Class Hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 12345]

Cpappso::AaCode	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
Cpappso::AaStringCodeMassMatching::aaCodeAndMassRange
Cpappso::specpeptidoms::AaPosition
Cpappso::AaStringCodec	Code and decode amino acid string sequence to unique integer
Cpappso::AaStringCodeMassMatching	Convert a list of mass to amino acid string codes
Cpappso::masschroq::Peptide::AlignedPeakPositionElement	Internal structure to compute consensus retention times
Cpappso::specpeptidoms::Alignment
Cpappso::masschroq::AlignmentMethod
Cpappso::specglob::AminoAcidModel
Cpappso::specpeptidoms::AminoAcidModel
Cpappso::AreNamespaceClassnamePairsEqual
►Cpappso::AtomNumberInterface
►Cpappso::AaBase
Cpappso::Aa
Cpappso::AaModification
Cpappso::ChemicalFormula
►Cpappso::PeptideInterface
Cpappso::Peptide
Cpappso::PeptideFragment
Cpappso::PeptideFragmentIon
Cpappso::PeptideNaturalIsotope
Cpappso::spectree::Bucket
Cpappso::spectree::BucketClustering
Cpappso::masschroq::CborOutputStream
►Cpappso::cbor::CborStreamReaderInterface
►Cpappso::cbor::psm::PsmFileReaderBase
Cpappso::cbor::psm::PsmCbor2Json
Cpappso::cbor::psm::PsmFileAppend
►Cpappso::cbor::psm::PsmFileScanProcess	Basic PSM file reader to process scan (parallelized scan processing)
►Cpappso::cbor::psm::PsmFileScanProcessAndCopy	Basic PSM file reader to process scan (parallelized scan processing) and write a new resulting PSM file
Cpappso::cbor::psm::PsmFeatures
Cpappso::cbor::psm::PsmIonSeries	Computes spectrum isotope match for each PSM and stores ion series in "props"
Cpappso::cbor::psm::PsmNewEval
Cpappso::cbor::psm::PsmSpecGlob
Cpappso::cbor::psm::PsmSpecPeptidOms
Cpappso::CodeToMass
Cpappso::ColorMapPlotConfig
CContainsAny
Cpappso::specpeptidoms::CorrectionTree
Cpappso::CosineSimilarity
Cpappso::cbor::psm::MzIdentMlReader::CvParam
Cpappso::DataPoint
Cpappso::FilterChargeDeconvolution::DataPointInfo
Cpappso::DeepProtEnumStr
Cpappso::Enzyme
►Cpappso::EnzymeProductInterface
Cpappso::PeptideBuilder	Builds a peptide shared pointer from peptide string and adds fixed modifications
Cpappso::PeptideMethioninRemove	Potential remove Nter Methionin
Cpappso::PeptideModificatorPipeline
Cpappso::PeptideSemiEnzyme	Cut a regular peptide obtained with an enzyme at any position from Nter or Cter
Cpappso::PeptideSizeFilter	Filter peptide string by size
Cpappso::specglob::ExperimentalSpectrumDataPoint
►Cpappso::FastaFileIndexerInterface
Cpappso::FastaFileIndexer
►Cpappso::FastaHandlerInterface
Cpappso::FastaSeqHandler
Cpappso::cbor::psm::SageReader::FastaSeq
Cpappso::FastaReader
►Cpappso::FastaWriterInterface
Cpappso::FastaOutputStream
►Cpappso::FilterInterface	Generic interface to apply a filter on a trace
Cpappso::FilterFloorY	Apply std::floor (round to lowest integer) to all Y values
Cpappso::FilterGreatestY	Keep N datapoints form the greatest intensities to the lowest
Cpappso::FilterGreatestYperWindow	Keep N datapoints form the greatest intensities to the lowest within a mass range in dalton
Cpappso::FilterHighPass	Remove datapoints below a given Y value (intensity)
Cpappso::FilterHighPassPercentage	Remove datapoints below a given intensity percentage (ratio) of the maximum intensity
Cpappso::FilterLocalMaximum	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
Cpappso::FilterLowPass	Remove datapoints higher than a given Y value (intensity)
Cpappso::FilterMorphoMaxMin	Transform the trace with the maximum of the minimum equivalent of the erode filter for pictures
Cpappso::FilterMorphoMinMax	Transform the trace with the minimum of the maximum equivalent of the dilate filter for pictures
►Cpappso::FilterNameInterface	Interface that allows to build filter objects from strings
Cpappso::FilterCeilingAmplitudePercentage	Redefines the ceiling intensity of the Trace
Cpappso::FilterChargeDeconvolution
Cpappso::FilterComplementIonEnhancer	Try to detect complementary ions and assign maximum intensity of both elements
Cpappso::FilterFloorAmplitudePercentage	Redefines the floor intensity of the Trace
Cpappso::FilterLowIntensitySignalRemoval	Redefines the floor intensity of the Trace
Cpappso::FilterMorphoAntiSpike	Anti spike filter set to zero alone values inside the window
Cpappso::FilterMorphoBackground	Compute background of a trace compute background noise on a trace
►Cpappso::FilterMorphoWindowBase	Base class that apply a signal treatment based on a window
Cpappso::FilterMorphoMax	Transform the trace into its maximum over a window
Cpappso::FilterMorphoMean	Mean filter apply mean of y values inside the window : this results in a kind of smoothing
Cpappso::FilterMorphoMedian	Median filter apply median of y values inside the window
Cpappso::FilterMorphoMin	Transform the trace into its minimum over a window
Cpappso::FilterMorphoSum	Test purpose
Cpappso::FilterMzExclusion
Cpappso::FilterNormalizeIntensities	Sets the maximum intensity of the trace to the provided value
Cpappso::FilterQuantileBasedRemoveY	Removes a value found by quantile to all Y values
Cpappso::FilterRemoveY	Removes a value to all Y values
Cpappso::FilterSavitzkyGolay	Uses Savitsky-Golay filter on trace
Cpappso::FilterSuiteString
Cpappso::FilterPeakDelta
Cpappso::FilterRemoveC13
Cpappso::FilterResampleKeepGreater
Cpappso::FilterResampleKeepPointInPolygon
Cpappso::FilterResampleKeepSmaller
Cpappso::FilterResampleKeepXRange
Cpappso::FilterResampleRemoveXRange
Cpappso::FilterRescaleY	Rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored
Cpappso::FilterRoundY	Apply std::round (round to nearest integer) to all Y values
Cpappso::FilterScaleFactorY	Rescales Y values given a tranformation factor
Cpappso::FilterSuite	Apply a suite of filters from a vector
Cpappso::FilterTriangle
Cpappso::FrameIdDescr
Cpappso::TimsDiaSlices::FrameSliceRange
Cpappso::GrpExperiment
Cpappso::GrpGroup
►Cpappso::GrpGroupingMonitorInterface
Cpappso::GrpGroupingMonitor
Cpappso::GrpMapPeptideToGroup
Cpappso::GrpMapPeptideToSubGroupSet
Cpappso::GrpPeptide
Cpappso::GrpPeptideSet
Cpappso::GrpProtein
Cpappso::GrpSubGroup
Cpappso::GrpSubGroupSet
CInHousePolynomialSolverResult
►Cpappso::IntegrationScopeBase
►Cpappso::IntegrationScope
Cpappso::IntegrationScopeRect
Cpappso::IntegrationScopeRhomb
Cpappso::IntegrationScopeSpec
►Cpappso::Ion
Cpappso::PeptideInterface
Cpappso::IonIsotopeRatioScore
Cpappso::IonMobilityGrid
Cpappso::IsotopeCount
Cpappso::spectree::ItemCart	Container for spectree items
Cpappso::masschroq::JsonInput
Cpappso::specpeptidoms::KeyCell
Cpappso::cbor::psm::SageTsvHandler::Line
Cpappso::LinearRegression
Cpappso::specpeptidoms::Location
Cpappso::specpeptidoms::LocationSaver
►Cstd::map< K, T >	STL class
Cpappso::MapTrace
Cpappso::spectree::SpecTree::MapSimilarityCount
Cpappso::spectree::SpecTree::MapSimilarityCountElement
►Cpappso::MassDataCombinerInterface
►Cpappso::MassSpectrumCombiner
Cpappso::MassSpectrumMinusCombiner
Cpappso::MassSpectrumPlusCombiner
►Cpappso::TraceCombiner
Cpappso::TraceMinusCombiner
Cpappso::TracePlusCombiner
►Cpappso::MassSpectrumFilterInterface	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
Cpappso::FilterTandemDeisotope	Deisotope the mass spectrum this mass spectrum is iterated over and according to a data point-based moving window progression does the following tests:
Cpappso::MassSpectrumFilterGreatestItensities
Cpappso::MassSpectrumFilterResampleKeepMzRange
Cpappso::MassSpectrumFilterResampleRemoveMzRange
Cpappso::TimsMs2CentroidFilter
Cpappso::MassSpectrumId
Cpappso::MassSpectrumLineData
Cpappso::masschroq::PeptideMeasurementsBase::Measurement
Cpappso::MgfOutput
Cpappso::cbor::psm::MzIdentMlReader::Modification
Cpappso::MorpheusScore
Cpappso::MsDataFormatEnumStr	Static functions to convert mz file formats
Cpappso::MsFileAccessor
►Cpappso::MsFileReader
Cpappso::BafAsciiFileReader
Cpappso::PwizMsFileReader
Cpappso::TimsMsFileReader
Cpappso::XyMsFileReader
Cpappso::TimsDiaSlices::MsMsWindow
Cpappso::masschroq::MsRun
Cpappso::MsRunDataSetTree
Cpappso::MsRunDataSetTreeNode
Cpappso::MsRunDataSetTreeNodeVisitorInterface
Cpappso::masschroq::MsRunGroup
Cpappso::MsRunId	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)
Cpappso::masschroq::MsRunPeptideList
Cpappso::MsRunReadConfig
►Cpappso::MsRunReader	Base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Cpappso::BafAsciiMsRunReader
Cpappso::PwizMsRunReader
►Cpappso::TimsMsRunReaderBase
Cpappso::TimsFramesMsRunReader
Cpappso::TimsMsRunReader
Cpappso::TimsMsRunReaderDia
►Cpappso::TimsMsRunReaderMs2
Cpappso::TimsMsRunReaderMs2Selected
Cpappso::XyMsRunReader
Cpappso::MsRunRetentionTime< T >
Cpappso::MsRunRetentionTime< QString >
Cpappso::MsRunRetentionTimeSeamarkPoint< T >
Cpappso::MsRunRetentionTimeSeamarkPoint< QString >
Cpappso::MsRunSlice
Cpappso::masschroq::Peptide::MsRunXicCoordCharge	Internal structure to store msrun + charge + intensity + xic coordinate
Cpappso::MsRunXicExtractorFactory	Factory to build different kinds of XIC extractors
►Cpappso::MsRunXicExtractorInterface
►Cpappso::MsRunXicExtractor
►Cpappso::MsRunXicExtractorDisk
Cpappso::MsRunXicExtractorDiskBuffer
►Cpappso::TimsXicExtractorInterface
Cpappso::TimsDirectXicExtractor
Cpappso::MsRunXicExtractor::MsRunXicExtractorPoints
►Cpappso::MzCalibrationInterface
►Cpappso::MzCalibrationModel1
Cpappso::MzCalibrationModel1Cached
Cpappso::MzCalibrationStore
Cpappso::cbor::psm::MzIdentMlReader::MzidDBSequence
Cpappso::cbor::psm::MzIdentMlReader::MzidPeptideEvidence
Cpappso::cbor::psm::MzIdentMlReader::MzidSearchDatabase
Cpappso::cbor::psm::MzIdentMlReader::MzidSpectraData
Cpappso::MzRange
Cpappso::MzxmlOutput
Cpappso::NamespaceClassnameAsKeyHash
Cpappso::OboPsiMod
►Cpappso::OboPsiModHandlerInterface
Cpappso::FilterOboPsiModMap
Cpappso::FilterOboPsiModSink
Cpappso::FilterOboPsiModTermAccession
Cpappso::FilterOboPsiModTermDiffMono
Cpappso::FilterOboPsiModTermLabel
Cpappso::FilterOboPsiModTermName
Cpappso::OboListModel::OboPsiModHandler
Cpappso::OboPsiModTerm
Cpappso::OboPsiMs
Cpappso::OboUnimod
Cpappso::masschroq::PeptideObservation::Observation
►COdsDocHandlerInterface
Cpappso::cbor::psm::SageTsvHandler
►Cpappso::PeakIonMatch
Cpappso::PeakIonIsotopeMatch
►Cpappso::masschroq::PeptideBase
Cpappso::masschroq::Peptide
Cpappso::masschroq::PeptideLabel
Cpappso::PeptideFragmentIonListBase
Cpappso::PeptideIsotopeSpectrumMatch
►Cpappso::masschroq::PeptideMeasurementsBase
Cpappso::masschroq::MbrPeptideMeasurements
Cpappso::masschroq::PeptideMeasurements
►Cpappso::PeptideModificatorInterface
►Cpappso::PeptideModificatorBase
Cpappso::PeptideFixedModificationBuilder
►Cpappso::PeptideVariableModificationBuilder	Modify a peptide shared pointer with a variable modification on one AA
Cpappso::PeptideVariableModificationReplacement
Cpappso::PeptideModificatorPipeline
Cpappso::PeptideModificatorTee
Cpappso::MsRunRetentionTime< T >::PeptideMs2Point
Cpappso::PeptideNaturalIsotopeAverage
Cpappso::PeptideNaturalIsotopeList
Cpappso::masschroq::PeptideObservation
Cpappso::PeptideProFormaParser
Cpappso::PeptideRawFragmentMasses
►Cpappso::PeptideSinkInterface
Cpappso::PeptideMethioninRemove	Potential remove Nter Methionin
Cpappso::PeptideSemiEnzyme	Cut a regular peptide obtained with an enzyme at any position from Nter or Cter
Cpappso::PeptideSizeFilter	Filter peptide string by size
Cpappso::specglob::PeptideSpectrumDataPoint
Cpappso::PeptideSpectrumMatch
►Cpappso::PeptideSpSinkInterface
Cpappso::PeptideBuilder	Builds a peptide shared pointer from peptide string and adds fixed modifications
Cpappso::PeptideModificatorBase
Cpappso::PeptideModificatorPipeline
Cpappso::PeptideStrParser
Cpappso::specglob::PostTreatment
►Cpappso::PrecisionBase
Cpappso::DaltonPrecision
Cpappso::PpmPrecision
Cpappso::ResPrecision
Cpappso::PrecisionFactory
Cpappso::masschroq::Precursor	A Precursor object represents the parent/precursor of the MS level 2 scan with number _scan_num in the mzxml file
Cpappso::PrecursorIonData
Cpappso::ProjectParam
Cpappso::ProjectParameters
Cpappso::masschroq::Protein
Cpappso::Protein
Cpappso::ProteinIntegerCode
CProteinPeptideList
Cpappso::ProteinPresenceAbsenceMatrix
Cpappso::cbor::psm::SageTsvHandler::Psm
Cpappso::cbor::psm::PsmCborUtils	Utilities to help managing data in PSM CBOR data file
Cpappso::PsmFeatures
Cpappso::cbor::psm::PsmFile
Cpappso::cbor::psm::PsmProtein
Cpappso::cbor::psm::PsmProteinMap	Store PsmProtein in a map with accession as key
Cpappso::cbor::psm::PsmCborUtils::PsmProteinRef
Cpappso::cbor::psm::PsmFileReaderBase::PsmProteinRef
►CQCborMap
►Cpappso::cbor::psm::CborScanMapBase
Cpappso::cbor::psm::PsmFeaturesScan
Cpappso::cbor::psm::PsmIonSeriesScan
Cpappso::cbor::psm::PsmSpecGlobScan
Cpappso::cbor::psm::PsmSpecPeptidOmsScan
►CQCborStreamReader
Cpappso::cbor::CborStreamReader
►CQCborStreamWriter
Cpappso::cbor::CborStreamWriter
►CQCustomPlot
►Cpappso::BasePlotWidget
►Cpappso::BaseColorMapPlotWidget
Cpappso::DriftSpecMassSpecColorMapPlotWidget
Cpappso::TicXicChromDriftSpecColorMapPlotWidget
Cpappso::TicXicChromMassSpecColorMapPlotWidget
►Cpappso::BaseTracePlotWidget
Cpappso::DriftSpecTracePlotWidget
Cpappso::MassSpecTracePlotWidget
Cpappso::TicXicChromTracePlotWidget
Cpappso::QCPSpectrum
Cpappso::QCPXic
►CQException
►Cpappso::PappsoException
Cpappso::ExceptionInterrupted
Cpappso::ExceptionNotFound
Cpappso::ExceptionNotImplemented
Cpappso::ExceptionNotPossible
Cpappso::ExceptionNotRecognized	Excetion to use when an item type is not recognized
Cpappso::ExceptionOutOfRange
Cpappso::XtandemError
►CQObject
►Cpappso::BasePlotContext
Cpappso::MassSpecTracePlotContext
Cpappso::DataPointJs
Cpappso::MassSpectrumJs	JavaScript wrapper around MassSpectrum
Cpappso::MzIntegrationParams	Parameters definining how m/z !
Cpappso::QPointFJs
Cpappso::TandemWrapperRun
Cpappso::TraceJs
►CQPushButton
Cpappso::HttpButton
Cpappso::SwitchWidget
►CQSortFilterProxyModel
Cpappso::OboListProxyModel
►CQStringListModel
Cpappso::OboListModel
►CQTextStream
Cpappso::cbor::JsonStreamWriter
Cpappso::QualifiedMassSpectrum	Class representing a fully specified mass spectrum
►Cpappso::QualifiedXic
Cpappso::XicPeptideFragmentIonNaturalIsotope
►Cpappso::XicPeptideInterface
Cpappso::XicPeptideFragmentIon
Cpappso::masschroq::QuantificationMethod
►CQWidget
►CGraphicDeviceWidget
Cpappso::MassSpectrumWidget
Cpappso::XicWidget
Cpappso::OboChooserWidget
Cpappso::OboListWidget
Cpappso::OboTermForm
Cpappso::PrecisionWidget
►CQXmlStreamWriter
Cpappso::MzIdentMlWriter
Cpappso::cbor::psm::SageFileReader
Cpappso::cbor::psm::SageReader::SageModification
Cpappso::cbor::psm::SageReader
Cpappso::cbor::psm::SageTsvHandler::Sample
Cpappso::cbor::psm::PsmFileAppend::SampleStorage
Cpappso::SavGolParams	Parameters for the Savitzky-Golay filter
Cpappso::cbor::psm::SageTsvHandler::Scan
Cpappso::specpeptidoms::Scenario
Cpappso::specpeptidoms::ScenarioCell
Cpappso::specglob::ScoreValues
Cpappso::specpeptidoms::ScoreValues
Cpappso::SelectionPolygon
Cpappso::SelectionPolygonSpec
Cpappso::specself::SelfSpectrum
Cpappso::specself::SelfSpectrumDataPoint
Cpappso::specpeptidoms::SemiGlobalAlignment
Cpappso::SimplePeakIonMatch
Cpappso::specglob::SpectralAlignment
Cpappso::specglob::SpectralAlignmentDataPoint
Cpappso::spectree::SpecTree
Cpappso::spectree::SpecTree::SpecTreeNode
►Cpappso::SpectrumCollectionHandlerInterface	Interface to collect spectrums from the MsRunReader class
Cpappso::MsRunQualifiedSpectrumLoader	Load all qualified spectrum into a vector
Cpappso::MsRunReaderRetentionTimeLine	Collect retention times along MS run
Cpappso::MsRunReaderScanNumberMultiMap	Multimap to find quickly spectrum index from scan number
Cpappso::MsRunReaderTicChromatogram	Calculate a TIC chromatogram
Cpappso::MsRunSimpleStatistics	Example of interface to count MS levels of all spectrum in an MSrun
Cpappso::MsRunXicExtractor::MsRunXicExtractorReadPoints	Class to read retention time points of MsRun
Cpappso::MzxmlOutput::Translater
Cpappso::masschroq::PrecursorParser
Cpappso::TimsDdaPrecursors::SpectrumDescr
Cpappso::cbor::psm::MzIdentMlReader::SpectrumIdentificationItem
Cpappso::cbor::psm::MzIdentMlReader::SpectrumIdentificationResult
►Cpappso::spectree::SpecXtractInterface	Yield similarities between pairs of ItemCart
Cpappso::spectree::SpecXtractMap	Store all similarities in vectors an map : very costly for memory and CPU
Cpappso::specpeptidoms::SpOMSAa
Cpappso::specglob::TheoreticalPeakDataPoint
Cpappso::TimsBinDec
Cpappso::TimsData
Cpappso::TimsDataFastMap	Replacement for std::map
Cpappso::TimsDataFastMap::TimsDataFastMapElement
Cpappso::TimsDdaPrecursors
Cpappso::TimsDiaSlices
►Cpappso::TimsFrameBase
►Cpappso::TimsFrame
Cpappso::TimsFrameType1
Cpappso::TimsFrameMobilityTraces
Cpappso::TimsFrameRawDataChunck
Cpappso::TimsFrameRecord
Cpappso::TimsFrameBase::TofIndexIntensityPair
►Cpappso::TraceDetectionInterface
Cpappso::TraceDetectionMoulon
Cpappso::TraceDetectionZivy
►Cpappso::TraceDetectionSinkInterface
Cpappso::TracePeakList
Cpappso::TracePeak
►Cpappso::UiMonitorInterface
►Cpappso::UiMonitorText
Cpappso::UiMonitorTextPercent
Cpappso::UiMonitorVoid
Cpappso::cbor::psm::MzIdentMlReader::UserParam
Cpappso::masschroq::Utils
Cpappso::Utils
►Cstd::vector< T >	STL class
Cpappso::FilterSuite	Apply a suite of filters from a vector
Cpappso::TimsDiaSlices::MsMsWindowGroup
Cpappso::TimsDiaSlices::MsMsWindowGroupList
►Cpappso::Trace	A simple container of DataPoint instances
Cpappso::MassSpectrum	Class to represent a mass spectrum
Cpappso::Xic
Cpappso::TracePeakList
Cpappso::specglob::ExperimentalSpectrum
Cpappso::specglob::PeptideModel
Cpappso::specglob::PeptideSpectrum
Cpappso::specpeptidoms::PeptideModel	Modelize peptide sequence to facilitate rendering in bracket or proforma
Cpappso::specpeptidoms::SpOMSProtein
Cpappso::specpeptidoms::SpOMSSpectrum
Cpappso::TimsFrame::XicComputeStructure
►Cpappso::XicCoord	Coordinates of the XIC to extract and the resulting XIC after extraction
Cpappso::XicCoordTims	Coordinates of the XIC to extract and the resulting XIC after extraction
►Cpappso::XmlStreamReaderInterface	Convenient xml reader helper
Cpappso::WrapTandemInput
Cpappso::WrapTandemResults
Cpappso::XtandemPresetReader
Cpappso::cbor::psm::MzIdentMlReader
Cpappso::XtandemHyperscore
Cpappso::XtandemHyperscoreBis
Cpappso::XtandemSpectrumProcess