information for ContactPerson objects |
| CDataProcessingVisualizer | Class that displays all meta information for DataProcessing objects |
| CDigestionVisualizer | Class that displays all meta information of digestion objects |
| CDocumentIdentifierVisualizer | Class that displays all meta information for DocumentIdentifier objects |
| CExperimentalSettingsVisualizer | Class that displays all meta information for ExperimentalSettings objects |
| CGradientVisualizer | GradientVisualizer is a visualizer class for objects of type gradient |
| CHPLCVisualizer | Class that displays all meta information for HPLC objects |
| CInstrumentSettingsVisualizer | Class that displays all meta information for InstrumentSettings objects |
| CInstrumentVisualizer | Class that displays all meta information for an MS instrument |
| CIonDetectorVisualizer | Class that displays all meta information for IonDetector objects |
| CIonSourceVisualizer | Class that displays all meta information for IonSource objects |
| CMassAnalyzerVisualizer | Class that displays all meta information for MassAnalyzer objects |
| CMetaInfoDescriptionVisualizer | Class that displays all meta information for MetaInfoDescription objects |
| CMetaInfoVisualizer | MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member |
| CModificationVisualizer | Class that displays all meta information of modification objects |
| CPeptideHitVisualizer | Class that displays all meta information for PeptideHit objects |
| CPeptideIdentificationVisualizer | Class that displays all meta information for PeptideIdentification objects |
| CPrecursorVisualizer | Class that displays all meta information for Precursor objects |
| CProductVisualizer | Class that displays all meta information for Product objects |
| CProteinHitVisualizer | Class that displays all meta information for ProteinHit objects |
| CProteinIdentificationVisualizer | Class that displays all meta information for ProteinIdentification objects |
| CSampleVisualizer | Class that displays all meta information of sample objects |
| CScanWindowVisualizer | Class that displays all meta information for ScanWindow objects |
| CSoftwareVisualizer | Class that displays all meta information for Software objects |
| CSourceFileVisualizer | Class that displays all meta information for SourceFile objects |
| CSpectrumSettingsVisualizer | Class that displays all meta information for SpectrumSettings objects |
| CTaggingVisualizer | Class that displays all meta information of tagging objects |
| ►NOpenSwath | |
| ►NScoring | Scoring functions used by MRMScoring |
| Cpair_hash | Simple hash function for Scoring::pos2D |
| CXCorrArrayType | |
| Cmean_and_stddev | Functor to compute the mean and stddev of sequence using the std::foreach algorithm |
| CIDataFrameWriter | |
| CDataMatrix | |
| CCSVWriter | |
| COSBinaryDataArray | The datastructures used by the OpenSwath interfaces |
| COSChromatogramMeta | Identifying information for a chromatogram |
| COSChromatogram | A single chromatogram |
| ►COSSpectrumMeta | Identifying information for a spectrum |
| CRTLess | Comparator for the retention time |
| COSSpectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
| CISpectrumAccess | The interface of a mass spectrometry experiment |
| CIFeature | |
| CIMRMFeature | |
| CITransitionGroup | |
| CISignalToNoise | |
| CMockFeature | Mock object implementing IFeature |
| CMockMRMFeature | Mock object implementing IMRMFeature |
| CMockTransitionGroup | Mock object implementing ITransitionGroup |
| CMockSignalToNoise | Mock object implementing ISignalToNoise |
| CSwathMap | Data structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2 |
| CLightTransition | |
| CLightModification | |
| CLightCompound | |
| CLightProtein | |
| CLightTargetedExperiment | |
| CTransitionHelper | |
| CPeptide | |
| CProtein | |
| CTargetedExperiment | |
| CMRMScoring | This class implements different scores for peaks found in SRM/MRM |
| CSwathQC | Quality Control function for OpenSwath |
| NSQLite | |
| ►Nstd | STL namespace |
| Chash< OpenMS::Index > | |
| Chash< OpenMS::String > | |
| NUi | |
1.9.1 
