Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

Npappso	Tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multicharge peaks to monocharge
Ncbor
Nmzcbor
CBinaryDataArray
CConvertToMzml
CCvParam
CCvParamMap
CIsolationWindow
CMzcborBuildIndexReader
CMzcborCopyReplaceBase	Base class to transform mzCBOR stream in a new mzCBOR output stream
CMzcborIndexReader
CMzcborPrecursorFinder	Base class to transform mzCBOR stream in a new mzCBOR output stream
CMzcborReaderBase	Base class to initialize mzCBOR file parsing
CMzcborSpectrumCollectionReader
CMzmlConvert
CPrecursor
CQcborSpectrum
CQcborSpectrumPrecursor
CScan
CSelectedIon
CSpectrum
CSpectrumTube
Npsm
CCborScanMapBase
CMzIdentMlReader
CCvParam
CModification
CMzidDBSequence
CMzidSearchDatabase
CMzidSpectraData
CMzidPeptideEvidence
CUserParam
CSpectrumIdentificationItem
CSpectrumIdentificationResult
CPsmCbor2Json
CPsmCborUtils	Utilities to help managing data in PSM CBOR data file
CPsmProteinRef
CPsmFeatures
CPsmFeaturesScan
CPsmFile
CPsmFileAppend
CSampleStorage
CPsmFileReaderBase
CPsmProteinRef
CPsmFileScanProcess	Basic PSM file reader to process scan (parallelized scan processing)
CPsmFileScanProcessAndCopy	Basic PSM file reader to process scan (parallelized scan processing) and write a new resulting PSM file
CPsmIonSeries	Computes spectrum isotope match for each PSM and stores ion series in "props"
CPsmIonSeriesScan
CPsmNewEval
CPsmProtein
CPsmProteinMap	Store PsmProtein in a map with accession as key
CPsmSpecGlob
CPsmSpecGlobScan
CPsmSpecPeptidOms
CPsmSpecPeptidOmsScan
CSageFileReader
CSageReader
CSageModification
CFastaSeq
CSageTsvHandler
CLine
CPsm
CScan
CSample
CCborStreamReader	Simple override of the raw QCborStreamReader This adds convenient functions to put CBOR data into C++ structures
CCborStreamReaderInterface	Base class to start a CBOR reader
CCborStreamWriter	Overrides QCborStreamWriter base class to provide convenient functions
CJsonStreamWriter	Helper class to write json text using CBOR data structures
Nmasschroq
CAlignmentMethod
CCborOutputStream
CJsonInput
CMbrPeptideMeasurements
CMsRun
CMsRunGroup
CMsRunPeptideList
CPeptide
CAlignedPeakPositionElement	Internal structure to compute consensus retention times
CMsRunXicCoordCharge	Internal structure to store msrun + charge + intensity + xic coordinate
CPeptideBase
CPeptideLabel
CPeptideMeasurements
CPeptideMeasurementsBase
CMeasurement
CPeptideObservation
CObservation
CPrecursor	A Precursor object represents the parent/precursor of the MS level 2 scan with number _scan_num in the mzxml file
CPrecursorParser
CProtein
CQuantificationMethod
CUtils
Nspecglob
CAminoAcidModel
CExperimentalSpectrum
CExperimentalSpectrumDataPoint
CPeptideModel
CPeptideSpectrum
CPeptideSpectrumDataPoint
CPostTreatment
CScoreValues
CSpectralAlignment
CSpectralAlignmentDataPoint
CTheoreticalPeakDataPoint
Nspecpeptidoms
CAaPosition
CAlignment
CAminoAcidModel
CCorrectionTree
CKeyCell
CLocation
CLocationSaver
CPeptideModel	Modelize peptide sequence to facilitate rendering in bracket or proforma
CScenario
CScenarioCell
CScoreValues
CSemiGlobalAlignment
CSpOMSAa
CSpOMSProtein
CSpOMSSpectrum
Nspecself
CSelfSpectrum
CSelfSpectrumDataPoint
Nspectree
CBucket
CBucketClustering
CItemCart	Container for spectree items
CSpecTree
CSpecTreeNode
CMapSimilarityCountElement
CMapSimilarityCount
CSpecXtractInterface	Yield similarities between pairs of ItemCart
CSpecXtractMap	Store all similarities in vectors an map : very costly for memory and CPU
CAa
CAaBase
CAaCode	Collection of integer code for each amino acid 0 => null 1 to 20 => amino acid sorted by there mass (lower to higher). Leucine is replaced by Isoleucine
CAaModification
CAaStringCodec	Code and decode amino acid string sequence to unique integer
CAaStringCodeMassMatching	Convert a list of mass to amino acid string codes
CaaCodeAndMassRange
CAtomNumberInterface
CBafAsciiFileReader
CBafAsciiMsRunReader
CBaseColorMapPlotWidget
CBasePlotContext
CBasePlotWidget
CBaseTracePlotWidget
CChemicalFormula
CCodeToMass
CColorMapPlotConfig
CCosineSimilarity
CCubicSplineModel
CDaltonPrecision
CDataPoint
CDeepProtEnumStr
CDriftSpecMassSpecColorMapPlotWidget
CDriftSpecTracePlotWidget
CEnzyme
CEnzymeProductInterface
CExceptionInterrupted
CExceptionNotFound
CExceptionNotImplemented
CExceptionNotPossible
CExceptionNotRecognized	Excetion to use when an item type is not recognized
CExceptionOutOfRange
CFastaFileIndexer
CFastaFileIndexerInterface
CFastaHandlerInterface
CFastaOutputStream
CFastaReader
CFastaSeqHandler
CFastaWriterInterface
CFilterCeilingAmplitudePercentage	Redefines the ceiling intensity of the Trace
CFilterChargeDeconvolution
CDataPointInfo
CFilterComplementIonEnhancer	Try to detect complementary ions and assign maximum intensity of both elements
CFilterFloorAmplitudePercentage	Redefines the floor intensity of the Trace
CFilterFloorY	Apply std::floor (round to lowest integer) to all Y values
CFilterGreatestY	Keep N datapoints form the greatest intensities to the lowest
CFilterGreatestYperWindow	Keep N datapoints form the greatest intensities to the lowest within a mass range in dalton
CFilterHighPass	Remove datapoints below or equal to the given Y value (intensity)
CFilterHighPassPercentage	Remove datapoints below a given intensity percentage (ratio) of the maximum intensity
CFilterInterface	Generic interface to apply a filter on a trace
CFilterLocalMaximum	Finds all local maxima, i.e. any point that has a greater y value than both of its neighboring points and only keep those points
CFilterLowIntensitySignalRemoval	Redefines the floor intensity of the Trace
CFilterLowPass	Remove datapoints higher or equal to a given Y value (intensity)
CFilterMorphoAntiSpike	Anti spike filter set to zero alone values inside the window
CFilterMorphoBackground	Compute background of a trace compute background noise on a trace
CFilterMorphoMax	Transform the trace into its maximum over a window
CFilterMorphoMaxMin	Transform the trace with the maximum of the minimum equivalent of the erode filter for pictures
CFilterMorphoMean	Mean filter apply mean of y values inside the window : this results in a kind of smoothing
CFilterMorphoMedian	Median filter apply median of y values inside the window
CFilterMorphoMin	Transform the trace into its minimum over a window
CFilterMorphoMinMax	Transform the trace with the minimum of the maximum equivalent of the dilate filter for pictures
CFilterMorphoSum	Test purpose
CFilterMorphoWindowBase	Base class that apply a signal treatment based on a window
CFilterMzExclusion
CFilterNameInterface	Interface that allows to build filter objects from strings
CFilterNormalizeIntensities	Sets the maximum intensity of the trace to the provided value
CFilterOboPsiModMap
CFilterOboPsiModSink
CFilterOboPsiModTermAccession
CFilterOboPsiModTermDiffMono
CFilterOboPsiModTermLabel
CFilterOboPsiModTermName
CFilterPeakDelta
CFilterQuantileBasedRemoveY	Removes a value found by quantile to all Y values
CFilterRemoveC13
CFilterRemoveY	Removes a value to all Y values
CFilterResampleKeepGreater
CFilterResampleKeepPointInPolygon
CFilterResampleKeepSmaller
CFilterResampleKeepXRange
CFilterResampleRemoveXRange
CFilterRescaleY	Rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored
CFilterRoundY	Apply std::round (round to nearest integer) to all Y values
CFilterSavitzkyGolay	Uses Savitsky-Golay filter on trace
CFilterScaleFactorY	Rescales Y values given a tranformation factor
CFilterSuite	Apply a suite of filters from a vector
CFilterSuiteString
CFilterTandemDeisotope	Deisotope the mass spectrum this mass spectrum is iterated over and according to a data point-based moving window progression does the following tests:
CFilterTriangle
CFrameIdDescr
CGrpExperiment
CGrpGroup
CGrpGroupingMonitor
CGrpGroupingMonitorInterface
CGrpMapPeptideToGroup
CGrpMapPeptideToSubGroupSet
CGrpPeptide
CGrpPeptideSet
CGrpProtein
CGrpSubGroup
CGrpSubGroupSet
CHighResPeakPicker
CParameters
CPeakRange
CHttpButton
CIntegrationScope
CIntegrationScopeBase
CIntegrationScopeRect
CIntegrationScopeRhomb
CIntegrationScopeSpec
CIon
CIonIsotopeRatioScore
CIonMobilityGrid
CIsotopeCount
CLinearRegression
CLocalSignalToNoiseEstimator
CParameters
CGaussianEstimateParams
CMapTrace
CMassDataCombinerInterface
CMassSpecTracePlotContext
CMassSpecTracePlotWidget
CMassSpectrum	Class to represent a mass spectrum
CMassSpectrumCombiner
CMassSpectrumFilterGreatestItensities
CMassSpectrumFilterInterface	Generic interface to apply a filter on a MassSpectrum This is the same as FilterInterface, but some filter are only relevant if they are used on MassSpectrum using this interface means the filter can only be applied on MassSpectrum and not on Trace
CMassSpectrumFilterResampleKeepMzRange
CMassSpectrumFilterResampleRemoveMzRange
CMassSpectrumId
CMassSpectrumLineData
CMassSpectrumMinusCombiner
CMassSpectrumPlusCombiner
CMassSpectrumWidget
CMgfOutput
CMorpheusScore
CMsDataFormatEnumStr	Static functions to convert mz file formats
CMsFileAccessor
CMsFileReader
CMsRunDataSetTree
CMsRunDataSetTreeNode
CMsRunDataSetTreeNodeVisitorInterface
CMsRunId	MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informations on its location (local disk path or URL)
CMsRunQualifiedSpectrumLoader	Load all qualified spectrum into a vector
CMsRunReadConfig
CMsRunReader	Base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
CMsRunReaderRetentionTimeLine	Collect retention times along MS run
CMsRunReaderScanNumberMultiMap	Multimap to find quickly spectrum index from scan number
CMsRunReaderTicChromatogram	Calculate a TIC chromatogram
CMsRunRetentionTime
CPeptideMs2Point
CMsRunRetentionTimeSeamarkPoint
CMsRunSimpleStatistics	Example of interface to count MS levels of all spectrum in an MSrun
CMsRunSlice
CMsRunXicExtractor
CMsRunXicExtractorPoints
CMsRunXicExtractorReadPoints	Class to read retention time points of MsRun
CMsRunXicExtractorDisk
CMsRunXicExtractorDiskBuffer
CMsRunXicExtractorFactory	Factory to build different kinds of XIC extractors
CMsRunXicExtractorInterface
CMzCalibrationInterface
CMzCalibrationModel1
CMzCalibrationModel1Cached
CMzCalibrationStore
CMzcborMsFileReader
CMzcborMsRunReader
CMzIdentMlWriter
CMzIntegrationParams	Parameters definining how m/z integrations must be performed
CMzRange
CMzxmlOutput
CTranslater
COboChooserWidget
COboListModel
COboPsiModHandler
COboListProxyModel
COboListWidget
COboPsiMod
COboPsiModHandlerInterface
COboPsiModTerm
COboPsiMs
COboTermForm
COboUnimod
CPappsoException
CPeakIonIsotopeMatch
CPeakIonMatch
CPeptide
CPeptideBuilder	Builds a peptide shared pointer from peptide string and adds fixed modifications
CPeptideFixedModificationBuilder
CPeptideFragment
CPeptideFragmentIon
CPeptideFragmentIonListBase
CPeptideInterface
CPeptideIsotopeSpectrumMatch
CPeptideMethioninRemove	Potential remove Nter Methionin
CPeptideModificatorBase
CPeptideModificatorInterface
CPeptideModificatorPipeline
CPeptideModificatorTee
CPeptideNaturalIsotope
CPeptideNaturalIsotopeAverage
CPeptideNaturalIsotopeList
CPeptideProFormaParser
CPeptideRawFragmentMasses
CPeptideSemiEnzyme	Cut a regular peptide obtained with an enzyme at any position from Nter or Cter
CPeptideSinkInterface
CPeptideSizeFilter	Filter peptide string by size
CPeptideSpectrumMatch
CPeptideSpSinkInterface
CPeptideStrParser
CPeptideVariableModificationBuilder	Modify a peptide shared pointer with a variable modification on one AA
CPeptideVariableModificationReplacement
CPpmPrecision
CPrecisionBase
CPrecisionFactory
CPrecisionWidget
CPrecursorIonData
CProjectParam
CProjectParameters
CProtein
CProteinIntegerCode
CProteinPresenceAbsenceMatrix
CPsmFeatures
CPwizMsFileReader
CPwizMsRunReader
CQCPSpectrum
CQCPXic
CQualifiedMassSpectrum	Class representing a fully specified mass spectrum
CQualifiedXic
CResPrecision
CSavGolParams	Parameters for the Savitzky-Golay filter
CSelectionPolygon
CSelectionPolygonSpec
CSimplePeakIonMatch
CSpectrumCollectionHandlerInterface	Interface to collect spectrums from the MsRunReader class
CSwitchWidget
CTandemWrapperRun
CTicXicChromDriftSpecColorMapPlotWidget
CTicXicChromMassSpecColorMapPlotWidget
CTicXicChromTracePlotWidget
CTimsBinDec
CTimsData
CTimsDataFastMap	Replacement for std::map
CTimsDataFastMapElement
CTimsDdaPrecursors
CSpectrumDescr
CTimsDiaSlices
CMsMsWindow
CMsMsWindowGroup
CMsMsWindowGroupList
CFrameSliceRange
CTimsDirectXicExtractor
CTimsFrame
CXicComputeStructure
CTimsFrameBase
CTofIndexIntensityPair
CTimsFrameMobilityTraces
CTimsFrameRawDataChunck
CTimsFrameRecord
CTimsFramesMsRunReader
CTimsFrameType1
CTimsMs2CentroidFilter
CTimsMsFileReader
CTimsMsRunReader
CTimsMsRunReaderBase
CTimsMsRunReaderDia
CTimsMsRunReaderMs2
CTimsMsRunReaderMs2Selected
CTimsXicExtractorInterface
CTrace	A simple container of DataPoint instances
CTraceCombiner
CTraceDetectionInterface
CTraceDetectionMoulon
CTraceDetectionSinkInterface
CTraceDetectionZivy
CTraceMinusCombiner
CTracePeak
CTracePeakList
CTracePlusCombiner
CUiMonitorInterface
CUiMonitorText
CUiMonitorTextPercent
CUiMonitorVoid
CUtils
CWrapTandemInput
CWrapTandemResults
CXic
CXicCoord	Coordinates of the XIC to extract and the resulting XIC after extraction
CXicCoordTims	Coordinates of the XIC to extract and the resulting XIC after extraction
CXicPeptideFragmentIon
CXicPeptideFragmentIonNaturalIsotope
CXicPeptideInterface
CXicWidget
CXmlStreamReaderInterface	Convenient xml reader helper
CXtandemError
CXtandemHyperscore
CXtandemHyperscoreBis
CXtandemPresetReader
CXtandemSpectrumProcess
CXyMsFileReader
CXyMsRunReader
CContainsAny
CFilterComplement	Try to detect complementary ions and assign maximum intensity of both elements
CFilterMs1WindowSelection	Try to detect complementary ions and assign maximum intensity of both elements
CGraphicDeviceWidget
CInHousePolynomialSolverResult
CProteinPeptideList