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

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