Class Hierarchy

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

[detail level 1234]

►Cpappso::AtomNumberInterface
►Cpappso::AaBase
Cpappso::Aa
Cpappso::AaModification
►Cpappso::PeptideInterface
Cpappso::Peptide
Cpappso::PeptideFragment
Cpappso::PeptideFragmentIon
Cpappso::PeptideNaturalIsotope
Cpappso::BasePlotContext
Cpappso::ColorMapPlotConfig
CContainsAny
Cralab::base::resample::Convert2Dense
Cpappso::DataPoint
Cpappso::FilterChargeDeconvolution::DataPointInfo
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::FastaFileIndexerInterface
Cpappso::FastaFileIndexer
Cpappso::FastaHandlerInterface
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::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::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::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::FilterNameInterface	Interface that allows to build filter objects from strings
Cpappso::FilterChargeDeconvolution
Cpappso::FilterComplementIonEnhancer	Try to detect complementary ions and assign maximum intensity of both elements
Cpappso::FilterSuiteString
Cpappso::FilterPseudoCentroid
Cpappso::FilterRemoveC13
Cpappso::FilterResampleKeepGreater
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::FilterSavitzkyGolay	Uses Savitsky-Golay filter on trace
Cpappso::FilterScaleFactorY	Rescales Y values given a tranformation factor
Cpappso::FilterSuite	Apply a suite of filters from a vector
Cpappso::FilterTriangle
Cpappso::GrpExperiment
Cpappso::GrpGroup
►Cpappso::GrpGroupingMonitorInterface
Cpappso::GrpGroupingMonitor
Cpappso::GrpMapPeptideToGroup
Cpappso::GrpMapPeptideToSubGroupSet
Cpappso::GrpPeptide
Cpappso::GrpPeptideSet
Cpappso::GrpProtein
Cpappso::GrpSubGroup
Cpappso::GrpSubGroupSet
►Cpappso::Ion
Cpappso::PeptideInterface
Cpappso::IonIsotopeRatioScore
Cpappso::LinearRegression
Cralab::base::ms::LocalMinPeakArea< TReal >
►Cstd::map< K, T >	STL class
Cpappso::MapTrace
►Cpappso::MassDataCombinerInterface
►Cpappso::MassSpectrumCombiner
Cpappso::MassSpectrumMinusCombiner
Cpappso::MassSpectrumPlusCombiner
►Cpappso::TraceCombiner
Cpappso::TraceMinusCombiner
Cpappso::TracePlusCombiner
Cpappso::MassSpecTracePlotContext
Cpappso::MassSpectrumCombinerFactory
►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::MgfOutput
Cpappso::MorpheusScore
Cpappso::MsFileAccessor
►Cpappso::MsFileReader
Cpappso::PwizMsFileReader
Cpappso::TimsMsFileReader
Cpappso::XyMsFileReader
Cpappso::MsRunAlignment
Cpappso::MsRunDataSetTree
Cpappso::MsRunDataSetTreeNode
Cpappso::MsRunDataSetTreeNodeVisitorInterface
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::MsRunReader	Base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Cpappso::PwizMsRunReader
Cpappso::TimsMsRunReader
►Cpappso::TimsMsRunReaderMs2
Cpappso::TimsMsRunReaderMs2Selected
Cpappso::XyMsRunReader
Cpappso::MsRunRetentionTime< T >
Cpappso::MsRunRetentionTimeSeamarkPoint< T >
Cpappso::MsRunSlice
Cpappso::MsRunXicExtractorFactory	Factory to build different kinds of XIC extractors
►Cpappso::MsRunXicExtractorInterface
►Cpappso::MsRunXicExtractor
►Cpappso::MsRunXicExtractorDisk
Cpappso::MsRunXicExtractorDiskBuffer
Cpappso::MsRunXicExtractorInterface::MsRunXicExtractorPoints
►Cpappso::MzCalibrationInterface
►Cpappso::MzCalibrationModel1
Cpappso::MzCalibrationModel1Cached
Cpappso::MzCalibrationStore
Cpappso::MzIntegrationParams	Parameters definining how m/z !
Cpappso::MzRange
Cpappso::MzxmlOutput
Cpappso::OboPsiMod
►Cpappso::OboPsiModHandlerInterface
Cpappso::FilterOboPsiModSink
Cpappso::FilterOboPsiModTermAccession
Cpappso::FilterOboPsiModTermDiffMono
Cpappso::FilterOboPsiModTermLabel
Cpappso::FilterOboPsiModTermName
Cpappso::OboPsiModTerm
►Cpappso::PeakIonMatch
Cpappso::PeakIonIsotopeMatch
Cralab::base::ms::PeakPicker< TReal, TIntegrator >
Cpappso::PeptideFragmentIonListBase
Cpappso::PeptideIsotopeSpectrumMatch
►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::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::PeptideSpectrumMatch
►Cpappso::PeptideSpSinkInterface
Cpappso::PeptideBuilder	Builds a peptide shared pointer from peptide string and adds fixed modifications
Cpappso::PeptideModificatorBase
Cpappso::PeptideModificatorPipeline
Cpappso::PeptideStrParser
►Cpappso::PrecisionBase
Cpappso::DaltonPrecision
Cpappso::MzPrecision
Cpappso::PpmPrecision
Cpappso::ResPrecision
Cpappso::PrecisionFactory
Cpappso::PrecursorIonData
Cpappso::Protein
CProteinPeptideList
►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::ExceptionNotFound
Cpappso::ExceptionNotImplemented
Cpappso::ExceptionNotPossible
Cpappso::ExceptionNotRecognized	Excetion to use when an item type is not recognized
Cpappso::ExceptionOutOfRange
►CQObject
Cpappso::TandemWrapperRun
Cpappso::QualifiedMassSpectrum	Class representing a fully specified mass spectrum
►Cpappso::QualifiedXic
Cpappso::XicPeptideFragmentIonNaturalIsotope
►Cpappso::XicPeptideInterface
Cpappso::XicPeptideFragmentIon
►CQWidget
►CGraphicDeviceWidget
Cpappso::MassSpectrumWidget
Cpappso::XicWidget
Cpappso::PrecisionWidget
►CQXmlDefaultHandler
Cpappso::XtandemInputSaxHandler
Cpappso::XtandemOutputSaxHandler
Cpappso::XtandemPresetSaxHandler
Cpappso::RtPoint
Cpappso::SavGolParams	Parameters for the Savitzky-Golay filter
Cralab::base::ms::SimplePeakArea< TReal >
Cpappso::SimplePeakIonMatch
Cralab::base::ms::SimplePicker< TReal >	Computes first derivative of a sequence, looks for zero crossings
►Cpappso::SpectrumCollectionHandlerInterface	Interface to collect spectrums from the MsRunReader class
Cpappso::MsRunReaderScanNumberMultiMap	Multimap to find quickly spectrum index from scan number
Cpappso::MsRunSimpleStatistics	Example of interface to count MS levels of all spectrum in an MSrun
Cpappso::MsRunXicExtractorInterface::MsRunXicExtractorReadPoints	Class to read retention time points of MsRun
Cpappso::MzxmlOutput::Translater
CRetentionTimeReader
Cpappso::TimsBinDec
Cpappso::TimsData
►Cpappso::TimsFrameBase
Cpappso::TimsFrame
CTimsXic
►Cpappso::TimsXicExtractorInterface
Cpappso::TimsDirectXicExtractor
Cpappso::TimsXicStructure	Structure needed to extract XIC from Tims data
►Cpappso::TraceDetectionInterface
Cpappso::TraceDetectionMoulon
Cpappso::TraceDetectionZivy
Cpappso::TraceDetectionSinkInterface
Cpappso::TracePeak
Cpappso::Utils
►Cstd::vector< T >	STL class
Cpappso::FilterSuite	Apply a suite of filters from a vector
►Cpappso::Trace	A simple container of DataPoint instances
Cpappso::MassSpectrum	Class to represent a mass spectrum
Cpappso::Xic
Cpappso::TimsFrame::XicComputeStructure
Cpappso::XtandemHyperscore
Cpappso::XtandemHyperscoreBis
Cpappso::XtandemSpectrumProcess