| ►Nboost | |
| ►Nmsclr | |
| Cpinned_gcroot | Pinned_gcroot: a slightly modified gcroot that pins its GCHandle |
| ►Npwiz | |
| ►Nanalysis | |
| Canalyzer_strings | This auxilliary class should be specialized for MSDataAnalyzers whose instantiation is controlled by user-supplied strings (via command line, config file, etc.) |
| Canalyzer_strings< MetadataReporter > | |
| Canalyzer_strings< RegionSIC > | |
| Canalyzer_strings< RegionSlice > | |
| Canalyzer_strings< RegionTIC > | |
| Canalyzer_strings< RunSummary > | |
| Canalyzer_strings< SpectrumBinaryData > | |
| Canalyzer_strings< SpectrumTable > | |
| CChromatogramDataFilter | |
| ►CChromatogramList_Filter | ChromatogramList filter, for creating Chromatogram sub-lists |
| CPredicate | Client-implemented filter predicate – called during construction of ChromatogramList_Filter to create the filtered list of chromatograms |
| CChromatogramList_FilterPredicate_IndexSet | |
| CChromatogramList_LockmassRefiner | ChromatogramList implementation to replace peak profiles with picked peaks |
| CChromatogramList_SavitzkyGolaySmoother | ChromatogramList implementation to return native centroided chromatogram data |
| CChromatogramList_XICGenerator | ChromatogramList implementation to return native centroided chromatogram data |
| CChromatogramListFactory | Factory for instantiating and wrapping ChromatogramLists |
| CChromatogramListWrapper | Inheritable pass-through implementation for wrapping a ChromatogramList |
| CCubicHermiteSpline | An implementation of the IInterpolation interface that acts as a wrapper for a cSpline |
| CCwtPeakDetector | |
| CDemuxDebugReader | A class for reading demux matrices from file |
| CDemuxDebugWriter | A class for writing demux matrices to file |
| CDemuxSolver | Interface for solver that can be used for demultiplexing |
| CDemuxWindow | A container for describing the isolation windows that are dedicated to columns of the design matrix for demultiplexing |
| CExtraZeroSamplesFilter | Removes (most) zero samples in signal profiles, except those flanking nonzero samples simply looks for runs of 0 values, removes all but start and end of run |
| CFeatureDetector | |
| ►CFeatureDetectorPeakel | FeatureDetectorPeakel implements a 'template method', delegating to 'strategies' encapsulated by the following interfaces: PeakExtractor PeakelGrower PeakelPicker |
| CConfig | Convenience construction |
| CFeatureDetectorSimple | FeatureDetectorSimple detects 'rectangular' features, ie number of peaks in isotope envelope is the same for each scan included in the feature |
| CFeatureModeler | Interface for fitting and scoring Feature data to a model |
| CFeatureModeler_Gaussian | Gaussian implementation |
| CIDemultiplexer | Interface for calculating demultiplexing scheme |
| CIPrecursorMaskCodec | Interface for generating and accessing precursor masks for a demultiplexing scheme |
| CIsolationWindow | A container that wraps DemuxWindow to preserve the full precision window boundaries |
| CIsolationWindowFilter | |
| CIsoWindowHasher | A method of hashing an isolation window to a unique long value mz is and m/z of a unique point in the isolation window, such as the lower bound, upper bound, or center |
| CLocalMaximumPeakDetector | |
| CMatrixIO | Provides static methods for writing and reading matrices to/from files |
| CMetadataReporter | Writes file-level metadata to a file |
| ►CMS2Deisotoper | |
| CConfig | PrecursorMassFilter's parameters |
| ►CMS2NoiseFilter | |
| CConfig | MS2NoiseFilter's parameters |
| ►CMSDataAnalyzer | Interface for MSData analyzers |
| CDataInfo | Information about the data to be analyzed |
| CMSDataAnalyzerContainer | Container of MSDataAnalyzer (composite pattern) |
| ►CMSDataAnalyzerDriver | Event generator for MSDataAnalyzer |
| CProgressCallback | Progress callback interface |
| ►CMSDataCache | Simple memory cache for common MSData info |
| CConfig | MSDataCache configuration |
| ►CMSXDemultiplexer | Implementation of the IDemultiplexer interface that is able to handle both MSX experiments, including ones with overlap |
| CParams | User-defined options for demultiplexing |
| CMZRTField | MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT |
| CNNLSSolver | Implementation of the DemuxSolver interface as a non-negative least squares (NNLS) problem |
| CNoise | |
| CNoiseCalculator | |
| ►CNoiseCalculator_2Pass | |
| CConfig | |
| CNoVendorPeakPickingException | |
| ►COverlapDemultiplexer | Implementation of the IDemultiplexer interface that is able to handle overlap experiments |
| CParams | User-defined options for demultiplexing |
| CPeak | Some generic metadata about a peak detected in a signal |
| CPeakDetector | |
| CPeakelGrower | Interface for growing Peakels |
| ►CPeakelGrower_Proximity | Simple PeakelGrower implementation, based on proximity of Peaks |
| CConfig | |
| CPeakelPicker | Interface for picking Peakels and arranging into Features; note: Peakels are actually removed from the PeakelField |
| ►CPeakelPicker_Basic | Basic implementation |
| CConfig | |
| CPeakExtractor | Class for extracting Peak objects from an array of ordered pairs; in design pattern lingo, this is a "template method" delegating peak finding and peak fitting to "strategies" |
| CPeakFamilyDetector | Interface for peak family (isotope envelope) detection |
| ►CPeakFamilyDetectorFT | FT-specific implementation of PeakFamilyDetector |
| CConfig | |
| CNoDataException | FT-specific exception |
| CPeakFinder | Interface for finding peaks in an array of ordered pairs |
| ►CPeakFinder_SNR | PeakFinder implementation based on signal-to-noise ratio |
| CConfig | |
| CPeakFitter | Interface for fitting peaks in an array of ordered pairs |
| ►CPeakFitter_Parabola | PeakFitter implementation based on fitting a parabola |
| CConfig | |
| ►CPepxmlRecordReader | |
| CConfig | |
| Crecord | |
| ►CPrecursorMaskCodec | Implementation of the IPrecursorMaskCodec interface that is able to handle both overlapping MSX experiments |
| CDemuxBoundary | Simple container that is useful for breaking up DemuxWindows into their edges and resolving overlap |
| ►CPrecursorMassFilter | |
| CConfig | PrecursorMassFilter's parameters |
| ►CPrecursorRecalculator | |
| CPrecursorInfo | |
| ►CPrecursorRecalculatorDefault | |
| CConfig | |
| ►CProteinList_DecoyGenerator | ProteinList decoy generator for creating decoy proteins on the fly |
| CPredicate | Client-implemented generator predicate – called during construction of ProteinList_DecoyGenerator to create a decoy protein from a target protein |
| CProteinList_DecoyGeneratorPredicate_Reversed | Creates a reversed copy of every target protein with the specified decoy string prefixed to the id |
| CProteinList_DecoyGeneratorPredicate_Shuffled | Creates a randomly shuffled copy of every target protein with the specified decoy string prefixed to the id |
| ►CProteinList_Filter | ProteinList filter, for creating Protein sub-lists |
| CPredicate | Client-implemented filter predicate – called during construction of ProteinList_Filter to create the filtered list of proteins |
| CProteinList_FilterPredicate_IdSet | |
| CProteinList_FilterPredicate_IndexSet | |
| CProteinListFactory | Factory for instantiating and wrapping ProteinLists |
| ►CRegionAnalyzer | Analyzes a rectangular region of m/z-time space |
| CConfig | |
| CSpectrumStats | |
| CStats | |
| ►CRegionSIC | Writes data samples from a single rectangular region |
| CConfig | |
| ►CRegionSlice | Writes data samples from a single rectangular region |
| CConfig | |
| ►CRegionTIC | Writes data samples from a single rectangular region |
| CConfig | |
| CRTMatches_Any | Predicate always returns true |
| CRTMatches_Contains | Predicate returns true iff the object's retention time range contains the specified retention time |
| CRTMatches_IsContainedIn | Predicate returns true iff the object's retention time range is completely contained within the range of the specified reference object, up to the specified tolerance |
| ►CRunSummary | Writes table of spectrum metadata to a file |
| CConfig | |
| CSavitzkyGolaySmoother | |
| CSmoother | Interface for a one-dimensional smoothing algorithm |
| ►CSpectrumBinaryData | Writes table of spectrum metadata to a file |
| CConfig | |
| CSpectrumDataFilter | |
| CSpectrumList_3D | SpectrumList implementation that can create 3D spectra of ion mobility drift time and m/z |
| CSpectrumList_ChargeFromIsotope | SpectrumList implementation that assigns (probable) charge states to tandem mass spectra |
| CSpectrumList_ChargeStateCalculator | SpectrumList implementation that assigns (probable) charge states to tandem mass spectra |
| ►CSpectrumList_Demux | SpectrumList decorator implementation that can demultiplex spectra of several precursor windows acquired in the same scan |
| CParams | User-defined options for demultiplexing |
| ►CSpectrumList_Filter | SpectrumList filter, for creating Spectrum sub-lists |
| CPredicate | Client-implemented filter predicate – called during construction of SpectrumList_Filter to create the filtered list of spectra |
| CSpectrumList_FilterPredicate_ActivationType | |
| CSpectrumList_FilterPredicate_AnalyzerType | |
| CSpectrumList_FilterPredicate_ChargeStateSet | |
| CSpectrumList_FilterPredicate_DefaultArrayLengthSet | |
| CSpectrumList_FilterPredicate_IdSet | |
| CSpectrumList_FilterPredicate_IndexSet | |
| CSpectrumList_FilterPredicate_MSLevelSet | |
| CSpectrumList_FilterPredicate_MzPresent | |
| CSpectrumList_FilterPredicate_Polarity | |
| CSpectrumList_FilterPredicate_PrecursorMzSet | |
| CSpectrumList_FilterPredicate_ScanEventSet | |
| CSpectrumList_FilterPredicate_ScanNumberSet | |
| CSpectrumList_FilterPredicate_ScanTimeRange | |
| CSpectrumList_FilterPredicate_ThermoScanFilter | |
| CSpectrumList_IonMobility | SpectrumList implementation that provides access to vendor-specific ion mobility functions |
| CSpectrumList_LockmassRefiner | SpectrumList implementation to replace peak profiles with picked peaks |
| CSpectrumList_MetadataFixer | SpectrumList implementation to add (or replace) base peak and total ion metadata with new values calculated from the current binary data |
| CSpectrumList_MZRefiner | |
| CSpectrumList_MZWindow | SpectrumList filter, for creating Spectrum sub-lists |
| CSpectrumList_PeakFilter | SpectrumList implementation that returns spectra with the specified SpectrumDataFilter operation applied |
| CSpectrumList_PeakPicker | SpectrumList implementation to replace peak profiles with picked peaks |
| CSpectrumList_PrecursorRecalculator | SpectrumList wrapper that recalculates precursor info on spectrum() requests |
| ►CSpectrumList_PrecursorRefine | SpectrumList wrapper that recalculates precursor info on spectrum() requests |
| CPrecursorInfo | |
| CSpectrumList_ScanSummer | Provides a custom-sorted spectrum list |
| CSpectrumList_Smoother | SpectrumList implementation to return smoothed spectral data |
| ►CSpectrumList_Sorter | Provides a custom-sorted spectrum list |
| CPredicate | Client-implemented sort predicate – called during construction of SpectrumList_Sorter to sort the underlying spectrum list |
| CSpectrumList_SorterPredicate_ScanStartTime | |
| CSpectrumList_TitleMaker | SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user-specified format |
| CSpectrumList_ZeroSamplesFilter | SpectrumList implementation to return spectra with or without extra zero samples |
| CSpectrumListFactory | Factory for instantiating and wrapping SpectrumLists |
| CSpectrumPeakExtractor | Extracts sets of centroided peaks from spectra using a user-defined list of peaks to extract |
| ►CSpectrumTable | Writes table of spectrum metadata to a file |
| CConfig | |
| CTabularConfig | |
| CThresholdFilter | |
| CVersion | |
| CWhittakerSmoother | |
| CZeroSampleFiller | Fills in missing zero samples around signal profiles |
| ►Nchemistry | |
| ►Ndetail | |
| CElement | |
| CIsotope | |
| ►NElement | Scope for declarations related to elements |
| ►NInfo | Class for obtaining information about elements |
| CRecord | |
| CFormula | Class to represent a chemical formula |
| CIsotopeCalculator | |
| ►CIsotopeEnvelopeEstimator | Class used for calculating a theoretical isotope envelope for a given mass, based on an estimate of the elemental composition for that mass |
| CConfig | |
| CIsotopeTable | Class representing a table of isotope distributions for collections of multiple atoms of a single element; the table is computed on instantiation, based on the element's mass distribution, a maximum atom count, and abundance cutoff value |
| CMassAbundance | Struct for holding isotope information |
| CMZTolerance | Struct for expressing m/z tolerance in either amu or ppm |
| ►Ncv | |
| CCV | Information about an ontology or CV source and a short 'lookup' tag to refer to |
| CCVTermInfo | Structure for holding CV term info |
| ►Ndata | |
| ►Ndiff_impl | |
| CHasID | |
| CSame | |
| CSameDeep | |
| ►Npeakdata | |
| CFeature | |
| CFeatureFile | |
| CHandlerFeature | |
| CHandlerPeak | |
| CHandlerPeakel | |
| CPeak | |
| CPeakData | |
| CPeakel | Struct for an eluted peak (PEAK ELution) |
| CPeakFamily | |
| CScan | |
| ►CSoftware | |
| CParameter | |
| ►Npepxml | |
| CAlternativeProtein | |
| CAminoAcidModification | |
| CAnalysisResult | |
| CAnalysisSummary | |
| CAnalysisTimestamp | Reference for analysis applied to current run (time corresponds with analysis_summary/, id corresponds with analysis_result/) |
| CDataFilter | |
| CDatasetDerivation | Source and filtering criteria used to generate dataset |
| CDistributionPoint | |
| CEnzymaticSearchConstraint | |
| CErrorPoint | |
| CMatch | |
| CMatchData | |
| CMixtureModel | |
| CModAminoAcidMass | |
| CModificationInfo | |
| CMSMSPipelineAnalysis | |
| CMSMSRunSummary | |
| CParameter | |
| CPeptideProphetResult | |
| CPeptideProphetSummary | |
| CQ3RatioResult | |
| CRocDataPoint | |
| CSampleEnzyme | |
| CSearchDatabase | |
| CSearchHit | |
| CSearchResult | |
| CSearchScore | |
| CSearchSummary | Database search settings |
| CSpecificity | |
| CSpectrumQuery | |
| CBaseDiffConfig | |
| CBinaryIndexStream | Index implementation in a stream (intended for fstreams but any iostream works); find(string id) is O(logN); find(ordinal index) is O(1); memory footprint is negligible |
| CCalibrationParameters | |
| CCVParam | Tag-value pair, where the tag comes from the controlled vocabulary |
| CCVParamIs | Functor for finding CVParam with specified exact CVID in a collection of CVParams: |
| CCVParamIsChildOf | Functor for finding children of a specified CVID in a collection of CVParams: |
| CCVTranslator | Translates text to CV terms |
| CDiff | Calculate diffs of objects in a ProteoWizard data model hierarchy |
| CFrequencyData | Class for binary storage of complex frequency data |
| ►CIndex | Generic interface for creating and using an index on a stream of serialized objects |
| CEntry | Generic type identifying an indexed item by string id, ordinal index, and stream offset |
| CMemoryIndex | Index implementation in memory; find(string id) is O(logN); find(ordinal index) is O(1); memory footprint is basically (number of entries * 2) |
| COBO | Represents a selectively parsed OBO file |
| CParamContainer | The base class for elements that may contain cvParams, userParams, or paramGroup references |
| CParamGroup | A collection of CVParam and UserParam elements that can be referenced from elsewhere in this mzML document by using the 'paramGroupRef' element in that location to reference the 'id' attribute value of this element |
| CSampleDatum | |
| CTerm | Single controlled vocabulary term |
| CUserParam | Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead |
| ►Nfrequency | |
| ►NDerivativeTest | |
| CAdaptedErrorDerivative | |
| CAdaptedErrorFunction | |
| CParametrizedDerivativeSlice | |
| CParametrizedFunctionSlice | |
| CVectorFunction | |
| CFrequencyEstimator | Interface for frequency estimator modules |
| ►CFrequencyEstimatorPhysicalModel | Physical model implementation of the FrequencyEstimator interface |
| CConfig | |
| CFrequencyEstimatorSimple | Simple implementation of the FrequencyEstimator interface |
| CMagnitudeLorentzian | |
| CParameterEstimator | |
| ►CParametrizedFunction | |
| CErrorFunction | |
| CPeakDetector | Interface for finding peaks in frequency data |
| ►CPeakDetectorMatchedFilter | MatchedFilter implementation of the PeakDetector interface |
| CConfig | Structure for holding configuration |
| CScore | Structure for holding the matched filter calculation results |
| CPeakDetectorNaive | Naive implementation of the PeakDetector interface |
| CTruncatedLorentzian | |
| CTruncatedLorentzianEstimator | |
| CTruncatedLorentzianParameters | Struct for holding parameters for a Truncated Lorentzian function |
| ►Nidentdata | |
| CAmbiguousResidue | Implementation of AmbiguousResidueType from the mzIdentML schema |
| CAnalysisCollection | Implementation of AnalysisCollectionType from the mzIdentML schema |
| CAnalysisData | Implementation of AnalysisDataType from the mzIdentML schema |
| CAnalysisProtocolCollection | Implementation of AnalysisProtocolCollectionType from the mzIdentML schema |
| CAnalysisSampleCollection | Implementation of AnalysisSampleCollectionType from mzIdentML schema |
| CAnalysisSoftware | Implementation of AnalysisSoftwareType from the mzIdentML schema |
| CBibliographicReference | Implementation for the BibliographicReferenceType tag in the mzIdentML schema |
| CContact | Implementation of ContactType from mzIdentML |
| CContactRole | Implementation of ContactRoleType from the mzIdentML schema |
| CCVIDMatchCVMap | |
| CCVMap | |
| CDatabaseTranslation | Implementation of DatabaseTranslationType from the mzIdentML schema |
| CDataCollection | Implementation of DataCollectionType from the mzIdentML schema |
| CDBSequence | Implementation of DBSequenceType from the mzIdentML schema |
| Cdbsequence_p | |
| CDefaultReaderList | Default Reader list |
| CDelimReader | |
| CDelimWriter | |
| CDiffConfig | |
| CEnzyme | Implementation of EnzymeType from the mzIdentML schema |
| CEnzymes | Implementation of EnzymesType from the mzIdentML schema |
| CFilter | Implementation of FilterType from the mzIdentML schema |
| CFragmentArray | Implementation of FragmentArrayType from the mzIdentML schema |
| Cid_p | |
| CIdentData | Implementation of the MzIdentMLType from the mzIdentML schema |
| ►CIdentDataFile | IdentData object plus file I/O |
| CWriteConfig | Configuration for write() |
| CIdentifiable | Parent class representing extensions of the IdentifiableType from the mzIdentML schema |
| CIdentifiableParamContainer | Parent class of all Identifiable objects that have ParamGroups |
| CInputs | Implementation of the InputsType from the mzIdentML schema |
| CIonType | Implementation of IonTypeType from the mzIdentML schema |
| CMascotReader | |
| CMassTable | Implementation of MassTableType from the mzIdentML schema |
| CMeasure | Implementation of MeasureType from the mzIdentML schema |
| CModification | Implementation of ModificationType from the mzIdentML schema |
| COrganization | Implementation of AbstractOrganizationType from the mzIdentML schema |
| Corganization_p | |
| CPep2MzIdent | Translates data from a MinimumPepXML object into a IdentData object tree when a translation is known |
| CPeptide | Implementation of PeptideType from the mzIdentML schema |
| CPeptideEvidence | Implementation of PeptideEvidenceType from the mzIdentML schema |
| CPeptideHypothesis | Implementation of PeptideHypothesisType from the mzIdentML schema |
| CPepXMLSpecificity | |
| CPerson | Implementation of PersonType from the mzIdentML schema |
| Cperson_p | |
| CProteinAmbiguityGroup | Implementation of ProteinAmbiguityGroupType from the mzIdentML schema |
| CProteinDetection | Implementation of ProteinDetectionType from the mzIdentML schema |
| CProteinDetectionHypothesis | Implementation of ProteinDetectionHypothesisType from the mzIdentML schema |
| CProteinDetectionList | Implementation of ProteinDetectionListType from the mzIdentML schema |
| CProteinDetectionProtocol | Implementation of ProteinDetectionProtocolType from the mzIdentML schema |
| CProvider | Implementation of ProviderType from the mzIdentML schema |
| ►CReader | Interface for file readers |
| CConfig | HACK: provide an option to read only file-level metadata; once we have an enumerable ResultList implementation this will be deprecated |
| CReaderFail | |
| CReaderList | Reader container (composite pattern) |
| CRegexCVMap | |
| CResidue | Implementation of ResidueType from the mzIdentML schema |
| CSample | Implementation of the SampleType from the mzIdentML schema |
| CSearchDatabase | Implementation of SearchDatabaseType from the mzIdentML schema |
| CSearchModification | Implementation of SearchModificationType from the mzIdentML schema |
| Cseq_p | |
| Csequence_p | |
| CSequenceCollection | Implementation of SequenceCollectionType from the mzIdentML schema |
| ►CSerializer_mzIdentML | MZIDData <-> mzIdentML stream serialization |
| CConfig | Serializer_mzIdentML configuration |
| ►CSerializer_pepXML | MZIDData <-> pepXML stream serialization |
| CConfig | Serializer_pepXML configuration |
| ►CSerializer_protXML | MZIDData <-> pepXML stream serialization |
| CConfig | Serializer_protXML configuration |
| ►CSerializer_Text | Serializer_Text reads in and writes out an id file in tab format |
| CConfig | < Controls the format of the text file |
| Csoftware_p | |
| CSourceFile | Implementation of SourceFileType from the mzIdentML schema |
| CSpectraData | Implementation of SpectraDataType from the mzIdentML schema |
| CSpectrumIdentification | Implementation of SpectrumIdentificationType from the mzIdentML schema |
| CSpectrumIdentificationItem | Implementation of SpectrumIdentificationItemType from the mzIdentML schema |
| CSpectrumIdentificationList | Implementation of SpectrumIdentificationListType from the mzIdentML schema |
| CSpectrumIdentificationProtocol | Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema |
| CSpectrumIdentificationResult | Implementation of SpectrumIdentificationResultType from the mzIdentML schema |
| CStringMatchCVMap | |
| CSubstitutionModification | Implementation of SubstitutionModificationType from the mzIdentML schema |
| CTextWriter | |
| CTranslationTable | Implementation of TranslationTableType from the mzIdentML schema |
| CVersion | |
| ►Nmath | |
| ►NMatchedFilter | |
| CCorrelation | |
| ►CKernelTraits | |
| CDummy | |
| CKernelTraitsBase | |
| CKernelTraitsBase< Y(*)(X)> | |
| CProductSpace | |
| CSampledData | |
| CLinearLeastSquares | |
| CLinearLeastSquares< LinearLeastSquaresType_LU > | |
| CLinearLeastSquares< LinearLeastSquaresType_QR > | |
| CLinearSolver | |
| CLinearSolver< LinearSolverType_LU > | |
| CLinearSolver< LinearSolverType_QR > | |
| COrderedPair | |
| COrderedPairContainerRef | Wrapper class for accessing contiguous data as a container of OrderedPairs; note that it does not own the underlying data |
| CParabola | |
| CStats | |
| ►Nminimxml | |
| ►NSAXParser | An extended SAX interface for custom XML stream parsing |
| ►CHandler | SAX event handler interface |
| ►CAttributes | |
| Cattribute | |
| CStatus | Handler returns the Status struct as a means of changing the parser's behavior |
| Csaxstring | |
| ►Cbasic_charcounter | |
| Ccategory | |
| ►CXMLWriter | Simple, tag-level XML syntax writing |
| CAttributes | Vector of name/value pairs to be written as XML attributes |
| CConfig | Initial configuration of the XMLWriter |
| COutputObserver | Interface to allow outside observation of data sent to output stream |
| ►Nmsdata | |
| ►Ndetail | |
| CChromatogramList_ABI | |
| CChromatogramList_Agilent | |
| CChromatogramList_Bruker | |
| CChromatogramList_Shimadzu | |
| CChromatogramList_Thermo | |
| CChromatogramList_Waters | |
| CSpectrumList_ABI | |
| CSpectrumList_ABI_T2D | |
| CSpectrumList_Agilent | |
| CSpectrumList_Bruker | |
| CSpectrumList_Shimadzu | |
| CSpectrumList_Thermo | |
| CSpectrumList_UIMF | |
| CSpectrumList_UNIFI | |
| ►CSpectrumList_Waters | |
| CVendorOptions | |
| CActivation | The type and energy level used for activation |
| CBinaryDataArray | The structure into which encoded binary data goes. Byte ordering is always little endian (Intel style). Computers using a different endian style MUST convert to/from little endian when writing/reading mzML |
| ►CBinaryDataEncoder | Binary-to-text encoding |
| CConfig | Encoding/decoding configuration |
| CChromatogram | A single chromatogram |
| CChromatogramIdentity | Identifying information for a chromatogram |
| CChromatogramList | Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML) |
| CChromatogramList_mzML | Implementation of ChromatogramList, backed by an mzML file |
| CChromatogramListBase | Common functionality for base ChromatogramList implementations |
| CChromatogramListSimple | Simple writeable in-memory implementation of ChromatogramList |
| CComponent | A component of an instrument corresponding to a source (i.e. ion source), an analyzer (i.e. mass analyzer), or a detector (i.e. ion detector) |
| CComponentList | List with the different components used in the mass spectrometer. At least one source, one mass analyzer and one detector need to be specified |
| CContact | Structure allowing the use of a controlled (cvParam) or uncontrolled vocabulary (userParam), or a reference to a predefined set of these in this mzML file (paramGroupRef) |
| CDataProcessing | Description of the way in which a particular software was used |
| CDefaultReaderList | Default Reader list |
| CDiffConfig | Configuration struct for diffing MSData types |
| CExtendedReaderList | Default ReaderList, extended to include vendor readers |
| CFileContent | This summarizes the different types of spectra that can be expected in the file. This is expected to aid processing software in skipping files that do not contain appropriate spectrum types for it |
| CFileDescription | Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here |
| CIndex_mzML | |
| CIndexList | |
| CInstrumentConfiguration | Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST have one (and only one) of the three different components used for an analysis. For hybrid instruments, such as an LTQ-FT, there MUST be one configuration for each permutation of the components that is used in the document. For software configuration, reference the appropriate ScanSettings element |
| CIsolationWindow | This element captures the isolation (or 'selection') window configured to isolate one or more precursors |
| CLegacyAdapter_Instrument | Interface for legacy access to Instrument |
| CLegacyAdapter_Software | Interface for legacy access to Software |
| CMemoryMRUCache | MRU cache for SpectrumPtrs or ChromatogramPtrs |
| CMSData | This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to capture the use of a mass spectrometer, the data generated, and the initial processing of that data (to the level of the peak list) |
| ►CMSDataFile | MSData object plus file I/O |
| CWriteConfig | Configuration for write() |
| CMSDataMerger | |
| CMSnHeader | |
| CMZIntensityPair | The data point type of a mass spectrum |
| CPrecursor | The method of precursor ion selection and activation |
| CProcessingMethod | Description of the default peak processing method. This element describes the base method used in the generation of a particular mzML file. Variable methods should be described in the appropriate acquisition section - if no acquisition-specific details are found, then this information serves as the default |
| CProduct | Product ion information |
| ►CReader | Interface for file readers |
| CConfig | Reader configuration |
| CReader_ABI | |
| CReader_ABI_T2D | |
| CReader_Agilent | |
| CReader_Bruker | |
| CReader_BTDX | |
| CReader_MGF | |
| CReader_MSn | |
| CReader_mz5 | |
| CReader_mzML | |
| CReader_mzXML | |
| CReader_Shimadzu | |
| CReader_Thermo | |
| CReader_UIMF | |
| CReader_UNIFI | |
| CReader_Waters | |
| CReaderFail | |
| CReaderList | Reader container (composite pattern) |
| CRun | A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument |
| CSample | Expansible description of the sample used to generate the dataset, named in sampleName |
| CScan | Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile |
| CScanList | List and descriptions of scans |
| CScanSettings | Description of the acquisition settings of the instrument prior to the start of the run |
| CScanWindow | TODO |
| CSelectedIon | TODO |
| CSerializer_MGF | MSData <-> MGF stream serialization |
| CSerializer_MSn | MSData <-> MSn stream serialization |
| ►CSerializer_mzML | MSData <-> mzML stream serialization |
| CConfig | Serializer_mzML configuration |
| ►CSerializer_mzXML | MSData <-> mzXML stream serialization |
| CConfig | Serializer_mzXML configuration |
| CSHA1OutputObserver | |
| CSoftware | A piece of software |
| CSourceFile | Description of the source file, including location and type |
| CSpectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
| CSpectrumIdentity | Identifying information for a spectrum |
| CSpectrumIdentityFromMzXML | Identifying information for a spectrum as read from mzML or mzXML subclassed to add private information for faster file IO in mzXML |
| CSpectrumIdentityFromXML | Identifying information for a spectrum subclassed to add private information for faster file IO in mzML and mzXML |
| ►CSpectrumInfo | Simple structure for holding Spectrum info |
| CPrecursorInfo | Structure for Precursor info |
| ►CSpectrumIterator | SpectrumIterator provides convenient iteration through a set of scans in a SpectrumList |
| CConfig | SpectrumIterator configuration – note that constructors allow automatic conversion from IntegerSet or Sieve to Config |
| CSieve | Interface for filtering based on ScanInfo |
| CSpectrumList | Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML) |
| CSpectrumList_BTDX | SpectrumList backed by a Bruker BioTools DataExchange XML file |
| CSpectrumList_MGF | Implementation of SpectrumList, backed by an MGF file |
| CSpectrumList_MSn | Implementation of SpectrumList, backed by an MGF file |
| CSpectrumList_mzML | Implementation of SpectrumList, backed by an mzML file |
| ►CSpectrumList_mzXML | Implementation of SpectrumList, backed by an mzXML file |
| Cindex_not_found | Exception thrown if create(*,*,true) is called and the mzXML index cannot be found |
| CSpectrumListBase | Common functionality for base SpectrumList implementations |
| ►CSpectrumListCache | Adds a level of flexible MRU caching to a SpectrumList processor chain |
| CCacheEntry | Cache mapping spectrum indices to SpectrumPtrs |
| CSpectrumListIonMobilityBase | |
| CSpectrumListSimple | Simple writeable in-memory implementation of SpectrumList |
| CSpectrumListWrapper | Inheritable pass-through implementation for wrapping a SpectrumList |
| CSpectrumWorkerThreads | |
| CTarget | TODO |
| CTextWriter | |
| CTimeIntensityPair | The data point type of a chromatogram |
| CVersion | |
| ►Npeptideid | |
| CFlatRecordBuilder | |
| Clocation_less | |
| CMSInspectRecordBuilder | |
| CnativeID_less | |
| ►CPeptideID | This is an interface for classes that allow access to data sources of identified peptides |
| CIterator | Iterator for |
| CIteratorInternal | Interface for |
| CLocation | |
| CRecord | |
| CPeptideID_flat | This class allows access to peptides listed in a flat tab delimited text file |
| CPeptideID_pepXml | This class allows access to identified proteins in PeptideProphet files |
| CPeptideIDMap | |
| ►Nproteome | |
| ►NAminoAcid | Scope for types related to amino acids |
| ►NInfo | Class for accessing information about the amino acids |
| CRecord | Struct for holding data for a single amino acid |
| CDefaultReaderList | Default Reader list |
| CDiffConfig | Configuration struct for diffs |
| CDigestedPeptide | Peptide subclass that contains extra metadata provided by digestion |
| ►CDigestion | Enumerates the peptides from proteolytic digestion of a polypeptide or protein; |
| CConfig | Sets constraints for valid peptides produced by iterating the digestion |
| Cconst_iterator | Forward-only, read-only iteration to enumerate peptides |
| CFragmentation | Fragment ion masses for a peptide |
| CIndexList | |
| ►CIPIFASTADatabase | Class for accessing data in ipi.*.fasta files |
| CRecord | Structure for holding peptide info |
| CModification | Post-translational modification (PTM) modification formula or masses must be provided at instantiation |
| CModificationList | List of modifications on a single amino acid |
| CModificationMap | Maps peptide/protein sequence indexes (0-based) to a modification list |
| CPeptide | Peptide or polypeptide (a sequence of amino acids) |
| CProtein | |
| CProteinList | |
| CProteinListCache | Adds a level of flexible MRU caching to a ProteinList processor chain |
| CProteinListSimple | |
| CProteinListWrapper | Inheritable pass-through implementation for wrapping a ProteinList |
| CProteomeData | |
| ►CProteomeDataFile | ProteomeData object plus file I/O |
| CWriteConfig | Configuration for write() |
| CReader | Interface for file readers |
| ►CReader_FASTA | FASTA -> ProteomeData stream serialization |
| CConfig | Reader_FASTA configuration |
| CReaderFail | |
| CReaderList | Reader container (composite pattern) |
| ►CSerializer_FASTA | ProteomeData <-> FASTA stream serialization |
| CConfig | Serializer_FASTA configuration |
| CTextWriter | |
| CVersion | |
| ►Ntradata | |
| CCompound | Chemical compound other than a peptide for which one or more transitions |
| CConfiguration | Instrument configuration used in the validation or optimization of the transitions |
| CContact | |
| CDefaultReaderList | Default Reader list |
| CDiffConfig | Configuration struct for diffs |
| CEvidence | Information about empirical mass spectrometer observations of the peptide |
| CInstrument | Instrument on which transitions are validated |
| CInterpretation | A possible interpration of the product ion for a transition |
| CModification | A molecule modification specification |
| CPeptide | Peptide for which one or more transitions are intended to identify |
| CPrecursor | Precursor (Q1) of the transition |
| CPrediction | Information about a prediction for a suitable transition using some software |
| CProduct | Product (Q3) of the transition |
| CProtein | |
| CPublication | |
| CReader | Interface for file readers |
| CReaderFail | |
| CReaderList | Reader container (composite pattern) |
| CRetentionTime | |
| CSerializer_traML | TraData <-> traML stream serialization |
| CSoftware | |
| CTarget | A peptide or compound that is to be included or excluded from a target list of precursor m/z values |
| CTargetList | List of precursor m/z targets to include or exclude |
| CTextWriter | |
| CTraData | |
| ►CTraDataFile | TraData object plus file I/O |
| CWriteConfig | Configuration for write() |
| CTransition | |
| CValidation | Information about the state of validation of a transition on a given instrument model |
| CVersion | |
| ►Nutil | |
| ►CBinaryData | A custom vector class that can store its contents in either a std::vector or a cli::array (when compiled with .NET) |
| Cconst_iterator | |
| Citerator | |
| CCharIndexedVector | Wrapper for boost::array that is indexable by character; supports indexes 0-127 |
| CCharIndexedVectorConstIterator | Const_iterator for CharIndexedVector |
| CCharIndexedVectorIterator | Iterator for CharIndexedVector |
| CClickwrapPrompter | Barrier to force end users to agree/disagree to a prompt before continuing |
| CDefaultTabHandler | |
| ►CImage | Wrapper class for using 'gd' graphics library |
| CColor | Struct for holding rgb values (in [0,255]) |
| CPoint | Struct for holding pixel coordinates |
| ►CIntegerSet | Virtual container of integers, accessible via an iterator interface, stored as union of intervals |
| CInterval | Single closed interval of integers |
| CIterator | Forward iterator providing readonly access to the virtual container |
| ►CIterationListener | Interface to be implemented by clients who want progress callbacks |
| CUpdateMessage | |
| CIterationListenerRegistry | Handles registration of IterationListeners and broadcast of update messages |
| CLock | |
| Cmru_list | |
| ►CMSIHandler | |
| CRecord | |
| Conce_flag_proxy | |
| Crandom_access_compressed_ifstream | |
| CReaderTestConfig | |
| CSHA1_ostream | Ostream filter for calculating a SHA-1 hash of data on the fly |
| CSHA1Calculator | |
| CSHA1Filter | Model of boost::iostreams::Filter |
| CSHA1SymmetricFilter | Model of boost::iostreams::SymmetricFilter |
| Cshared_map | Copy semantics of shared_ptr<map<K,V> > with a std::map interface |
| CTabHandler | |
| CTabReader | |
| CTestPathPredicate | Test implementations derive from this to define which paths should be tested |
| CTimer | |
| Cusage_exception | |
| Cuser_error | |
| CVectorTabHandler | |
| Cvirtual_map | Wrapper for std::map that will behave properly with polymorphism |
| ►Nvendor_api | |
| CVersion | |
| ►Nralab | EQUISPACEINTERPOL Interpolation on a equidistantly spaced grid |
| ►Nbase | |
| ►Nbase | |
| ►Nutilities | |
| CCosineInterpolate | CosineInterpolate Functor Linear interpolation results in discontinuities at each point |
| CCubicInterpolate | CubicInterpolate Functor |
| CHermiteInterpolate | HermiteInterpolation |
| CLinearInterpolate | LinearInterpolate Functor |
| CSeqMinus | |
| CSeqPlus | |
| ►Nfilter | |
| ►Nutilities | |
| CGauss | Gauss function |
| CGauss_1deriv | First derivative of Gaussian |
| CMexican_Hat | Mexican hat wavelet |
| CMexican_Hat2 | Mexican hat wavelet Version 2 |
| ►Nms | |
| CLocalMinPeakArea | Extends peak to the left and to the right to the next local minimum or a predefined threshol or a maximum allowed extension |
| CPeakPicker | Resamples spectrum, apply smoothing, determines zero crossings, integrates peaks |
| CSimplePeakArea | Resamples spectrum, apply smoothing, determines zero crossings, integrates peaks |
| CSimplePicker | |
| ►Nresample | |
| ►Nutilities | |
| Cmeanfunctor | |
| CBin1D | |
| CBucket1D | |
| CConvert2Dense | |
| CDaCompFunctor | Da Comparator - constant mass error |
| CFTMSCompFunctor | FTMS Comparator |
| CPPMCompFunctor | TODO Do checking on TReal thats a real |
| CSamplingWith | |
| CSquareRoot | |
| ►Nstats | |
| CNthPower | |
| CAnotherRootHandler | |
| CBadListener | |
| CCancelListener | |
| CCancelProgressCallback | |
| CCSHA1 | |
| CCubicHermiteSplineTest | |
| CCustomPair | |
| CDatum | |
| CDefaultArrayLengthSorter | |
| CDemuxDebugRWTest | |
| CDemuxHelpersTest | |
| CDemuxSolverTest | |
| ►CDemuxTest | |
| CMSDPair | |
| CDigestedPeptideLessThan | |
| CEnumConstantNotPresentException | An exception class inspired by Java's EnumConstantNotPresentException |
| CEnzymePtr_missedCleavages | |
| CEnzymePtr_specificity | |
| CEvenMS2Predicate | |
| CEvenPredicate | |
| CEvenRequester | |
| CFifth | |
| CFifthHandler | |
| CFilterWrapper | |
| CFirst | |
| CFirstHandler | |
| CFTSieve | |
| CGoober | |
| CHasBinaryDataPredicate | |
| CIInterpolation | Interface for interpolating between points in a discrete data set |
| CIs_T2D_Directory | |
| CIsDirectory | |
| CIsIMSData | |
| CisoChain | |
| CisotopeChain | |
| CIsRawData | |
| CIsRawFile | |
| CIsTDF | |
| CIsWiffFile | |
| CMatrixIOTest | |
| CMSDataWithSettableVersion | |
| CMSLevelSorter | |
| CMyBase | |
| CMyPred | |
| CMyWrapper | |
| CmzrtEqual | |
| CNestedHandler | |
| COneMinusAbs | |
| CpairData | |
| CParametrizedCosine | |
| CparentIon | |
| CprecursorGroup | |
| CPrintAttribute | |
| CPrintEventHandler | |
| CRawMassDatum | |
| ►CReader1 | |
| CConfig | |
| CReaderConfig | |
| ►CReader2 | |
| CConfig | |
| CReaderConfig | |
| CridgeLine | |
| CRoot | |
| CRootHandler | |
| CrtimeMap | |
| CscoreChain | |
| CSecond | |
| CSecondHandler | |
| CSelectedIndexPredicate | |
| CSetRetentionTime | |
| CSHA1_WORKSPACE_BLOCK | |
| CSimple | |
| CSimpleAnalyzer | |
| CSimpleProgressCallback | |
| CSpectrumPeakExtractorTest | |
| CTestAminoAcid | |
| CTestChargeStateCalculator | |
| CTestData | |
| CTestDatum | |
| CTestDeisotopeCalculator | |
| CTestDeisotoper | |
| CTestETDMassFilter | |
| CTestFormula | |
| CTestFragmentation | |
| CTestInfo | |
| CTestIterationListener | |
| CTestIterationListener_WithCancel | |
| CTestListener | |
| CTestMetadataFixer | |
| CTestModification | |
| CTestModifiedPeptide | |
| CTestMS2Denoise | |
| CTestOperator | |
| CTestOutputObserver | |
| CTestPair | |
| CTestPathmask | |
| CTestPeptide | |
| CTestReader | |
| CTestScanSummerCalculator | |
| CTestSpectrumInfo | |
| CTestThresholder | |
| CThreadStatus | |
| CUserParamNameIs | |
| CWriteCVParam | |
