| ►NEigen | |
| CSparseVector | |
| ►Neol_bspline | |
| CBSpline | |
| NH5 | |
| NIsoSpec | |
| ►NKDTree | |
| ►C_Alloc_base | |
| CNoLeakAlloc | |
| C_Base_iterator | |
| C_Bracket_accessor | |
| C_Iterator | |
| C_Node | |
| C_Node_base | |
| C_Node_compare | |
| C_Region | |
| Calways_true | |
| CKDTree | |
| Csquared_difference | |
| Csquared_difference_counted | |
| ►Nms | |
| ►Nnumpress | |
| NMSNumpress | |
| ►NOpenMS | Main OpenMS namespace |
| ►NConstants | Mathematical and physical constants namespace |
| NUserParam | |
| ►NDataArrays | |
| CFloatDataArray | Float data array class |
| CIntegerDataArray | Integer data array class |
| CStringDataArray | String data array class |
| ►NDetail | |
| CMetaKeyGetter | |
| Ndetail | |
| NDIAHelpers | |
| ►NException | Exception namespace |
| CBaseException | Exception base class |
| CBufferOverflow | Buffer overflow exception |
| CConversionError | Invalid conversion exception |
| CDepletedIDPool | Exception used if no more unique document ID's can be drawn from ID pool |
| CDivisionByZero | Division by zero error exception |
| CElementNotFound | Element could not be found exception |
| CExternalExecutableNotFound | External executable (e.g. comet.exe) not found exception |
| CFailedAPICall | A call to an external library (other than OpenMS) went wrong |
| CFileEmpty | File is empty |
| CFileNameTooLong | Filename is too long to be writable/readable by the filesystem |
| CFileNotFound | File not found exception |
| CFileNotReadable | File not readable exception |
| CFileNotWritable | File not writable exception |
| CGlobalExceptionHandler | OpenMS global exception handler |
| CIllegalArgument | A method or algorithm argument contains illegal values |
| CIllegalPosition | Invalid 3-dimensional position exception |
| CIllegalSelfOperation | Illegal self operation exception |
| CIllegalTreeOperation | Illegal tree operation exception |
| CIncompatibleIterators | Incompatible iterator exception |
| CIndexOverflow | Int overflow exception |
| CIndexUnderflow | Int underflow exception |
| CInternalToolError | A tool or algorithm which was called internally raised an exception |
| CInvalidFileType | Invalid file type exception |
| CInvalidIterator | Invalid iterator exception |
| CInvalidParameter | Exception indicating that an invalid parameter was handed over to an algorithm |
| CInvalidRange | Invalid range exception |
| CInvalidSize | Invalid UInt exception |
| CInvalidValue | Invalid value exception |
| CIOException | General IOException |
| CMissingInformation | Not all required information provided |
| CNotImplemented | Not implemented exception |
| CNotSorted | Array not sorted exception |
| CNullPointer | Null pointer argument is invalid exception |
| COutOfGrid | Out of grid exception |
| COutOfMemory | Out of memory exception |
| COutOfRange | Out of range exception |
| CParseError | Parse Error exception |
| CPostcondition | Postcondition failed exception |
| CPrecondition | Precondition failed exception |
| CRequiredParameterNotGiven | A required parameter was not given |
| CSizeUnderflow | UInt underflow exception |
| CSqlOperationFailed | SqlOperation failed exception |
| CUnableToCalibrate | Exception used if an error occurred while calibrating a dataset |
| CUnableToCreateFile | Unable to create file exception |
| CUnableToFit | Exception used if an error occurred while fitting a model to a given dataset |
| CUnregisteredParameter | An unregistered parameter was accessed |
| CWrongParameterType | A parameter was accessed with the wrong type |
| NFastLowessSmoothing | LOWESS (locally weighted scatterplot smoothing) |
| ►NGUIHelpers | |
| ►CColorBrewer | |
| CDistinct | |
| CGUILock | RAII class to disable the GUI and set a busy cursor and go back to the original state when this class is destroyed |
| COverlapDetector | A heuristic: Given a set of levels (rows), try to add items at to topmost row which does not overlap an already placed item in this row (according to its x-coordinate) |
| NHelpers | |
| ►NIdentificationDataInternal | |
| CAdductCompare | Comparator for adducts |
| CAppliedProcessingStep | |
| CDBSearchParam | Parameters specific to a database search step |
| CIdentifiedCompound | |
| CIdentifiedMolecule | Variant type holding Peptide/Compound/Oligo references and convenience functions |
| CIdentifiedSequence | Representation of an identified sequence (peptide or oligonucleotide) |
| CInputFile | Information about input files that were processed |
| CIteratorWrapper | Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi_index_containers |
| CObservation | Representation of an observation, e.g. a spectrum or feature, in an input data file |
| CObservationMatch | Representation of a search hit (e.g. peptide-spectrum match) |
| CObservationMatchGroup | : Group of related (co-identified) input matches |
| CParentGroup | : Group of ambiguously identified parent sequences (e.g. protein group) |
| CParentGroupSet | Set of groups of ambiguously identified parent sequences (e.g. results of running a protein inference algorithm) |
| CParentMatch | Meta data for the association between an identified molecule (e.g. peptide) and a parent sequence (e.g. protein) |
| CParentSequence | Representation of a parent sequence that is identified only indirectly (e.g. a protein) |
| CProcessingSoftware | Information about software used for data processing |
| CProcessingStep | Data processing step that is applied to the data (e.g. database search, PEP calculation, filtering, ConsensusID) |
| CScoredProcessingResult | Base class for ID data with scores and processing steps (and meta info) |
| CScoreType | Information about a score type |
| ►Nims | |
| ►CIMSAlphabet | Holds an indexed list of bio-chemical elements |
| 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 |
| CChromatogram | A single chromatogram |
| CChromatogramMeta | Identifying information for a chromatogram |
| CIChromatogramsReader | The interface of read-access to a list of chromatograms |
| CIChromatogramsWriter | |
| CIMSDataConsumer | The interface of a consumer of spectra and chromatograms |
| CISpectraReader | The interface of read-access to a list of spectra |
| CISpectraWriter | |
| CSpectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
| CSpectrumMeta | Identifying information for a spectrum |
| ►NInternal | Namespace used to hide implementation details from users |
| NClassTest | Namespace for class tests |
| NSqliteHelper | |
| CAcqusHandler | Read-only acqus File handler for XMass Analysis |
| ►CAreaIterator | Forward iterator for an area of peaks in an experiment |
| CParam | |
| CArgs | Custom arguments to allow for looping calls |
| CCachedMzMLHandler | An class that uses on-disk caching to read and write spectra and chromatograms |
| CCommand | |
| CConsensusXMLHandler | This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation |
| CDIntervalBase | A base class for D-dimensional interval |
| CFeatureXMLHandler | This class provides Input/Output functionality for feature maps |
| CFFIDAlgoExternalIDHandler | Class for handling external peptide identifications in feature finding |
| CFidHandler | Read-only fid File handler for XMass Analysis |
| CFileMapping | Maps input/output files to filenames for the external program |
| CFilterableList | A widget which shows a list of text items, which can be filtered |
| CFilterList | A widget which shows a list of DataFilter items |
| CFLASHDeconvTabWidget | A multi-tabbed widget for the FLASHDeconvWizard offering setting of parameters, input-file specification and running FLASHDeconv and more |
| ►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 |
| CIdentification | |
| CIdentificationHit | Represents a object which can store the information of an analysisXML instance |
| CIndexedMzMLHandler | A low-level class to read an indexedmzML file |
| CInputFileList | A widget shows a list of input files (i.e. existing files on a mounted drive), which allows adding/removing files and supports drag'n'drop from the window manager |
| CIntensityIteratorWrapper | An iterator wrapper to access peak intensities instead of the peak itself |
| CListEditorDelegate | Internal delegate class |
| CListTable | |
| CLooper | |
| CLooper< grid_size, grid_size, EvalResult, Tuple, TupleTypes... > | |
| CLooper< param_index, grid_size, EvalResult, Tuple, FirstTupleType, TupleTypes... > | |
| CMappingParam | Filename mappings for all input/output files |
| CMascotXMLHandler | Handler that is used for parsing MascotXML data |
| CMessagePasserFactory | |
| CMzDataHandler | |
| CMzDataValidator | Semantically validates MzXML files |
| ►CMzIdentMLDOMHandler | XML DOM handler for MzIdentMLFile |
| CAnalysisSoftware | Struct to hold the used analysis software for that file |
| CDatabaseInput | Struct to hold the information from the DatabaseInput xml tag |
| CDBSequence | Struct to hold the information from the DBSequence xml tag |
| CModificationParam | Struct to hold the information from the ModificationParam xml tag |
| CPeptideEvidence | Struct to hold the PeptideEvidence information |
| CSpectrumIdentification | Struct to hold the information from the SpectrumIdentification xml tag |
| CSpectrumIdentificationProtocol | Struct to hold the information from the SpectrumIdentificationProtocol xml tag |
| CMzIdentMLHandler | XML STREAM handler for MzIdentMLFile |
| CMzIdentMLValidator | Semantically validates MzXML files |
| ►CMzMLHandler | Handler for mzML file format |
| CChromatogramData | Data necessary to generate a single chromatogram |
| CSpectrumData | Data necessary to generate a single spectrum |
| ►CMzMLHandlerHelper | Helper for mzML file format |
| CBinaryData | Representation for binary data in mzML |
| CMzMLSqliteHandler | Sqlite handler for storing spectra and chromatograms in sqMass format |
| CMzMLSqliteSwathHandler | Sqlite handler for SWATH data sets |
| CMzMLValidator | Semantically validates MzXML files |
| ►CMzXMLHandler | |
| CSpectrumData | Data necessary to generate a single spectrum |
| COMSFileLoad | Helper class for loading .oms files (SQLite format) |
| COMSFileStore | Helper class for storing .oms files (SQLite format) |
| COpenMSBuildInfo | Struct with some static methods to get informations on the build configuration |
| COpenMSLineEdit | Custom QLineEdit which emits a signal when losing focus (such that we can commit its data) |
| COpenMSOSInfo | |
| CParamEditorDelegate | Internal delegate class for QTreeWidget |
| CParamTree | QTreeWidget that emits a signal whenever a new row is selected |
| CParamXMLHandler | XML Handler for Param files |
| CPlot1DPrefDialog | Preferences dialog for Plot1DWidget |
| CPlot2DPrefDialog | Preferences dialog for Plot2DWidget |
| CPlot3DPrefDialog | Preferences dialog for Plot3DWidget |
| CPTMXMLHandler | Handler that is used for parsing PTMXML data |
| CPythonModuleRequirement | |
| CPythonSelector | |
| ►CSemanticValidator | Semantically validates XML files using CVMappings and a ControlledVocabulary |
| CCVTerm | Representation of a parsed CV term |
| Cshared_xerces_ptr | |
| CSpectrumIdentification | |
| CStringManager | |
| CSwathTabWidget | A multi-tabbed widget for the SwathWizard offering setting of parameters, input-file specification and running Swath and more |
| CToolDescription | |
| CToolDescriptionHandler | XML handler for ToolDescriptionFile |
| CToolDescriptionInternal | ToolDescription Class |
| CToolExternalDetails | |
| CTOPPViewPrefDialog | Preferences dialog for TOPPView |
| CTraMLHandler | XML handler for TraMLFile |
| CTraMLValidator | Semantically validates MzXML files |
| CUnimodXMLHandler | Handler that is used for parsing XTandemXML data |
| Cunique_xerces_ptr | |
| CWizardGUILock | RAII class to switch to certain TabWidget, disable the GUI and go back to the orignal Tab when this class is destroyed |
| CXMLFile | Base class for loading/storing XML files that have a handler derived from XMLHandler |
| ►CXMLHandler | Base class for XML handlers |
| CEndParsingSoftly | Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file is needed) |
| CXQuestResultXMLHandler | XMLHandler for the result files of XQuest |
| REvaluator | |
| ►NLogger | Log streams |
| CLogStream | Log Stream Class |
| ►CLogStreamBuf | Stream buffer used by LogStream |
| CLogCacheStruct | Holds a counter of occurrences and an index for the occurrence sequence of the corresponding log message |
| CStreamStruct | Holds a stream that is connected to the LogStream. It also includes the minimum and maximum level at which the LogStream redirects messages to this stream |
| CLogStreamNotifier | |
| ►NMath | Math namespace |
| CAdaptiveQuantileResult | Result of adaptiveQuantile computation |
| CBasicStatistics | Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation |
| CBilinearInterpolation | Provides access to bilinearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero |
| ►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 |
| CLinearInterpolation | Provides access to linearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero |
| CLinearRegression | This class offers functions to perform least-squares fits to a straight line model, \( Y(c,x) = c_0 + c_1 x \) |
| CLinearRegressionWithoutIntercept | This class offers functions to perform least-squares fits to a straight line model, \( Y(c,x) = c_0 + c_1 x \) |
| CPosteriorErrorProbabilityModel | Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture |
| CQuadraticRegression | |
| CRandomShuffler | |
| CRANSAC | This class provides a generic implementation of the RANSAC outlier detection algorithm. Is implemented and tested after the SciPy reference: http://wiki.scipy.org/Cookbook/RANSAC |
| CRansacModel | Generic plug-in template base class using 'Curiously recurring template pattern' (CRTP) to allow for arbitrary RANSAC models (e.g. linear or quadratic fits) |
| CRansacModelLinear | Implementation of a linear RANSAC model fit |
| CRansacModelQuadratic | Implementation of a quadratic RANSAC model fit |
| CRANSACParam | A simple struct to carry all the parameters required for a RANSAC run |
| ►CROCCurve | ROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cutoff values |
| Csimsortdec | Predicate for sort() |
| CSummaryStatistics | Helper class to gather (and dump) some statistics from a e.g. vector<double> |
| NNNLS | |
| NNuXLPresets | |
| ►NStringConversions | |
| ►NDetail | |
| CBK_PrecPolicyFull | |
| CBK_PrecPolicyShort | |
| NStringUtils | |
| ►NTargetedExperimentHelper | This class stores helper structures that are used in multiple classes of the TargetedExperiment (e.g. ReactionMonitoringTransition and IncludeExcludeTarget) |
| CCompound | Represents a compound (small molecule) |
| CConfiguration | |
| CContact | |
| CCV | |
| CInstrument | |
| CInterpretation | Product ion interpretation |
| ►CPeptide | Represents a peptide (amino acid sequence) |
| CModification | |
| CPeptideCompound | Base class to represent either a peptide or a compound |
| CPrediction | |
| CProtein | |
| CPublication | |
| CRetentionTime | This class stores a retention time structure that is used in TargetedExperiment (representing a TraML file) |
| CTraMLProduct | Represents a product ion |
| NTest | |
| CAA | |
| CAAIndex | Representation of selected AAIndex properties |
| ►CAASequence | Representation of a peptide/protein sequence |
| CConstIterator | ConstIterator for AASequence |
| CIterator | Iterator class for AASequence |
| CAbsoluteQuantitation | AbsoluteQuantitation is a class to support absolute or relative quantitation for targeted or untargeted quantitation workflows (e.g., Isotope Dilution Mass Spectrometry) |
| CAbsoluteQuantitationMethod | AbsoluteQuantitationMethod is a class to hold information about the quantitation method and for applying and/or generating the quantitation method |
| CAbsoluteQuantitationMethodFile | File adapter for AbsoluteQuantitationMethod files |
| ►CAbsoluteQuantitationStandards | 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 |
| CAbsoluteQuantitationStandardsFile | Load files containing runConcentration data |
| ►CAccurateMassSearchEngine | An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB) |
| CCompareEntryAndMass_ | |
| CMappingEntry_ | |
| CAccurateMassSearchResult | |
| ►CACNode | |
| CDepthHits | Internal struct to steal one bit from depth to use as hit indicator |
| CAcquisition | Information about one raw data spectrum that was combined with several other raw data spectra |
| CAcquisitionInfo | Description of the combination of raw data to a single spectrum |
| CAcquisitionInfoVisualizer | Class that displays all meta information for AcquisitionInfo objects |
| CAcquisitionVisualizer | Class that displays all meta information for Acquisition objects |
| CACScout | Spin-off search path through the trie, which can deal with ambiguous AAs and mismatches |
| CACTrie | An Aho Corasick trie (a set of nodes with suffix links mainly) |
| CACTrieState | |
| CAdduct | |
| CAdductInfo | |
| ►CAnnotatedMSRun | Class for storing MS run data with peptide and protein identifications |
| CPairIterator | Iterator for pairs of spectra and peptide identifications |
| CAnnotation1DCaret | An annotation item which paints a set of carets on the canvas |
| CAnnotation1DDistanceItem | An annotation item which represents a measured distance between two peaks |
| CAnnotation1DItem | An abstract class acting as an interface for the different 1D annotation items |
| CAnnotation1DPeakItem | A peak annotation item |
| CAnnotation1DTextItem | An annotation item which represents an arbitrary text on the canvas |
| CAnnotation1DVerticalLineItem | An annotation item which represents a vertical line (or more precisely a line along the gravity axis, i.e. it could also be horizontal) and text label on top |
| CAnnotations1DContainer | Container for annotations to content of Plot1DCanvas |
| CAnnotationStatistics | |
| CArea | |
| CAScore | Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the most probable phosphorylation-site(s). For each phosphorylation site a probability score is calculated. The algorithm is implemented according to Beausoleil et al. (Nat. Biotechnol. 2006) |
| CAverageLinkage | AverageLinkage ClusterMethod |
| CAxisPainter | Draws a coordinate axis. It has only static methods, that's why the constructor is private |
| CAxisTickCalculator | Calculates ticks for a given value range |
| CAxisWidget | Widget that represents an axis of a graph |
| ►CBase64 | Class to encode and decode Base64 |
| CReinterpreter32_ | Internal class needed for type-punning |
| CReinterpreter64_ | Internal class needed for type-punning |
| ►CBaseFeature | A basic LC-MS feature |
| CQualityLess | Compare by quality |
| CBaseGroupFinder | The base class of all element group finding algorithms |
| CBaseModel | Abstract base class for 1-dimensional models |
| CBaseSuperimposer | The base class of all superimposer algorithms |
| CBaseVisualizer | A base class for all visualizer classes |
| CBaseVisualizerGUI | A base class for all visualizer classes |
| CBasicProteinInferenceAlgorithm | 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) |
| CBiGaussFitter1D | BiGaussian distribution fitter (1-dim.) approximated using linear interpolation |
| CBiGaussModel | |
| CBinaryTreeNode | Elements of a binary tree used to represent a hierarchical clustering process |
| CBinnedSharedPeakCount | Compare functor scoring the shared peaks for similarity measurement |
| CBinnedSpectralContrastAngle | Compare functor scoring the spectral contrast angle for similarity measurement |
| CBinnedSpectrum | This is a binned representation of a PeakSpectrum |
| CBinnedSpectrumCompareFunctor | Base class for compare functors of BinnedSpectra |
| CBinnedSumAgreeingIntensities | Sum of agreeing intensities for similarity measurement |
| ►CBiosaur2Algorithm | Implementation of the Biosaur2 feature detection workflow for LC-MS1 data |
| CFastHillEntry | Lightweight index entry for fast m/z-based hill lookup |
| CHill | Representation of a single hill (continuous m/z trace across adjacent scans) |
| CIsotopeCandidate | Candidate isotope peak that can be associated with a monoisotopic hill |
| CPatternCandidate | Internal representation of a candidate isotope pattern |
| CPeptideFeature | Aggregated properties of a detected peptide feature |
| CBitset | Custom bitset which uses a 32-bit integer to store bits (instead of 8 bytes for std::bitset<32> on Clang/GCC) |
| CBSpline2d | B spline interpolation |
| 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 |
| CCachedSwathFileConsumer | On-disk cached implementation of FullSwathFileConsumer |
| CCalibrationData | A helper class, holding all calibration points |
| CCentroidTolerances | Structure to hold centroid-based overlap tolerances |
| CChannelQC | Small quality control class, holding temporary data for reporting |
| CChargePair | Representation of a (putative) link between two Features, which stem from the same compound but have different charge (including different adduct ions (H+, Na+, ..) |
| CChromatogramExtractor | The ChromatogramExtractor extracts chromatograms (intensity vs retention time) from mass spectrometry data |
| ►CChromatogramExtractorAlgorithm | The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data |
| CExtractionCoordinates | |
| ►CChromatogramPeak | A 1-dimensional raw data point or peak for chromatograms |
| CIntensityLess | Comparator by intensity |
| CPositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for RTLess |
| CRTLess | Comparator by RT position |
| CChromatogramRangeManager | Range manager for chromatograms |
| CChromatogramSettings | Representation of chromatogram settings, e.g. SRM/MRM chromatograms |
| CChromatogramTools | Conversion class to convert chromatograms |
| CChromeleonFile | Load Chromeleon HPLC text file and save it into a MSExperiment |
| CChromExtractParams | ChromatogramExtractor parameters |
| CCitation | Stores Citations for individual TOPP tools |
| CClusterAnalyzer | Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's) |
| ►CClusterFunctor | Base class for cluster functors |
| CInsufficientInput | Exception thrown if not enough data (<2) is used |
| CClusterHierarchical | Hierarchical clustering with generic clustering functions |
| CClusteringGrid | Data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering |
| CClusterProxyKD | Proxy for a (potential) cluster |
| CCmpHypothesesByScore | |
| CCmpMassTraceByMZ | |
| CCoarseIsotopePatternGenerator | Isotope pattern generator for coarse isotope distributions |
| ►CColorizer | Color and style the fonts shown on cout/cerr (or other streams) |
| CColorWithUndo_ | |
| CColorSelector | A widget for selecting a color |
| CCompareMzTabMMatchRef | Data model of MzTabM files. Please see the official MzTabM specification at https://github.com/HUPO-PSI/mzTab/tree/master/specification_document-releases/2_0-Metabolomics-Release |
| CCompleteLinkage | CompleteLinkage ClusterMethod |
| CCompomer | Holds information on an edge connecting two features from a (putative) charge ladder |
| CCompressedInputSource | This class is based on xercesc::LocalFileInputSource |
| ►CConfidenceScoring | |
| CGLM_ | Binomial GLM |
| CRTNorm_ | Helper for RT normalization (range 0-100) |
| CConnectedComponent | |
| ►CConsensusFeature | A consensus feature spanning multiple LC-MS/MS experiments |
| CMapsLess | Compare by the sets of consensus elements (lexicographically) |
| CRatio | Slim struct to feed the need for systematically storing of ratios |
| CSizeLess | Compare by size(), the number of consensus elements |
| ►CConsensusIDAlgorithm | Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs) |
| CHitInfo | |
| CConsensusIDAlgorithmAverage | Calculates a consensus from multiple ID runs by averaging the search scores |
| CConsensusIDAlgorithmBest | Calculates a consensus from multiple ID runs by taking the best search score |
| CConsensusIDAlgorithmIdentity | Abstract base class for ConsensusID algorithms that compare only identical sequences |
| CConsensusIDAlgorithmPEPIons | Calculates a consensus from multiple ID runs based on PEPs and shared ions |
| CConsensusIDAlgorithmPEPMatrix | Calculates a consensus from multiple ID runs based on PEPs and sequence similarities |
| CConsensusIDAlgorithmRanks | Calculates a consensus from multiple ID runs based on the ranks of the search hits |
| CConsensusIDAlgorithmSimilarity | Abstract base class for ConsensusID algorithms that take peptide similarity into account |
| CConsensusIDAlgorithmWorst | Calculates a consensus from multiple ID runs by taking the worst search score (conservative approach) |
| ►CConsensusMap | A container for consensus elements |
| CColumnHeader | Description of the columns in a consensus map |
| CConsensusMapMergerAlgorithm | Merges identification data in ConsensusMaps |
| CConsensusMapNormalizerAlgorithmMedian | Algorithms of ConsensusMapNormalizer |
| CConsensusMapNormalizerAlgorithmQuantile | Algorithms of ConsensusMapNormalizer |
| CConsensusMapNormalizerAlgorithmThreshold | Algorithms of ConsensusMapNormalizer |
| CConsensusXMLFile | This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation |
| CConsoleUtils | |
| ►CConstRefVector | This vector holds pointer to the elements of another container |
| CConstRefVectorConstIterator | ConstIterator for the ConstRefVector |
| CConstRefVectorIterator | Mutable iterator for the ConstRefVector |
| CContactPerson | Contact person information |
| CContactPersonVisualizer | Class that displays all meta information for ContactPerson objects |
| ►CContaminants | This class is a metric for the QualityControl TOPP tool |
| CContaminantsSummary | Structure for storing results |
| ►CControlledVocabulary | |
| CCVTerm | Representation of a CV term |
| CFNV1aHasher | Ensure same hash on all platforms (for reproducibility)- |
| CConvexHull2D | |
| CCrossLinksDB | |
| CCrossValidation | Lightweight K-fold / LOO cross-validation utilities and 1-D grid search |
| CCsvFile | This class handles csv files. Currently only loading is implemented. Does NOT support comment lines! |
| 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 |
| CCVMappingFile | Used to load CvMapping files |
| CCVMappingRule | Representation of a CV Mapping rule used by CVMappings |
| CCVMappings | Representation of controlled vocabulary mapping rules (for PSI formats) |
| CCVMappingTerm | Representation of controlled vocabulary term |
| CCVReference | Controlled Vocabulary Reference |
| ►CCVTerm | Representation of controlled vocabulary term |
| CUnit | |
| CCVTermList | Representation of controlled vocabulary term list |
| CCVTermListInterface | Interface to the controlled vocabulary term list |
| CDataFilterDialog | Dialog for creating and changing a DataFilter |
| ►CDataFilters | DataFilter array providing some convenience functions |
| CDataFilter | Representation of a peak/feature filter combining FilterType, FilterOperation and a value (either double or String) |
| CDataProcessing | Description of the applied preprocessing steps |
| CDataProcessingVisualizer | Class that displays all meta information for DataProcessing objects |
| CDataSelectionTabs | A tabbed view, to browse lists of spectra or identifications |
| CDataTabBase | All tabs need to implement this interface |
| CDataValue | Class to hold strings, numeric values, lists of strings and lists of numeric values |
| CDate | Date Class |
| CDateTime | DateTime Class |
| CDaTrait | |
| CDBoundingBox | A D-dimensional bounding box |
| ►CDBSuitability | This class holds the functionality of calculating the database suitability |
| CSuitabilityData | Struct to store results |
| CDBSuitability_friend | |
| CDDAWorkflowCommons | Common functions for DDA workflows |
| CDeconvolvedSpectrum | A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroup instances representing masses. For MSn n>1, a PeakGroup representing the precursor mass is also added in this class. Properly assigning a precursor mass from the original precursor peak and its deconvolution result is very important in top down proteomics. This assignment is performed here for conventional acquired datasets. But for FLASHIda acquired datasets, the assignment is already done by FLASHIda. So this class simply use the results from FLASHIda log file for assignment. The parsing of FLASHIda log file is done in FLASHDeconv tool class |
| CDecoyGenerator | Methods to generate isobaric decoy sequences for DDA target-decoy searches |
| ►CDecoyHelper | Helper class for calculations on decoy proteins |
| CDecoyStatistics | Struct for intermediate results needed for calculations on decoy proteins |
| CResult | |
| CDefaultParamHandler | A base class for all classes handling default parameters |
| CDeisotoper | |
| 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 |
| CDIATreeTab | Hierarchical visualization and selection of spectra |
| 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) |
| CDimBase | A base class for a dimension which represents a certain unit (e.g. RT or m/z). Derived classes implement virtual functions, which receive a well-defined data type, e.g. a Feature, and return the appropriate value for their dimension (the DimRT class would return the RT of the feature). This makes it possible to extract dimensions using a runtime configuration of DimBase instances. Very useful when mapping units (RT, m/z) to axis when plotting etc |
| CDimIM | Dimension implementation for ion mobility values |
| CDimINT | Dimension implementation for intensity values |
| CDimMapper | Allows dynamical switching (at runtime) between a dimension (RT, m/z, int, IM, etc) and X,Y,Z coordinates. You can set either of them, and query the other. The Mapping is stored internally. The unit to which the X,Y,Z coordinates currently mapped onto can also be queried (useful for axis labels etc) |
| CDimMZ | Dimension implementation for m/z values |
| CDimRT | Dimension implementation for retention time values |
| CDistanceMatrix | A two-dimensional distance matrix, similar to OpenMS::Matrix |
| CDocumentIdentifier | Manage source document information |
| CDocumentIdentifierVisualizer | Class that displays all meta information for DocumentIdentifier objects |
| CDPeak | Metafunction to choose among Peak1D respectively Peak2D through a template argument |
| CDPosition | Representation of a coordinate in D-dimensional space |
| CDRange | A D-dimensional half-open interval |
| CDTA2DFile | DTA2D File adapter |
| CDTAFile | File adapter for DTA files |
| CEDTAFile | |
| ►CEGHTraceFitter | A RT Profile fitter using an Exponential Gaussian Hybrid background model |
| CEGHTraceFunctor | |
| CElement | Representation of an element |
| CElementDB | Singleton that stores elements and isotopes |
| CElutionModelFitter | Helper class for fitting elution models to features |
| CElutionPeakDetection | Extracts chromatographic peaks from a mass trace |
| ►CEmgFitter1D | Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization |
| CData | Helper struct (contains the size of an area and a raw data container) |
| CEgmFitterFunctor | |
| CEmgGradientDescent | Fit peaks to an Exponentially Modified Gaussian (EMG) model using gradient descent |
| CEmgGradientDescent_friend | |
| CEmgModel | |
| CEmgScoring | Scoring of an elution peak using an exponentially modified gaussian distribution model |
| CEmpiricalFormula | Representation of an empirical formula |
| CEnhancedTabBar | Convenience tab bar implementation |
| CEnhancedTabBarWidgetInterface | Widgets that are placed into an EnhancedTabBar must implement this interface |
| CEnhancedWorkspace | |
| CEnzymaticDigestion | Class for the enzymatic digestion of sequences |
| CEuclideanSimilarity | CompareFunctor for 2Dpoints |
| ►CExperimentalDesign | Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class |
| CMSFileSectionEntry | |
| CSampleSection | |
| CExperimentalDesignFile | Load an experimental design from a TSV file. (see ExperimentalDesign for details on the supported format) |
| CExperimentalSettings | Description of the experimental settings |
| CExperimentalSettingsVisualizer | Class that displays all meta information for ExperimentalSettings objects |
| CExposedVector | |
| CExtendedIsotopeFitter1D | Extended isotope distribution fitter (1-dim.) approximated using linear interpolation |
| CExtendedIsotopeModel | |
| CExternalProcess | A wrapper around QProcess to conveniently start an external program and forward its outputs |
| CExternalProcessMBox | A wrapper around ExternalProcess to conveniently show a MessageBox when an error occurs |
| CFAIMSHelper | Helper functions for FAIMS data |
| CFakeProcess | A FakeProcess class |
| ►CFalseDiscoveryRate | Calculates false discovery rates (FDR) from identifications |
| ►CDecoyStringHelper | Finds decoy strings in ProteinIdentification runs |
| CResult | Finds the most common decoy string in the accessions of proteins. Checks for suffix and prefix and some common decoy strings. Only successful if more than 30% had a common string |
| CFASTAContainer | Template parameter for vector-based FASTA access |
| CFASTAContainer< TFI_File > | FASTAContainer<TFI_File> will make FASTA entries available chunk-wise from start to end by loading it from a FASTA file. This avoids having to load the full file into memory. While loading, the container will memorize the file offsets of each entry, allowing to read an arbitrary i'th entry again from disk. If possible, only entries from the currently cached chunk should be queried, otherwise access will be slow |
| CFASTAContainer< TFI_Vector > | FASTAContainer<TFI_Vector> simply takes an existing vector of FASTAEntries and provides the same interface with a potentially huge speed benefit over FASTAContainer<TFI_File> since it does not need disk access, but at the cost of memory |
| ►CFASTAFile | This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusual symbols (such as translation end (*)), they will be kept! You can use aggregate methods load() and store() to read/write a set of protein sequences at the cost of memory |
| CFASTAEntry | FASTA entry type (identifier, description and sequence) The first String corresponds to the identifier that is written after the > in the FASTA file. The part after the first whitespace is stored in description and the text from the next line until the next > (exclusive) is stored in sequence |
| CFeature | An LC-MS feature |
| CFeatureDeconvolution | An algorithm to decharge features (i.e. as found by FeatureFinder) |
| ►CFeatureDistance | A functor class for the calculation of distances between features or consensus features |
| CDistanceParams_ | Structure for storing distance parameters |
| CFeatureEditDialog | Dialog for editing a feature |
| CFeatureFileOptions | Options for loading files containing features |
| CFeatureFinderAlgorithm | Abstract base class for FeatureFinder algorithms |
| ►CFeatureFinderAlgorithmMetaboIdent | |
| CFeatureCompare | Comparison functor for features |
| CFeatureFilterQuality | Predicate for filtering features by overall quality |
| CFeatureFinderMetaboIdentCompound | Compound in the assay library |
| CMassTraceBounds | Boundaries for a mass trace in a feature |
| CFeatureFinderAlgorithmPicked | FeatureFinderAlgorithm for picked peaks |
| ►CFeatureFinderAlgorithmPickedHelperStructs | Wrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes |
| CIsotopePattern | Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked |
| CMassTrace | Helper struct for mass traces used in FeatureFinderAlgorithmPicked |
| CMassTraces | Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked |
| CSeed | Helper structure for seeds used in FeatureFinderAlgorithmPicked |
| CTheoreticalIsotopePattern | Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked |
| ►CFeatureFinderDefs | The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes.
|
| CNoSuccessor | Exception that is thrown if a method an invalid IndexPair is given |
| ►CFeatureFinderIdentificationAlgorithm | |
| CFeatureCompare | Comparison functor for features |
| CFeatureFilterPeptides | Predicate for filtering features by assigned peptides: |
| CFeatureFilterQuality | Predicate for filtering features by overall quality: |
| CIMStats | Ion mobility statistics for a peptide in a specific RT region and charge state |
| CPeptideCompare | Comparison functor for (unassigned) peptide IDs |
| CRTRegion | Region in RT in which a peptide elutes: |
| CFeatureFinderMultiplexAlgorithm | |
| CFeatureFindingMetabo | Method for the assembly of mass traces belonging to the same isotope pattern, i.e., that are compatible in retention times, mass-to-charge ratios, and isotope abundances |
| CFeatureGroupingAlgorithm | Base class for all feature grouping algorithms |
| CFeatureGroupingAlgorithmKD | A feature grouping algorithm for unlabeled data |
| CFeatureGroupingAlgorithmLabeled | A map feature grouping algorithm for labeling techniques with two labels |
| CFeatureGroupingAlgorithmQT | A feature grouping algorithm for unlabeled data |
| CFeatureGroupingAlgorithmUnlabeled | A map feature grouping algorithm for unlabeled data |
| ►CFeatureHandle | Representation of a Peak2D, RichPeak2D or Feature |
| CFeatureHandleMutable_ | Helper class returned by FeatureHandle::asMutable(), which see |
| CIndexLess | Comparator by map and unique id |
| CFeatureHypothesis | Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis) |
| CFeatureMap | A container for features |
| ►CFeatureMapping | |
| CFeatureMappingInfo | Stores information required for preprocessing |
| CFeatureToMs2Indices | Stores preprocessed feature mapping information |
| CFeatureOpenMS | An implementation of the OpenSWATH Feature Access interface using OpenMS |
| CFeatureOverlapFilter | |
| ►CFeatureSummary | |
| CResult | |
| CFeatureXMLFile | This class provides Input/Output functionality for feature maps |
| CFIAMSDataProcessor | Data processing for FIA-MS data |
| CFIAMSScheduler | |
| ►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 |
| CFileHandler | Facilitates file handling by file type recognition |
| ►CFileTypeList | Holds a vector of known file types, e.g. as a way to specify supported input formats |
| CFilterElements_ | Hold filter items (for Qt dialogs) along with their OpenMS type |
| CFileTypes | Centralizes the file types recognized by FileHandler |
| CFileWatcher | Watcher that monitors file changes |
| CFineIsotopePatternGenerator | Isotope pattern generator for fine isotope distributions |
| CFitter1D | Abstract base class for all 1D-dimensional model fitter |
| CFlagSet | Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64 |
| CFLASHDeconvAlgorithm | FLASHDeconv algorithm: ultrafast mass deconvolution algorithm for top down mass spectrometry dataset From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps: i) decharging and select candidate masses - speed up via binning ii) collecting isotopes from the candidate masses and deisotoping - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups) |
| CFLASHDeconvFeatureFile | FLASHDeconv feature level output *.tsv, *.ms1ft (for Promex), *.feature (for TopPIC) file formats |
| CFLASHDeconvSpectrumFile | FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats |
| CFLASHDeconvWizardBase | Main window of the FLASHDeconvWizard tool |
| ►CFLASHHelperClasses | Wrapper struct for all the structs needed by the FLASHDeconv The following structures/classes are defined: PrecalculatedAveragine, MassFeature, IsobaricQuantities, LogMzPeak, Tag, and DAG for tagging. i) PrecalculatedAveragine - to match observed isotopic envelope against theoretical one, theoretical envelope from averagine model should be quickly calculated. To do so, precalculate averagines for different masses at the beginning of FLASHDeconv runs ii) MassFeature - the feature of the deconvolved masses (instead of m/zs for MS features). iii) IsobaricQuantities - the quantities from isobaric quantification (implemented within FLASHDeconv) iv) LogMzPeak - Log transformed peak from original peak. Contains information such as charge, isotope index, and uncharged mass. v) Tag - the sequence tag generated on deconvolved spectra in FLASHTaggerAlgorithm vi) DAG - the graph for sequence tagging in FLASHTaggerAlgorithm and for proteoform characterization in FLASHExtenderAlgorithm |
| CIsobaricQuantities | Isobaric quantities |
| CLogMzPeak | Log transformed peak. After deconvolution, all necessary information from deconvolution such as charge and isotope index is stored |
| CMassFeature | Mass feature (Deconvolved masses in spectra are traced by Mass tracing to generate mass features - like LC-MS features) |
| CPrecalculatedAveragine | Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine calculation |
| ►CFragmentIndex | Generates from a set of Fasta files a 2D-datastructure which stores all theoretical masses of all b and y ions from all peptides generated from the Fasta file. The datastructure is build such that on one axis the fragments are sorted by their own mass and the axis by the mass of their precursor/protein. The FI has two options: Bottom-up and Top Down. In later digestion is skiped and the fragments have a direct reference to the mass of the proteins instead of digested peptides |
| CFragment | One entry in the fragment index |
| CHit | |
| CPeptide | Compact descriptor of a peptide instance held by the FragmentIndex |
| CSpectrumMatch | Match between a query peak and an entry in the DB |
| CSpectrumMatchesTopN | Container for SpectrumMatch. Also keeps count of total number of candidates and total number of matches |
| ►CFragmentMassError | |
| CStatistics | Structure for storing results: average and variance of all FragmentMassErrors in ppm |
| CFullSwathFileConsumer | Abstract base class which can consume spectra coming from SWATH experiment stored in a single file |
| ►CFuzzyStringComparator | Fuzzy comparison of strings, tolerates numeric differences |
| CAbortComparison | Internal exception class |
| CInputLine | Stores information about the current input line (i.e., stream for the line and the current position in the stream) |
| CPrefixInfo_ | Wrapper for the prefix information computed for the failure report |
| CStreamElement_ | Stores information about characters, numbers, and white spaces loaded from the InputStream |
| CFWHM | QC metric calculating (un)calibrated m/z error |
| CGaussFilter | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data |
| CGaussFilterAlgorithm | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data |
| CGaussFitter1D | Gaussian distribution fitter (1-dim.) approximated using linear interpolation |
| CGaussModel | Normal distribution approximated using linear interpolation |
| ►CGaussTraceFitter | Fitter for RT profiles using a Gaussian background model |
| CGaussTraceFunctor | |
| CGNPSMetaValueFile | |
| CGNPSMGFFile | |
| CGNPSQuantificationFile | |
| CGradient | Representation of a HPLC gradient |
| CGradientVisualizer | GradientVisualizer is a visualizer class for objects of type gradient |
| CGravitator | Manipulates X or Y component of points in the X-Y plane, by assuming one axis (either X or Y axis) has gravity acting upon it |
| CGridBasedCluster | Basic data structure for clustering |
| CGridBasedClustering | 2D hierarchical clustering implementation optimized for large data sets containing many small clusters i.e. dimensions of clusters << dimension of entire dataset |
| CGridFeature | Representation of a feature in a hash grid |
| CGridSearch | |
| CGUIProgressLoggerImpl | Implements a GUI version of the ProgressLoggerImpl |
| CGzipIfstream | Decompresses files which are compressed in the gzip format (*.gzip) |
| CGzipInputStream | Implements the BinInputStream class of the xerces-c library in order to read gzip compressed XML files |
| CHasActivationMethod | Predicate that determines if a spectrum was generated using any activation method given in the constructor list |
| ►CHashGrid | Container for (2-dimensional coordinate, value) pairs |
| CConstIterator | Constant element iterator for the hash grid |
| CIterator | Element iterator for the hash grid |
| CHasMetaValue | Predicate that determines if a class has a certain metavalue |
| CHasPrecursorCharge | Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list |
| CHasScanMode | Predicate that determines if a spectrum has a certain scan mode |
| CHasScanPolarity | Predicate that determines if a spectrum has a certain scan polarity |
| CHDF5Connector | File adapter for HDF5 files |
| CHistogramDialog | Dialog that show a HistogramWidget |
| CHistogramWidget | |
| CHit | |
| CHPLC | Representation of a HPLC experiment |
| CHPLCVisualizer | Class that displays all meta information for HPLC objects |
| ►CHyperScore | An implementation of the X!Tandem HyperScore PSM scoring function |
| CPSMDetail | Compute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match |
| CIBSpectraFile | Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results |
| CIDConflictResolverAlgorithm | Resolves ambiguous annotations of features with peptide identifications |
| ►CIDDecoyProbability | IDDecoyProbability calculates probabilities using decoy approach |
| CTransformation_ | Struct to be used to store a transformation (used for fitting) |
| ►CIdentificationData | |
| CModifyMultiIndexAddProcessingStep | Helper functor for adding processing steps to elements in a boost::multi_index_container structure |
| CModifyMultiIndexAddScore | Helper functor for adding scores to elements in a boost::multi_index_container structure |
| CModifyMultiIndexRemoveParentMatches | Helper functor for removing invalid parent matches from elements in a boost::multi_index_container structure |
| CRefTranslator | Structure that maps references of corresponding objects after copying |
| ►CIdentificationDataConverter | |
| CPepIDCompare | Functor for ordering peptide IDs by RT and m/z (if available) |
| CStepOptCompare | Functor for ordering StepOpt (by date of the steps, if available): |
| ►CIdentificationSummary | |
| CResult | |
| CUniqueID | |
| ►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? |
| CHasMetaValue | Is a meta value with given key and value set on this hit? |
| CHasMinMetaValue | Predicate to check if a HitType object has a minimum meta value |
| CHasNoHits | Is the list of hits of this peptide/protein ID empty? |
| CPeptideDigestionFilter | Filter Peptide Hit by its digestion product |
| ►CIDMapper | Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications |
| CPeptideIdentificationListState | Result of a partitioning by identification state with mapPrecursorsToIdentifications() |
| CIDMergerAlgorithm | Algorithm for merging multiple protein and peptide identification runs |
| ►CIDRipper | Ripping protein/peptide identification according their file origin |
| CIdentificationRuns | Represents a set of IdentificationRuns |
| CRipFileContent | Represents the content of an IDRipper output file |
| CRipFileIdentifier | Identifies an IDRipper output file |
| CRipFileIdentifierIdxComparator | Provides a 'less' operation for RipFileIdentifiers that ignores the out_basename and origin_fullname members |
| ►CIDScoreGetterSetter | A class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps |
| CIsHitType | |
| CIsIDType | |
| ►CIDScoreSwitcherAlgorithm | This class is used to switch identification scores within identification or consensus feature maps |
| CIDSwitchResult | Structure holding score switching information for IDScoreSwitcherAlgorithm |
| CScoreSearchResult | Structure to hold score detection results for any ScoreType.
|
| CIdXMLFile | Used to load and store idXML files |
| CILPDCWrapper | |
| CIMDataConverter | This class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models |
| CIMTypes | |
| CIncludeExcludeTarget | This class stores a SRM/MRM transition |
| CIndentedStream | Class for writing data which spans multiple lines with an indentation for each line (all except the first) |
| CIndex | |
| CIndexedMzMLDecoder | A class to analyze indexedmzML files and extract the offsets of individual tags |
| CIndexedMzMLFileLoader | A class to load an indexedmzML file |
| CINIFileEditorWindow | Shows the ParamEditor widget in a QMainWindow with a toolbar |
| CInIntensityRange | Predicate that determines if a peak lies inside/outside a specific intensity range |
| CINIUpdater | |
| CInMSLevelRange | Predicate that determines if a spectrum lies inside/outside a specific MS level set |
| CInMzRange | Predicate that determines if a peak lies inside/outside a specific m/z range |
| CInPrecursorMZRange | Predicate that determines if a spectrum's precursor is within a certain m/z range |
| CInputFile | A simple widget with a line-edit and a browse button to choose filenames |
| CInRTRange | Predicate that determines if a spectrum lies inside/outside a specific retention time range |
| CInspectInfile | Inspect input file adapter |
| CInspectOutfile | |
| CInstrument | Description of a MS instrument |
| CInstrumentSettings | Description of the settings a MS Instrument was run with |
| CInstrumentSettingsVisualizer | Class that displays all meta information for InstrumentSettings objects |
| CInstrumentVisualizer | Class that displays all meta information for an MS instrument |
| ►CInternalCalibration | A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference masses |
| CCalibrantStats_ | Statistics when adding peptide calibrants |
| CLockMass | Helper class, describing a lock mass |
| CInterpolationModel | Abstract class for 1D-models that are approximated using linear interpolation |
| CIonDetector | Description of a ion detector (part of a MS Instrument) |
| CIonDetectorVisualizer | Class that displays all meta information for IonDetector objects |
| CIonIdentityMolecularNetworking | |
| CIonMobilityScoring | A class that calls the ion mobility scoring routines |
| CIonSource | Description of an ion source (part of a MS Instrument) |
| CIonSourceVisualizer | Class that displays all meta information for IonSource objects |
| CIPeptideIds | Abstract base class which defines an interface for PeptideIdentifications |
| CIsEmptySpectrum | Predicate that determines if a spectrum is empty |
| CIsInCollisionEnergyRange | Predicate that determines if an MSn spectrum was generated with a collision energy in the given range |
| CIsInIsolationWindow | Predicate that determines if the isolation window covers ANY of the given m/z values |
| CIsInIsolationWindowSizeRange | Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range |
| ►CIsobaricChannelExtractor | Extracts individual channels from MS/MS spectra for isobaric labeling experiments |
| CPurityState_ | Small struct to capture the current state of the purity computation |
| CIsobaricIsotopeCorrector | Performs isotope impurity correction on intensities extracted from isobaric labeling experiments |
| CIsobaricNormalizer | Performs median normalization on the extracted ratios of isobaric labeling experiment |
| CIsobaricQuantifier | Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing |
| CIsobaricQuantifierStatistics | Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion) |
| ►CIsobaricQuantitationMethod | Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix |
| CIsobaricChannelInformation | Summary of an isobaric quantitation channel |
| CIsoSpecGeneratorWrapper | Interface for the IsoSpec algorithm - a generator of infinitely-resolved theoretical spectra |
| CIsoSpecOrderedGeneratorWrapper | Generate the stream of configurations, ordered from most likely to least likely |
| CIsoSpecThresholdGeneratorWrapper | Provides a threshold-based generator of isotopologues: generates all isotopologues more probable than a given probability threshold |
| CIsoSpecThresholdWrapper | A non-generator version of IsoSpecThresholdGeneratorWrapper |
| CIsoSpecTotalProbGeneratorWrapper | Generate a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99) |
| CIsoSpecTotalProbWrapper | Create a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99) |
| CIsoSpecWrapper | A convenience class for the IsoSpec algorithm - easier to use than the IsoSpecGeneratorWrapper classes |
| ►CIsotopeCluster | Stores information about an isotopic cluster (i.e. potential peptide charge variants) |
| CChargedIndexSet | Index set with associated charge estimate |
| CIsotopeDistribution | |
| CIsotopeFitter1D | Isotope distribution fitter (1-dim.) approximated using linear interpolation |
| CIsotopeLabelingMDVs | IsotopeLabelingMDVs is a class to support and analyze isotopic labeling experiments (i.e. MDVs : Mass Distribution Vectors, also known as Mass Isotopomer Distribution (MID)) |
| CIsotopeModel | |
| CIsotopePatternGenerator | Provides an interface for different isotope pattern generator methods |
| CIsZoomSpectrum | Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum |
| ►CItraqConstants | Some constants used throughout iTRAQ classes |
| CChannelInfo | Stores information on an iTRAQ channel |
| CItraqEightPlexQuantitationMethod | ITRAQ 8 plex quantitation to be used with the IsobaricQuantitation |
| CItraqFourPlexQuantitationMethod | ITRAQ 4 plex quantitation to be used with the IsobaricQuantitation |
| CJavaInfo | Detect Java and retrieve information |
| CKDTreeFeatureMaps | 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 |
| CKroenikFile | File adapter for Kroenik (HardKloer sibling) files |
| CLabeledPairFinder | The LabeledPairFinder allows the matching of labeled features (features with a fixed distance) |
| CLayerAnnotatorAMS | |
| CLayerAnnotatorBase | |
| CLayerAnnotatorOSW | |
| CLayerAnnotatorPeptideID | |
| CLayerData1DBase | Base class for all 1D layers, a special case of LayerData |
| CLayerData1DChrom | |
| CLayerData1DIonMobility | |
| CLayerData1DPeak | |
| CLayerDataBase | Class that stores the data for one layer |
| CLayerDataChrom | Class that stores the data for one layer of type Chromatogram |
| CLayerDataConsensus | Class that stores the data for one layer of type ConsensusMap |
| ►CLayerDataDefs | |
| ►CProjectionData | Result of computing a projection on X and Y axis in a 2D Canvas; see LayerDataBase::getProjection() |
| CSummary | |
| CLayerDataFeature | Class that stores the data for one layer of type FeatureMap |
| CLayerDataIdent | Class that stores the data for one layer of type PeptideIdentifications |
| CLayerDataIonMobility | Class that stores the data for one layer of type IonMobility |
| CLayerDataPeak | Class that stores the data for one layer of type PeakMap |
| CLayerListView | Pimped QListView for Layers of a Canvas |
| CLayerStack | |
| CLayerStatistics | Compute summary statistics (count/min/max/avg) about a container, e.g. intensity, charge, meta values, .. |
| CLayerStatisticsConsensusMap | Computes statistics and distributions for a PeakMap |
| CLayerStatisticsDialog | Dialog showing statistics about the data of the current layer |
| CLayerStatisticsFeatureMap | Computes statistics and distributions for a PeakMap |
| CLayerStatisticsIdent | Computes statistics and distributions for a vector<PeptideIdentifications> |
| CLayerStatisticsPeakMap | Computes statistics and distributions for a PeakMap
|
| CLayerStoreData | Base class to store either the currently visible or all data of a canvas |
| CLayerStoreDataConsensusMapAll | Visitor which can save a full ConsensusMap; subsequently the data can be stored to a file |
| CLayerStoreDataConsensusMapVisible | Visitor which can save a visible piece of data; subsequently the data can be stored to a file |
| CLayerStoreDataFeatureMapAll | Visitor which can save a full FeatureMap; subsequently the data can be stored to a file |
| CLayerStoreDataFeatureMapVisible | Visitor which can save a visible piece of data; subsequently the data can be stored to a file |
| CLayerStoreDataIdentAll | Visitor which can save a full set of Identifications; subsequently the data can be stored to a file |
| CLayerStoreDataIdentVisible | Visitor which can save a visible piece of data; subsequently the data can be stored to a file |
| CLayerStoreDataPeakMapAll | Visitor which can save a full experiment; subsequently the data can be stored to a file |
| CLayerStoreDataPeakMapVisible | Visitor which can save a visible piece of data; subsequently the data can be stored to a file |
| ►CLevMarqFitter1D | Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization |
| CGenericFunctor | |
| CLinearResampler | Linear Resampling of raw data |
| CLinearResamplerAlign | Linear Resampling of raw data with alignment |
| CListEditor | Editor for editing int, double and string lists (including output and input file lists) |
| CListFilterDialog | Dialog for creating and changing a DataFilter |
| ►CListUtils | Collection of utility functions for management of vectors |
| CDoubleTolerancePredicate_ | Predicate to check double equality with a given tolerance |
| CLogConfigHandler | The LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream |
| CLogWindow | A log window (QTextEdit) with convenience functions |
| CLowessSmoothing | LOWESS (locally weighted scatterplot smoothing) |
| ►CLPWrapper | A wrapper class for linear programming (LP) solvers |
| CSolverParam | Struct that holds the parameters of the LP solver |
| CMapAlignmentAlgorithmIdentification | A map alignment algorithm based on peptide identifications from MS2 spectra |
| CMapAlignmentAlgorithmKD | An efficient reference-free feature map alignment algorithm for unlabeled data |
| CMapAlignmentAlgorithmPoseClustering | A map alignment algorithm based on pose clustering |
| CMapAlignmentAlgorithmTreeGuided | A map alignment algorithm based on peptide identifications from MS2 spectra |
| CMapAlignmentEvaluationAlgorithm | Base class for all Caap evaluation algorithms |
| CMapAlignmentEvaluationAlgorithmPrecision | Caap evaluation algorithm to obtain a precision value |
| CMapAlignmentEvaluationAlgorithmRecall | Caap evaluation algorithm to obtain a recall value |
| CMapAlignmentTransformer | This class collects functions for applying retention time transformations to data structures |
| CMapConversion | |
| CMapUtilities | Utilities for Feature and ConsensusMap |
| CMascotGenericFile | Read/write Mascot generic files (MGF) |
| CMascotRemoteQuery | Class which handles the communication between OpenMS and the Mascot server |
| CMascotXMLFile | Used to load Mascot XML files |
| CMassAnalyzer | Description of a mass analyzer (part of a MS Instrument) |
| CMassAnalyzerVisualizer | Class that displays all meta information for MassAnalyzer objects |
| CMassDecomposition | Class represents a decomposition of a mass into amino acids |
| CMassDecompositionAlgorithm | Mass decomposition algorithm, given a mass it suggests possible compositions |
| CMassExplainer | Computes empirical formulas for given mass differences using a set of allowed elements |
| CMassFeatureTrace | Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by SpectralDeconvolution In other words, per spectrum deconvolved masses are converted into deconvolved features Currently only works for MS1 spectra. (Top-down DIA is not yet used much). Every time an MS1 spectrum is deconvolved, the relevant information is stored in this class. This class also comes with tsv, TopFD feature file formats |
| CMassTrace | A container type that gathers peaks similar in m/z and moving along retention time |
| CMasstraceCorrelator | Correlates individual masstraces found in mass spectrometric maps |
| ►CMassTraceDetection | A mass trace extraction method that gathers peaks similar in m/z and moving along retention time |
| CApex | |
| CPeakCandidate | Encapsulates peak finding logic for both up and down directions |
| CTraceExtensionState | Encapsulates trace extension state |
| CMatchedIterator | For each element in the reference container the closest peak in the target will be searched. If no match is found within the tolerance window, the peak will be skipped over |
| CMatrix | A 2D matrix class with efficient buffer access for NumPy interoperability |
| CMaxLikeliFitter1D | Abstract base class for all 1D-model fitters using maximum likelihood optimization |
| CMetaboliteFeatureDeconvolution | An algorithm to decharge small molecule features (i.e. as found by FeatureFinder) |
| CMetaboliteSpectralMatching | |
| ►CMetaboTargetedAssay | This class provides methods for the extraction of targeted assays for metabolomics |
| CCompoundSpectrumPair | CompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum |
| CCompoundTargetDecoyPair | CompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum (target, decoy) |
| CTargetDecoyGroup | TargetDecoyGroup stores the mz, rt and file number in correspondence to the index of a MetaboTargetedAssay vector |
| ►CMetaboTargetedTargetDecoy | Resolve overlapping fragments and missing decoys for experimental specific decoy generation in targeted/pseudo targeted metabolomics |
| CMetaboTargetDecoyMassMapping | MetaboTargetDecoyMassMapping introduces a mapping of target and decoy masses and their respective compound reference using an identifier |
| CMetaDataBrowser | A meta data visualization widget |
| CMetaInfo | A Type-Name-Value tuple class |
| CMetaInfoDescription | Description of the meta data arrays of MSSpectrum |
| CMetaInfoDescriptionVisualizer | Class that displays all meta information for MetaInfoDescription objects |
| CMetaInfoInterface | Interface for classes that can store arbitrary meta information (Type-Name-Value tuples) |
| CMetaInfoInterfaceUtils | Utilities operating on containers inheriting from MetaInfoInterface |
| CMetaInfoRegistry | Registry which assigns unique integer indices to strings |
| CMetaInfoVisualizer | MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member |
| CMinimumDistance | Basic data structure for distances between clusters |
| CMissedCleavages | This class is a metric for the QualityControl TOPP Tool |
| ►CMobilityPeak1D | A 1-dimensional raw data mobility point or peak. The unit (ms, 1/K_0, etc) is implicit |
| CIntensityLess | |
| CMobilityLess | Comparator by mobility position |
| CPositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for MobilityLess |
| ►CMobilityPeak2D | A 2-dimensional raw data point or peak |
| CIMLess | Comparator by IM position |
| CIntensityLess | |
| CMZLess | Comparator by m/z position |
| CPositionLess | Comparator by position. Lexicographical comparison (first IM then m/z) is done |
| ►CMobilogram | The representation of a 1D ion mobilogram |
| CRTLess | Comparator for the RT of the mobilogram |
| CModelDescription | Stores the name and parameters of a model |
| CModificationDefinition | |
| CModificationDefinitionsSet | |
| CModificationsDB | Database which holds all residue modifications from UniMod |
| CModifiedNASequenceGenerator | |
| ►CModifiedPeptideGenerator | |
| CMapToResidueType | |
| ►CMorpheusScore | An implementation of the Morpheus PSM scoring function Inspired by a C# implementation by C. Wenger released under MIT license |
| CResult | Score and subscores |
| CMorphologicalFilter | This class implements baseline filtering operations using methods from mathematical morphology |
| CMRMAssay | Generate assays from a TargetedExperiment |
| CMRMBatchFeatureSelector | Batch processing wrapper for MRMFeatureSelector |
| CMRMDecoy | This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object |
| CMRMFeature | A multi-chromatogram MRM feature |
| CMRMFeatureFilter | The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria |
| CMRMFeatureFinderScoring | The MRMFeatureFinder finds and scores peaks of transitions that co-elute |
| CMRMFeatureOpenMS | An implementation of the OpenSWATH MRM Feature Access interface using OpenMS |
| ►CMRMFeaturePicker | MRMFeaturePicker defines the structures containing parameters to be used in MRMTransitionGroupPicker for components and components groups |
| CComponentGroupParams | Structure to contain information about a component group with its parameters |
| CComponentParams | Structure to contain information about a single component with its parameters |
| CMRMFeaturePickerFile | MRMFeaturePickerFile loads components and components groups parameters from a .csv file |
| ►CMRMFeatureQC | The MRMFeatureQC is a class to handle the parameters and options for MRMFeatureFilter |
| CComponentGroupPairQCs | Quality Controls (QCs) for multiple components (between or within component_groups) |
| CComponentGroupQCs | Quality Controls (QCs) within a component group |
| CComponentQCs | Quality Controls (QCs) for individual components |
| CMRMFeatureQCFile | File adapter for MRMFeatureQC files |
| ►CMRMFeatureSelector | A base class for selection of MRM Features through Linear Programming optimization |
| CSelectorParameters | |
| CMRMFeatureSelector_test | |
| CMRMFeatureSelectorQMIP | |
| CMRMFeatureSelectorScore | |
| CMRMIonSeries | Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy |
| CMRMMapping | A class to map targeted assays to chromatograms |
| CMRMRTNormalizer | The MRMRTNormalizer will find retention time peptides in data |
| CMRMTransitionGroup | The representation of a group of transitions in a targeted proteomics experiment |
| CMRMTransitionGroupPicker | The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors |
| CMS2AdductsOfSinglePrecursorAdduct | |
| CMS2File | |
| ►CMs2IdentificationRate | This class is a metric for the QualityControl-ToppTool |
| CIdentificationRateData | Structure for storing results |
| ►CMs2SpectrumStats | QC metric to determine the number of MS2 scans per MS1 scan over RT |
| CScanEvent | |
| ►CMSChromatogram | The representation of a chromatogram |
| CMZLess | Comparator for the precursor m/z time |
| CMSDataAggregatingConsumer | Aggregates spectra by retention time |
| CMSDataCachedConsumer | Transforming and cached writing consumer of MS data |
| CMSDataChainingConsumer | Consumer class that passes all consumed data through a set of operations |
| CMSDataSqlConsumer | A data consumer that inserts MS data into a SQLite database |
| CMSDataStoringConsumer | Consumer class that simply stores the data |
| CMSDataTransformingConsumer | Transforming consumer of MS data |
| CMSDataWritingConsumer | Consumer class that writes MS data to disk using the mzML format |
| ►CMSExperiment | In-Memory representation of a mass spectrometry run |
| CContainerAdd_ | Helper class to add either general data points in set2DData or use mass traces from meta values |
| CContainerAdd_< ContainerValueType, false > | |
| CContainerAdd_< ContainerValueType, true > | |
| CSumIntensityReduction | Calculates the sum of intensities for a range of elements |
| CMsInspectFile | |
| ►CMSNumpressCoder | Class to encode and decode data encoded with MSNumpress |
| CNumpressConfig | Configuration class for MSNumpress |
| CMSPFile | File adapter for MSP files (NIST spectra library) |
| CMSPGenericFile | Load MSP text file and save it into an MSExperiment |
| CMSPGenericFile_friend | |
| ►CMSSpectrum | The representation of a 1D spectrum |
| CChunk | Used to remember what subsets in a spectrum are sorted already to allow faster sorting of the spectrum |
| CChunks | Container for organizing and managing multiple chunks in a spectrum |
| CIMLess | Comparator for the ion mobility |
| CRTLess | Comparator for the retention time |
| ►CMSstatsFile | File adapter for MSstats files |
| CAggregatedConsensusInfo | |
| CMSstatsLine_ | |
| CMSstatsTMTLine_ | |
| CMultiGradient | A gradient of multiple colors and arbitrary distances between colors |
| CMultiGradientSelector | A widget witch allows constructing gradients of multiple colors |
| ►CMultiplexClustering | Clusters results from multiplex filtering |
| CMultiplexDistance | Scaled Euclidean distance for clustering |
| ►CMultiplexDeltaMasses | Data structure for mass shift pattern |
| CDeltaMass | Mass shift with corresponding label set |
| ►CMultiplexDeltaMassesGenerator | Generates complete list of all possible mass shifts due to isotopic labelling |
| CLabel | Complete label information |
| CMultiplexFilteredMSExperiment | Data structure storing all peaks (and optionally their raw data points) of an experiment corresponding to one specific peak pattern |
| CMultiplexFilteredPeak | Data structure storing a single peak that passed all filters |
| CMultiplexFiltering | Base class for filtering centroided and profile data for peak patterns |
| CMultiplexFilteringCentroided | Filters centroided data for peak patterns |
| CMultiplexFilteringProfile | Filters centroided and profile data for peak patterns |
| CMultiplexIsotopicPeakPattern | Data structure for pattern of isotopic peaks |
| CMultiplexSatelliteCentroided | Data structure storing a single satellite peak |
| CMultiplexSatelliteProfile | Data structure storing a single satellite data point |
| CMzCalibration | QC metric calculating (un)calibrated m/z error |
| CMzDataFile | File adapter for MzData files |
| CMzIdentMLFile | File adapter for MzIdentML files |
| ►CMzMLFile | File adapter for MzML files |
| CSpecInfo | |
| CMzMLSpectrumDecoder | A class to decode input strings that contain an mzML chromatogram or spectrum tag |
| CMzMLSwathFileConsumer | On-disk mzML implementation of FullSwathFileConsumer |
| CMzQCFile | File adapter for mzQC files used to load and store mzQC files |
| ►CMzTab | Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/ |
| CCMMzTabStream | |
| CIDMzTabStream | |
| CMzTabAssayMetaData | |
| CMzTabBase | |
| CMzTabBoolean | |
| CMzTabContactMetaData | |
| CMzTabCVMetaData | |
| CMzTabDouble | |
| CMzTabDoubleList | |
| CMzTabFile | File adapter for MzTab files |
| CMzTabInstrumentMetaData | |
| CMzTabInteger | |
| CMzTabIntegerList | |
| CMzTabM | Data model of MzTab-M files Please see the MzTab-M specification at https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc#use-cases-for-mztab |
| CMzTabMAssayMetaData | MztabM Assay Metadata |
| CMzTabMDatabaseMetaData | MztabM Database Metadata |
| CMzTabMetaData | All meta data of a mzTab file. Please refer to specification for documentation |
| CMzTabMFile | File adapter for MzTab-M files |
| CMzTabMMetaData | MztabM Metadata |
| CMzTabMMSRunMetaData | MztabM MSRun Metadata |
| CMzTabModification | Data model of MzTab files |
| CMzTabModificationList | |
| CMzTabModificationMetaData | |
| CMzTabMSmallMoleculeEvidenceSectionRow | SME Small molecule evidence section (mztab-m) |
| CMzTabMSmallMoleculeFeatureSectionRow | SMF Small molecule feature section (mztab-m) |
| CMzTabMSmallMoleculeSectionRow | SML Small molecule section (mztab-m) |
| CMzTabMSRunMetaData | |
| CMzTabMStudyVariableMetaData | MztabM StudyVariable Metadata |
| ►CMzTabNucleicAcidSectionRow | NUC - Nucleic acid section (table-based) |
| CRowCompare | Comparison operator for sorting rows |
| ►CMzTabOligonucleotideSectionRow | OLI - Oligonucleotide section (table-based) |
| CRowCompare | Comparison operator for sorting rows |
| ►CMzTabOSMSectionRow | OSM - OSM (oligonucleotide-spectrum match) section (table-based) |
| CRowCompare | Comparison operator for sorting rows |
| CMzTabParameter | |
| CMzTabParameterList | |
| ►CMzTabPeptideSectionRow | PEP - Peptide section (Table based) |
| CRowCompare | Comparison operator for sorting rows |
| ►CMzTabProteinSectionRow | PRT - Protein section (Table based) |
| CRowCompare | Comparison operator for sorting rows |
| ►CMzTabPSMSectionRow | PSM - PSM section (Table based) |
| CRowCompare | Comparison operator for sorting rows |
| CMzTabSampleMetaData | |
| CMzTabSmallMoleculeSectionRow | SML Small molecule section (table based) |
| CMzTabSoftwareMetaData | |
| CMzTabSpectraRef | |
| CMzTabString | |
| CMzTabStringList | |
| CMzTabStudyVariableMetaData | |
| ►CMZTrafoModel | Create and apply models of a mass recalibration function |
| CRTLess | Comparator by position. As this class has dimension 1, this is basically an alias for MZLess |
| CMzXMLFile | File adapter for MzXML 3.1 files |
| ►CNASequence | Representation of a nucleic acid sequence |
| CConstIterator | ConstIterator of NASequence class |
| CIterator | Iterator of NASequence class |
| CNeedlemanWunsch | 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 |
| ►CNeighborSeq | The Neighbor Peptide functionality is designed to find peptides (neighbors) in a given set of sequences (FASTA file) that are similar to a target peptide (aka relevant peptide) based on mass and spectral characteristics. This provides more power when searching complex samples, when only a subset of the peptides/proteins is of interest |
| CNeighborStats | Statistics of how many neighbors were found per reference peptide |
| CNetworkGetRequest | |
| CNLargest | NLargest removes all but the n largest peaks |
| CNonNegativeLeastSquaresSolver | Wrapper for a non-negative least squares (NNLS) solver |
| CNoopMSDataConsumer | Consumer class that performs no operation |
| CNoopMSDataWritingConsumer | Consumer class that perform no operation |
| CNormalizer | Normalizes the peak intensities spectrum-wise |
| CNucleicAcidSpectrumGenerator | Generates theoretical spectra for nucleic acid sequences |
| CNuXLAnnotateAndLocate | |
| CNuXLAnnotatedHit | |
| CNuXLConstants | |
| CNuXLDeisotoper | Deisotoping of nucleotide cross-link mass spectra |
| CNuXLFDR | Adapted FDR calculation for NA cross-links |
| CNuXLFragmentAdductDefinition | |
| ►CNuXLFragmentAnnotationHelper | Convenience functions to construct appealing fragment annotation strings and store them as PeptideHit::PeakAnnotation |
| CFragmentAnnotationDetail_ | Single fragment annotation |
| CNuXLFragmentIonGenerator | |
| CNuXLMarkerIonExtractor | |
| ►CNuXLModificationMassesResult | |
| CMyStringLengthCompare | |
| CNuXLModificationsGenerator | |
| CNuXLParameterParsing | |
| CNuXLProteinReport | Protein report |
| CNuXLReport | Create PSM report |
| CNuXLReportRow | Struct to hold a single report line |
| CNuXLReportRowHeader | Create header line |
| COMSFile | This class supports reading and writing of OMS files |
| COMSSACSVFile | |
| COMSSAXMLFile | Used to load OMSSAXML files |
| COnDiscMSExperiment | Representation of a mass spectrometry experiment on disk |
| COpenPepXLAlgorithm | Search for peptide pairs linked with a labeled cross-linker |
| ►COpenSearchModificationAnalysis | Utility class for analyzing modification patterns in open search results |
| CFuzzyDoubleComparator | Comparator for approximate comparison of double values |
| CModificationPattern | Stores details of a modification pattern found in the data |
| CModificationSummary | Data structure for modification summary output |
| COpenSwath_Ind_Scores | A structure to hold the individual scores computed for unique ion signatures (UIS) scores for the Inference of Peptidoforms (IPF) workflow |
| COpenSwath_Scores | A structure to hold the different scores computed by OpenSWATH |
| COpenSwath_Scores_Usage | A structure to store which scores should be used by the OpenSWATH Algorithm |
| COpenSwathCalibrationWorkflow | Execute all steps for retention time and m/z calibration of SWATH-MS data |
| COpenSwathDataAccessHelper | Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces |
| COpenSwathHelper | A helper class that is used by several OpenSWATH tools |
| COpenSwathOSWWriter | Class to write out an OpenSwath OSW SQLite output (PyProphet input) |
| COpenSwathScoring | A class that calls the scoring routines |
| COpenSwathWorkflow | Execute all steps in an OpenSwath analysis |
| COpenSwathWorkflowBase | |
| ►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 to reduce duplicated code |
| CPeptideIDScoreComparator | A comparator for PeptideIdentifications that compares the scores in the first PeptideHit |
| COPXLSpectrumProcessingAlgorithms | |
| COSWData | Holds all or partial information from an OSW file |
| ►COSWFile | This class serves for reading in and writing OpenSWATH OSW files |
| CPercolatorFeature | |
| COSWHierarchy | Hierarchy levels of the OSWData tree |
| COSWIndexTrace | |
| COSWPeakGroup | |
| COSWPeptidePrecursor | A peptide with a charge state |
| COSWProtein | A Protein is the highest entity and contains one or more peptides which were found/traced |
| COSWTransition | High-level meta data of a transition |
| COutputDirectory | A simple widget with a line-edit and a browse button to choose filenames |
| CPainter1DBase | A base class for painting all items from a data layer (as supported by class derived from here) onto a 1D Canvas |
| CPainter1DChrom | Painter1D for chromatograms |
| CPainter1DIonMobility | Painter1D for mobilograms |
| CPainter1DPeak | Painter1D for spectra |
| CPainter2DBase | A base class for painting all items from a data layer (as supported by class derived from here) onto a 2D Canvas |
| CPainter2DChrom | Painter2D for chromatograms |
| CPainter2DConsensus | Painter2D for ConsensusFeatures |
| CPainter2DFeature | Painter2D for Features |
| CPainter2DIdent | Painter2D for Identifications |
| CPainter2DIonMobility | Painter2D for ion mobilograms |
| CPainter2DPeak | Painter2D for spectra |
| CPainterBase | An empty base class with some static convenience functions |
| ►CParam | Management and storage of parameters / INI files |
| CParamEntry | Parameter entry used to store the actual information inside of a Param entry |
| ►CParamIterator | Forward const iterator for the Param class |
| CTraceInfo | Struct that captures information on entered / left nodes for ParamIterator |
| CParamNode | Node inside a Param object which is used to build the internal tree |
| CParamCTDFile | Serializes a Param class in paramCTD file format. Note: only storing is currently possible |
| CParamCWLFile | Exports .cwl files |
| CParamEditor | A GUI for editing or viewing a Param object |
| CParameterInformation | Struct that captures all information of a command line parameter |
| CParamJSONFile | Load from JSON (in a Common Workflow Language (CWL) compatible way) into the Param class |
| CParamValue | Class to hold strings, numeric values, vectors of strings and vectors of numeric values using the stl types |
| CParamXMLFile | The file pendant of the Param class used to load and store the param datastructure as paramXML (i.e. INI files) |
| ►CPeak1D | A 1-dimensional raw data point or peak |
| CIntensityLess | |
| CMZLess | Comparator by m/z position |
| CPositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for MZLess |
| ►CPeak2D | A 2-dimensional raw data point or peak |
| CIntensityLess | |
| CMZLess | Comparator by m/z position |
| CPositionLess | Comparator by position. Lexicographical comparison (first RT then m/z) is done |
| CRTLess | Comparator by RT position |
| CPeakAlignment | Make a PeakAlignment of two PeakSpectra |
| CPeakCandidate | A small structure to hold peak candidates |
| CPeakFileOptions | Options for loading files containing peak data |
| CPeakGroup | Class describing a deconvolved mass. A mass contains multiple (LogMz) peaks of different charges and isotope indices. PeakGroup is the set of such peaks representing a single monoisotopic mass. PeakGroup also contains features that define the quality of it. It is used for PeakGroupScoring calculation. DeconvolvedSpectrum consists of PeakGroups |
| CPeakGroupScoring | Scoring functions for PeakGroup. For now, only Qscore has been implemented. For Qscore, the weight vector has been determined by logistic regression. In the future, other technique such as deep learning would be used |
| CPeakIndex | Index of a peak or feature |
| ►CPeakIntegrator | Compute the area, background and shape metrics of a peak |
| CPeakArea | |
| CPeakBackground | |
| CPeakShapeMetrics | |
| CPeakPickerChromatogram | The PeakPickerChromatogram finds peaks a single chromatogram |
| ►CPeakPickerHiRes | This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width |
| CPeakBoundary | Structure for peak boundaries |
| CPeakPickerIM | Peak picking algorithm for ion mobility data |
| CPeakPickerIterative | This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data) |
| ►CPeakPickerMobilogram | The PeakPickerMobilogram finds peaks a single mobilogram |
| CPeakPositions | Struct to hold peak positions |
| CPeakSpectrumCompareFunctor | Base class for compare functors of spectra, that return a similarity value for two spectra |
| CPeakTypeEstimator | Estimates if the data of a spectrum is raw data or peak data |
| CPeakWidthEstimator | Rough estimation of the peak width at m/z |
| CPepNovoInfile | |
| CPepNovoOutfile | Representation of a PepNovo output file |
| ►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 |
| CPeptideEvidence | Representation of a peptide evidence |
| ►CPeptideHit | Represents a single spectrum match (candidate) for a specific tandem mass spectrum (MS/MS) |
| CPeakAnnotation | Contains annotations of a peak |
| CPepXMLAnalysisResult | Analysis Result (containing search engine / prophet results) |
| CRankLess | Lesser predicate for scores of hits |
| CScoreLess | Lesser predicate for scores of hits |
| CScoreMore | Greater predicate for scores of hits |
| CSequenceChargeEqual | Equality functor for PeptideHit based on sequence and charge |
| CSequenceChargeHash | Hash functor for PeptideHit based on sequence and charge |
| CSequenceLessComparator | Lesser predicate for (modified) sequence of hits |
| CPeptideHitVisualizer | Class that displays all meta information for PeptideHit objects |
| CPeptideIdentification | Represents the set of candidates (SpectrumMatches) identified for a single precursor spectrum |
| CPeptideIdentificationList | Container for peptide identifications from multiple spectra |
| CPeptideIdentificationVisualizer | Class that displays all meta information for PeptideIdentification objects |
| CPeptideIndexing | Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds target/decoy information |
| CPeptideMass | QC metric calculating theoretical mass of a peptide sequence |
| CPeptideProteinResolution | Resolves shared peptides based on protein scores |
| ►CPeptideSearchEngineFIAlgorithm | Fragment-index-based peptide database search algorithm (experimental) |
| CAnnotatedHit_ | Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space |
| ►CPepXMLFile | Used to load and store PepXML files |
| CAminoAcidModification | |
| CPepXMLFileMascot | Used to load Mascot PepXML files |
| ►CPercolatorFeatureSetHelper | Percolator feature set and integration helper |
| Clq_PeptideEvidence | For accession dependent sorting of PeptideEvidences |
| Clq_ProteinHit | For accession dependent sorting of ProteinHits |
| CPercolatorInfile | Class for storing Percolator tab-delimited input files |
| CPercolatorOutfile | Class for reading Percolator tab-delimited output files |
| CPlainMSDataWritingConsumer | Consumer class that writes MS data to disk using the mzML format |
| CPlot1DCanvas | Canvas for visualization of one or several spectra |
| CPlot1DGoToDialog | Simple goto/set visible area dialog for exact placement of the viewing window |
| CPlot1DWidget | Widget for visualization of several spectra |
| CPlot2DCanvas | Canvas for 2D-visualization of peak map, feature map and consensus map data |
| CPlot2DGoToDialog | GoTo dialog used to zoom to a m/z and retention time range or to a feature |
| CPlot2DWidget | Widget for 2D-visualization of peak map and feature map data |
| CPlot3DCanvas | Canvas for 3D-visualization of peak map data |
| CPlot3DOpenGLCanvas | OpenGL Canvas for 3D-visualization of map data |
| CPlot3DWidget | Widget for 3D-visualization of map data |
| CPlotCanvas | Base class for visualization canvas classes |
| CPlotWidget | Base class for spectrum widgets |
| CPoseClusteringAffineSuperimposer | A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation |
| CPoseClusteringShiftSuperimposer | A superimposer that uses a voting scheme, also known as pose clustering, to find a good shift transformation |
| CPpmTrait | |
| CPrecisionWrapper | Wrapper class to implement output with appropriate precision. See precisionWrapper() |
| CPrecursor | Precursor meta information |
| CPrecursorCorrection | This class provides methods for precursor correction |
| CPrecursorMassComparator | |
| ►CPrecursorPurity | Precursor purity or noise estimation |
| CPurityScores | |
| CPrecursorVisualizer | Class that displays all meta information for Precursor objects |
| CProbablePhosphoSites | |
| CProduct | Product meta information |
| CProductVisualizer | Class that displays all meta information for Product objects |
| ►CProgressLogger | Base class for all classes that want to report their progress |
| CProgressLoggerImpl | This class represents an actual implementation of a logger |
| CProteaseDB | Database for enzymes that digest proteins (proteases) |
| CProteaseDigestion | Class for the enzymatic digestion of proteins represented as AASequence or String |
| ►CProteinHit | Representation of a protein hit |
| CProteinHitAccessionHash | Hash of a ProteinHit based on its accession only! |
| CProteinHitPtrAccessionHash | |
| CScoreLess | Lesser predicate for scores of hits |
| CScoreMore | Greater predicate for scores of hits |
| CProteinHitVisualizer | Class that displays all meta information for ProteinHit objects |
| ►CProteinIdentification | Representation of a protein identification run |
| 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 |
| CProteinIdentificationVisualizer | Class that displays all meta information for ProteinIdentification objects |
| CProteinInference | [experimental class] given a peptide quantitation, infer corresponding protein quantities |
| ►CProteinModificationSummary | Map a protein position to all observed modifications and associated statistics |
| CStatistics | Basic modification statistic |
| CProtXMLFile | Used to load (storing not supported, yet) ProtXML files |
| CPScore | Implementation of the PScore PSM scoring algorithm |
| ►CPSMExplainedIonCurrent | |
| CStatistics | Structure for storing results: average and variance over all PSMs |
| CPTMXMLFile | Used to load and store PTMXML files |
| CPythonInfo | Detect Python and retrieve information |
| CQApplicationTOPP | Extension to the QApplication for running TOPPs GUI tools |
| ►CQCBase | This class serves as an abstract base class for all QC classes |
| CSpectraMap | Map to find a spectrum via its NativeID |
| ►CQcMLFile | File adapter for QcML files used to load and store QcML files |
| CAttachment | Representation of an attachment |
| CQualityParameter | Representation of a quality parameter |
| ►CQTCluster | A representation of a QT cluster used for feature grouping |
| CBulkData | Class to store the bulk internal data (neighbors, annotations, etc.) |
| CElement | |
| CNeighbor | |
| CQTClusterFinder | A variant of QT clustering for the detection of feature groups |
| CQuantmsIO | File adapter for writing PSM (Peptide Spectrum Match) data to parquet files |
| CQvalue | Qvalue : contains functions to calculate Qvalues from deconvolution quality score (Qscore) defined in PeakGroupScoring |
| CRAIICleanup | Exception-safe way of executing arbitrary code at the end of a scope |
| CRange | Internal structure to store a lower and upper bound of an m/z range |
| CRangeBase | Base class for a simple range with minimum and maximum |
| CRangeIntensity | |
| CRangeManager | Handles the management of a multidimensional range, e.g. RangeMZ and RangeIntensity for spectra |
| CRangeManagerContainer | |
| CRangeMobility | |
| CRangeMZ | |
| CRangeRT | |
| CRangeStats | Struct representing the statistics about a set of values |
| CRangeStatsType | Origin and name of a statistic |
| CRankScaler | Scales each peak by ranking the peaks per spectrum and assigning intensity according to rank |
| ►CReactionMonitoringTransition | This class stores a SRM/MRM transition |
| CNameLess | Comparator by name |
| CProductMZLess | Comparator by Product ion MZ |
| CRecentFilesMenu | Manages recent files opened by the user and provides a QMenu to go with it |
| CRegularSwathFileConsumer | In-memory implementation of FullSwathFileConsumer |
| 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) |
| CRichPeak2D | A 2-dimensional raw data point or peak with meta information |
| CRNaseDB | Database for enzymes that digest RNA (RNases) |
| CRNaseDigestion | Class for the enzymatic digestion of RNAs |
| CRTAlignment | Take the original retention time before map alignment and use the alignment's trafoXML for calculation of the new alignment retention times |
| CRWrapper | R-Wrapper Class |
| CSample | Meta information about the sample |
| CSampleVisualizer | Class that displays all meta information of sample objects |
| CSaveImageDialog | Dialog for saving an image |
| CSavitzkyGolayFilter | Computes the Savitzky-Golay filter coefficients using QR decomposition |
| CScanWindow | Scan window description |
| CScanWindowVisualizer | Class that displays all meta information for ScanWindow objects |
| CScoreToTgtDecLabelPairs | |
| CSearchEngineBase | Base class for Search Engine Adapters |
| CSeedListGenerator | Generate seed lists for feature detection |
| CSequestInfile | |
| CSequestOutfile | Representation of a Sequest output file |
| CSignalProvider | Signal mechanism (by deriving from QObject) for classes which are not allowed to have signals themselves |
| ►CSignalToNoiseEstimator | This class represents the abstract base class of a signal to noise estimator |
| CGaussianEstimate | Protected struct to store parameters my, sigma for a Gaussian distribution |
| CSignalToNoiseEstimatorMeanIterative | Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities |
| CSignalToNoiseEstimatorMedian | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) |
| ►CSignalToNoiseEstimatorMedianRapid | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based) |
| CNoiseEstimator | Class to compute the noise value at a given position |
| CSignalToNoiseOpenMS | An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS |
| CSimpleOpenMSSpectraFactory | A factory method that returns two ISpectrumAccess implementations |
| ►CSimpleSearchEngineAlgorithm | |
| CAnnotatedHit_ | Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space |
| ►CSimpleSVM | Simple interface to support vector machines for classification and regression (via LIBSVM) |
| CPrediction | SVM/SVR prediction result |
| ►CSimpleTSGXLMS | Generates theoretical spectra for cross-linked peptides |
| CLossIndex | |
| CSimplePeak | A simple struct to represent peaks with mz and charge and sort them easily |
| CSimplePeakComparator | Comparator to sort SimplePeaks by mz |
| CSingleLinkage | SingleLinkage ClusterMethod |
| CSiriusExportAlgorithm | |
| ►CSiriusFragmentAnnotation | |
| CSiriusTargetDecoySpectra | SiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from SIRIUS) |
| ►CSiriusMSFile | |
| CAccessionInfo | < class to store information about accessions |
| CCompoundInfo | |
| CSoftware | Description of the software used for processing |
| CSoftwareVisualizer | Class that displays all meta information for Software objects |
| CSourceFile | Description of a file location, used to store the origin of (meta) data |
| CSourceFileVisualizer | Class that displays all meta information for SourceFile objects |
| CSpecArrayFile | File adapter for SpecArray (.pepList) files |
| ►CSpectraIDViewTab | Tabular visualization / selection of identified spectra |
| CSelfResizingTableView_ | |
| CSpectralDeconvolution | FLASHDeconv algorithm: ultrafast mass deconvolution algorithm for top down mass spectrometry dataset From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps: i) decharging and select candidate masses - speed up via binning ii) collecting isotopes from the candidate masses and deisotope - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups) |
| CSpectralMatch | |
| CSpectralMatchScoreComparator | |
| ►CSpectraMerger | Offers spectra merging and averaging algorithms to increase the quality of a spectrum |
| CSpectraDistance_ | |
| CSpectraSTSimilarityScore | Similarity score of SpectraST |
| CSpectraTreeTab | Hierarchical visualization and selection of spectra |
| 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 |
| CSpectrumAddition | The SpectrumAddition is used to add up individual spectra |
| CSpectrumAlignment | Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) alignment if absolute tolerances are given. Scoring function is the m/z distance between peaks. Intensity does not play a role! |
| CSpectrumAlignmentDialog | Lets the user select two spectra and set the parameters for the spectrum alignment |
| CSpectrumAlignmentScore | Similarity score via spectra alignment |
| CSpectrumAnnotator | Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options |
| CSpectrumCheapDPCorr | SpectrumCheapDPCorr calculates an optimal alignment on stick spectra |
| CSpectrumCount | |
| CSpectrumLookup | Helper class for looking up spectra based on different attributes |
| ►CSpectrumMetaDataLookup | Helper class for looking up spectrum meta data |
| CSpectrumMetaData | Meta data of a spectrum |
| CSpectrumPrecursorComparator | SpectrumPrecursorComparator compares just the parent mass of two spectra |
| CSpectrumRangeManager | Advanced range manager for MS spectra with separate ranges for each MS level |
| CSpectrumSettings | Representation of 1D spectrum settings |
| CSpectrumSettingsVisualizer | Class that displays all meta information for SpectrumSettings objects |
| ►CSplineInterpolatedPeaks | Data structure for spline interpolation of MS1 spectra and chromatograms |
| CNavigator | Iterator class for access of spline packages |
| CSplinePackage | Fundamental data structure for SplineInterpolatedPeaks |
| CSqliteConnector | File adapter for Sqlite files |
| ►CSqMassFile | An class that uses on-disk SQLite database to read and write spectra and chromatograms |
| CSqMassConfig | Configuration class for SqMassFile |
| CSqrtScaler | Scales the intensity of peaks to the sqrt |
| CStablePairFinder | This class implements a pair finding algorithm for consensus features |
| CStatsCounter | Simple counting struct, for non-numerical occurrences of meta-values |
| CSteinScottImproveScore | Similarity score based of Stein & Scott |
| ►CStopWatch | This class is used to determine the current process' CPU (user and/or kernel) and wall time |
| CTimeDiff_ | |
| CStreamHandler | Provides a central class to register globally used output streams. Currently supported streams are |
| 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 |
| CSummary | Summary of fitting results |
| CSVOutStream | Stream class for writing to comma/tab/...-separated values files |
| CSwathFile | File adapter for Swath files |
| CSwathLibraryStats | A multi-tabbed widget for the SwathWizard offering setting of parameters, input-file specification and running Swath and more |
| CSwathMapMassCorrection | A class containing correction functions for Swath MS maps |
| CSwathWindowLoader | Class to read a file describing the Swath Windows |
| CSwathWizardBase | Main window of the SwathWizard tool |
| ►CSysInfo | Some functions to get system information |
| CMemUsage | A convenience class to report either absolute or delta (between two timepoints) RAM usage |
| CTableView | A better QTable for TOPPView, which supports exporting to TSV and conveniently adding data to cells and headers |
| CTagger | Calculate sequence tags from m/z values |
| ►CTargetedExperiment | A description of a targeted experiment containing precursor and production ions |
| CSummaryStatistics | |
| ►CTargetedSpectraExtractor | This class filters, annotates, picks, and scores spectra (e.g., taken from a DDA experiment) based on a target list |
| CBinnedSpectrumComparator | |
| CComparator | |
| CMatch | |
| CTextFile | |
| ►CTheoreticalSpectrumGenerationDialog | Dialog which allows to enter an AA or NA sequence and generates a theoretical spectrum for it |
| CCheckBox | Struct for all information about a check box of an ion |
| CTheoreticalSpectrumGenerator | Generates theoretical spectra for peptides with various options |
| ►CTheoreticalSpectrumGeneratorXLMS | |
| CLossIndex | |
| CThresholdMower | Removes all peaks below an intensity threshold |
| ►CTIC | |
| CResult | |
| 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 |
| CToolDescriptionFile | File adapter for ToolDescriptor files |
| CToolHandler | |
| CToolInfo | A struct to pass information about the tool as one parameter |
| CToolsDialog | TOPP tool selection dialog |
| CTopDownIsobaricQuantification | Isobaric quantification for Top down proteomics. The report ion ratios from multiple MS2 are merged when their precursor masses belong to the same deconvolved features (MassFeature instances) |
| CTOPPASBase | Main window of the TOPPAS tool |
| CTOPPASEdge | An edge representing a data flow in TOPPAS |
| CTOPPASInputFileDialog | Dialog which allows to specify an input file |
| CTOPPASInputFileListVertex | A vertex representing an input file list |
| CTOPPASInputFilesDialog | Dialog which allows to specify a list of input files |
| CTOPPASIOMappingDialog | Dialog which allows to configure the input/output parameter mapping of an edge |
| CTOPPASMergerVertex | A special vertex that allows to merge several inputs |
| CTOPPASOutputFileListVertex | A vertex representing an output file list |
| CTOPPASOutputFilesDialog | Dialog which allows to specify the directory for the output files |
| CTOPPASOutputFolderVertex | A vertex representing an output folder |
| CTOPPASOutputVertex | A vertex representing an output, either folder or files(s) |
| CTOPPASResource | Represents a data resource for TOPPAS workflows |
| CTOPPASResources | A dictionary mapping string keys to lists of TOPPASResource objects |
| ►CTOPPASScene | |
| CTOPPProcess | Stores the information for a TOPP process |
| CTOPPASSplitterVertex | A special vertex that allows to split a list of inputs |
| CTOPPASToolConfigDialog | TOPP tool configuration dialog |
| ►CTOPPASToolVertex | A vertex representing a TOPP tool |
| CIOInfo | Stores the information for input/output files/lists |
| CTOPPASTreeView | Tree view implementation for the list of TOPP tools |
| ►CTOPPASVertex | The base class of the different vertex classes |
| CTOPPASFilenames | |
| CVertexRoundPackage | Info for one edge and round, to be passed to next node |
| CTOPPASVertexNameDialog | Dialog which allows to change the name of an input/output vertex |
| CTOPPASWidget | Widget visualizing and allowing to edit TOPP pipelines |
| CTOPPBase | Base class for TOPP applications |
| ►CTOPPOpenSwathBase | |
| CCalibrationResult | Outputs of RT, m/z, IM calibration |
| CTOPPViewBase | Main window of TOPPView tool |
| ►CTOPPViewMenu | The file menu items for TOPPView |
| CActionRequirement_ | |
| CTOPPViewOpenDialog | Dataset opening options for TOPPView |
| ►CTraceFitter | Abstract fitter for RT profile fitting |
| CGenericFunctor | |
| CModelData | |
| CTraMLFile | File adapter for HUPO PSI TraML files |
| ►CTransformationDescription | Generic description of a coordinate transformation |
| CTransformationStatistics | Summary statistics before/after applying the transformation. For deviations before/after transformation, the percentiles 100, 99, 95, 90, 75, 50, 25 are returned |
| ►CTransformationModel | Base class for transformation models |
| CDataPoint | Coordinate pair (with optional annotation) |
| CTransformationModelBSpline | B-spline (non-linear) model for transformations |
| ►CTransformationModelInterpolated | Interpolation model for transformations |
| CInterpolator | The class defines a generic interpolation technique used in the TransformationModelInterpolated |
| CTransformationModelLinear | Linear model for transformations |
| CTransformationModelLowess | Lowess (non-linear) model for transformations |
| CTransformationXMLFile | Used to load and store TransformationXML files |
| CTransitionGroupOpenMS | An implementation of the OpenSWATH Transition Group Access interface using OpenMS |
| ►CTransitionPQPFile | This class supports reading and writing of PQP files |
| CPQPSqlQueryInfo | Holds information about a PQP SQL query and optional column availability |
| ►CTransitionTSVFile | |
| CTSVTransition | Internal structure to represent a transition |
| CTreeView | A better QTreeWidget for TOPPView, which supports header context menu and conveniently adding/getting headers names |
| ►CTriqlerFile | File adapter for Triqler files |
| CAggregatedConsensusInfo | |
| CTriqlerLine_ | |
| CTVControllerBase | Base behavior for different visualizaton modules in TOPPView |
| CTVDIATreeTabController | Behavior of TOPPView in spectra view mode |
| CTVIdentificationViewController | Behavior of TOPPView in identification mode |
| CTVSpectraViewController | Behavior of TOPPView in spectra view mode |
| CTVToolDiscovery | Scans for tools and generates a param for each asynchronously |
| CUnimodXMLFile | Used to load XML files from unimod.org files |
| CUniqueIdGenerator | A generator for unique ids |
| CUniqueIdIndexer | A base class for containers with elements derived from UniqueIdInterface. This adds functionality to convert a unique id into an index into the container |
| CUniqueIdInterface | A base class defining a common interface for all classes having a unique id |
| CUnnormalizedComparator | Exception thrown if clustering is attempted without a normalized compare functor |
| CUpdateCheck | Helper Functions to perform an update query to the OpenMS REST server |
| CValueTrait | Trait for MatchedIterator to find pairs with a certain distance, which is computed directly on the value_type of the container |
| CVecLowPrecision | |
| ►CVersionInfo | Version information class |
| CVersionDetails | |
| CWindowMower | Retains the highest peaks in a sliding or jumping window |
| CXFDRAlgorithm | Calculates false discovery rate estimates on crosslink identifications |
| CXMassFile | |
| CXMLValidator | Validator for XML files |
| CXQuestResultXMLFile | Used to load and store xQuest result files |
| CXQuestScores | An implementation of the scores for cross-link identification from the xQuest algorithm (O. Rinner et al., 2008, "Identification of cross-linked peptides from large sequence databases") |
| CXTandemInfile | XTandem input file |
| CXTandemXMLFile | Used to load XTandemXML files |
| CZhangSimilarityScore | Similarity score of Zhang |
| CZlibCompression | Compresses and uncompresses data using zlib |
| RIsFCMap | |
| RLessThanComparable | |
| RIsPeptideOrProteinIdentification | |
| RIsFeatureOrConsensusMap | |
| RIsNotIdentificationVector | Concept to exclude std::vector of identification types (used to disambiguate template overloads) |
| ►NOpenSwath | |
| ►NScoring | Scoring functions used by MRMScoring |
| Cpair_hash | Simple hash function for Scoring::pos2D |
| CXCorrArrayType | |
| CCSVWriter | |
| CDataMatrix | |
| CIDataFrameWriter | |
| CIFeature | |
| CIMRMFeature | |
| CISignalToNoise | |
| CISpectrumAccess | The interface of a mass spectrometry experiment |
| CITransitionGroup | |
| CLightCompound | |
| CLightModification | |
| CLightProtein | |
| CLightTargetedExperiment | |
| CLightTransition | |
| Cmean_and_stddev | Functor to compute the mean and stddev of sequence using the std::foreach algorithm |
| CMockFeature | Mock object implementing IFeature |
| CMockMRMFeature | Mock object implementing IMRMFeature |
| CMockSignalToNoise | Mock object implementing ISignalToNoise |
| CMockTransitionGroup | Mock object implementing ITransitionGroup |
| CMRMScoring | This class implements different scores for peaks found in SRM/MRM |
| COSBinaryDataArray | The datastructures used by the OpenSwath interfaces |
| COSChromatogram | A single chromatogram |
| COSChromatogramMeta | Identifying information for a chromatogram |
| COSSpectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
| ►COSSpectrumMeta | Identifying information for a spectrum |
| CRTLess | Comparator for the retention time |
| CPeptide | |
| CProtein | |
| CSwathMap | Data structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2 |
| CSwathQC | Quality Control function for OpenSwath |
| CTargetedExperiment | |
| CTransitionFlags | Packed boolean flags for transitions Reduces memory from 4 bytes (4 separate bools) to 1 byte |
| CTransitionHelper | |
| NSQLite | |
| ►Nstd | STL namespace |
| Chash< OpenMS::AASequence > | Hash function for OpenMS::AASequence |
| Chash< OpenMS::Adduct > | |
| Chash< OpenMS::AnnotatedMSRun > | Hash function for OpenMS::AnnotatedMSRun |
| Chash< OpenMS::ChargePair > | |
| Chash< OpenMS::ChromatogramPeak > | |
| Chash< OpenMS::ChromatogramSettings > | Hash function for OpenMS::ChromatogramSettings |
| Chash< OpenMS::Compomer > | |
| Chash< OpenMS::ConvexHull2D > | |
| Chash< OpenMS::CVTerm > | Hash function for CVTerm |
| Chash< OpenMS::CVTerm::Unit > | Hash function for CVTerm::Unit |
| Chash< OpenMS::CVTermList > | Hash function for CVTermList |
| Chash< OpenMS::CVTermListInterface > | Hash function for CVTermListInterface |
| Chash< OpenMS::DataValue > | Hash function for DataValue |
| Chash< OpenMS::DateTime > | |
| Chash< OpenMS::DBoundingBox< D > > | |
| Chash< OpenMS::DigestionEnzyme > | Std::hash specialization for DigestionEnzyme |
| Chash< OpenMS::DPosition< D, TCoordinateType > > | |
| Chash< OpenMS::DRange< D > > | |
| Chash< OpenMS::Element > | |
| Chash< OpenMS::EmpiricalFormula > | Hash function for OpenMS::EmpiricalFormula |
| Chash< OpenMS::FeatureHandle > | |
| Chash< OpenMS::FLASHHelperClasses::LogMzPeak > | Hash specialization for FLASHHelperClasses::LogMzPeak |
| Chash< OpenMS::FLASHHelperClasses::MassFeature > | Hash specialization for FLASHHelperClasses::MassFeature |
| Chash< OpenMS::IncludeExcludeTarget > | Std::hash specialization for OpenMS::IncludeExcludeTarget |
| Chash< OpenMS::Index > | |
| Chash< OpenMS::IonDetector > | Hash function for OpenMS::IonDetector |
| Chash< OpenMS::IonSource > | |
| Chash< OpenMS::IsotopeDistribution > | |
| Chash< OpenMS::MassAnalyzer > | Hash function for OpenMS::MassAnalyzer |
| Chash< OpenMS::MetaInfo > | |
| Chash< OpenMS::MetaInfoInterface > | Hash function for MetaInfoInterface |
| Chash< OpenMS::MobilityPeak1D > | |
| Chash< OpenMS::MobilityPeak2D > | |
| Chash< OpenMS::ModificationDefinition > | Hash function for OpenMS::ModificationDefinition |
| Chash< OpenMS::NASequence > | Hash function for OpenMS::NASequence |
| Chash< OpenMS::NuXLFragmentAdductDefinition > | Hash function for OpenMS::NuXLFragmentAdductDefinition |
| Chash< OpenMS::OPXLDataStructs::ProteinProteinCrossLink > | Std::hash specialization for ProteinProteinCrossLink |
| Chash< OpenMS::ParamValue > | |
| Chash< OpenMS::Peak1D > | |
| Chash< OpenMS::Peak2D > | |
| Chash< OpenMS::PeakGroup > | |
| Chash< OpenMS::PeptideEvidence > | |
| Chash< OpenMS::PeptideHit > | Hash function for OpenMS::PeptideHit |
| Chash< OpenMS::PeptideHit::PeakAnnotation > | Hash function for OpenMS::PeptideHit::PeakAnnotation |
| Chash< OpenMS::PeptideIdentification > | Hash function for OpenMS::PeptideIdentification |
| Chash< OpenMS::Precursor > | |
| Chash< OpenMS::Product > | Hash function for OpenMS::Product |
| Chash< OpenMS::ProteinHit > | Hash function for OpenMS::ProteinHit |
| Chash< OpenMS::ProteinIdentification > | Std::hash specialization for ProteinIdentification |
| Chash< OpenMS::ProteinIdentification::ProteinGroup > | Std::hash specialization for ProteinIdentification::ProteinGroup |
| Chash< OpenMS::ProteinIdentification::SearchParameters > | Std::hash specialization for ProteinIdentification::SearchParameters |
| Chash< OpenMS::ReactionMonitoringTransition > | Hash function for ReactionMonitoringTransition |
| Chash< OpenMS::Residue > | Hash specialization for OpenMS::Residue Hashes all fields used in operator== for consistency |
| Chash< OpenMS::ResidueModification > | Hash function for OpenMS::ResidueModification |
| Chash< OpenMS::Ribonucleotide > | Hash function for OpenMS::Ribonucleotide |
| Chash< OpenMS::Software > | Hash function for OpenMS::Software |
| Chash< OpenMS::SpectrumSettings > | Hash function for OpenMS::SpectrumSettings |
| Chash< OpenMS::String > | |
| Chash< OpenMS::TargetedExperimentHelper::Compound > | Hash function for TargetedExperimentHelper::Compound |
| Chash< OpenMS::TargetedExperimentHelper::Contact > | Hash function for TargetedExperimentHelper::Contact |
| Chash< OpenMS::TargetedExperimentHelper::CV > | Hash function for TargetedExperimentHelper::CV |
| Chash< OpenMS::TargetedExperimentHelper::Instrument > | Hash function for TargetedExperimentHelper::Instrument |
| Chash< OpenMS::TargetedExperimentHelper::Interpretation > | Hash function for TargetedExperimentHelper::Interpretation |
| Chash< OpenMS::TargetedExperimentHelper::Peptide > | Hash function for TargetedExperimentHelper::Peptide |
| Chash< OpenMS::TargetedExperimentHelper::PeptideCompound > | Hash function for TargetedExperimentHelper::PeptideCompound |
| Chash< OpenMS::TargetedExperimentHelper::Prediction > | Hash function for TargetedExperimentHelper::Prediction |
| Chash< OpenMS::TargetedExperimentHelper::Protein > | Hash function for TargetedExperimentHelper::Protein |
| Chash< OpenMS::TargetedExperimentHelper::Publication > | Hash function for TargetedExperimentHelper::Publication |
| Chash< OpenMS::TargetedExperimentHelper::RetentionTime > | Hash function for TargetedExperimentHelper::RetentionTime |
| Chash< OpenMS::TargetedExperimentHelper::TraMLProduct > | Hash function for TargetedExperimentHelper::TraMLProduct |
| Chash< OpenSwath::LightCompound > | Hash function for LightCompound |
| Chash< OpenSwath::LightModification > | Hash function for LightModification |
| Chash< OpenSwath::LightProtein > | Hash function for LightProtein |
| Chash< OpenSwath::LightTransition > | Hash function for LightTransition |
| NUi | |
1.9.8 