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

pappso::AtomNumberInterface |
pappso::AaBase |
pappso::Aa |
pappso::AaModification |
pappso::PeptideInterface |
pappso::Peptide |
pappso::PeptideFragment |
pappso::PeptideFragmentIon |
pappso::PeptideNaturalIsotope |
pappso::BasePlotContext |
pappso::MassSpecTracePlotContext |
pappso::ColorMapPlotConfig |
ContainsAny |
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::FastaFileIndexerInterface |
pappso::FastaFileIndexer |
pappso::FastaHandlerInterface |
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 a 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 than a given Y value (intensity)
pappso::FilterMorphoBackground | Compute background of a trace compute background noise on a trace
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::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::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::FilterMzExclusion |
pappso::FilterQuantileBasedRemoveY | Removes a value found by quantile to all Y values
pappso::FilterSavitzkyGolay | Uses Savitsky-Golay filter on trace
pappso::FilterSuiteString |
pappso::FilterRemoveC13 |
pappso::FilterRemoveY | Removes a value to all Y values
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::TimsData::FrameIdDescr |
pappso::GrpExperiment |
pappso::GrpGroup |
pappso::GrpGroupingMonitorInterface |
pappso::GrpGroupingMonitor |
pappso::GrpMapPeptideToGroup |
pappso::GrpMapPeptideToSubGroupSet |
pappso::GrpPeptide |
pappso::GrpPeptideSet |
pappso::GrpProtein |
pappso::GrpSubGroup |
pappso::GrpSubGroupSet |
pappso::Ion |
pappso::PeptideInterface |
pappso::IonIsotopeRatioScore |
pappso::LinearRegression |
std::map< K, T > | STL class
pappso::MapTrace |
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::MgfOutput |
pappso::MorpheusScore |
pappso::MsFileAccessor |
pappso::MsFileReader |
pappso::PwizMsFileReader |
pappso::TimsMsFileReader |
pappso::XyMsFileReader |
pappso::MsRunAlignment |
pappso::MsRunDataSetTree |
pappso::MsRunDataSetTreeNode |
pappso::MsRunDataSetTreeNodeVisitorInterface |
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::MsRunReader | Base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
pappso::PwizMsRunReader |
pappso::TimsMsRunReader |
pappso::TimsMsRunReaderMs2 |
pappso::TimsMsRunReaderMs2Selected |
pappso::XyMsRunReader |
pappso::MsRunRetentionTime< T > |
pappso::MsRunRetentionTimeSeamarkPoint< T > |
pappso::MsRunSlice |
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::MzFormatEnumStr | Static functions to convert mz file formats
pappso::MzIntegrationParams | Parameters definining how m/z !
pappso::MzRange |
pappso::MzxmlOutput |
pappso::OboPsiMod |
pappso::OboPsiModHandlerInterface |
pappso::FilterOboPsiModSink |
pappso::FilterOboPsiModTermAccession |
pappso::FilterOboPsiModTermDiffMono |
pappso::FilterOboPsiModTermLabel |
pappso::FilterOboPsiModTermName |
pappso::OboListModel::OboPsiModHandler |
pappso::OboPsiModTerm |
pappso::PeakIonMatch |
pappso::PeakIonIsotopeMatch |
pappso::PeptideFragmentIonListBase |
pappso::PeptideIsotopeSpectrumMatch |
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::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::PeptideSpectrumMatch |
pappso::PeptideSpSinkInterface |
pappso::PeptideBuilder | Builds a peptide shared pointer from peptide string and adds fixed modifications
pappso::PeptideModificatorBase |
pappso::PeptideModificatorPipeline |
pappso::PeptideStrParser |
pappso::PrecisionBase |
pappso::DaltonPrecision |
pappso::PpmPrecision |
pappso::ResPrecision |
pappso::PrecisionFactory |
pappso::PrecursorIonData |
pappso::Protein |
ProteinPeptideList |
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::TandemWrapperRun |
QPushButton |
pappso::HttpButton |
pappso::SwitchWidget |
QSortFilterProxyModel |
pappso::OboListProxyModel |
QStringListModel |
pappso::OboListModel |
pappso::QualifiedMassSpectrum | Class representing a fully specified mass spectrum
pappso::QualifiedXic |
pappso::XicPeptideFragmentIonNaturalIsotope |
pappso::XicPeptideInterface |
pappso::XicPeptideFragmentIon |
QWidget |
GraphicDeviceWidget |
pappso::MassSpectrumWidget |
pappso::XicWidget |
pappso::OboChooserWidget |
pappso::OboListWidget |
pappso::OboTermForm |
pappso::PrecisionWidget |
pappso::SavGolParams | Parameters for the Savitzky-Golay filter
pappso::SelectionPolygon |
pappso::SelectionPolygonSpec |
pappso::SimplePeakIonMatch |
pappso::SpectrumCollectionHandlerInterface | Interface to collect spectrums from the MsRunReader class
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::TimsData::SpectrumDescr |
pappso::TimsBinDec |
pappso::TimsData |
pappso::TimsFrameBase |
pappso::TimsFrame |
pappso::TimsFrameType1 |
pappso::TraceDetectionInterface |
pappso::TraceDetectionMoulon |
pappso::TraceDetectionZivy |
pappso::TraceDetectionSinkInterface |
pappso::TracePeakList |
pappso::TracePeak |
pappso::UiMonitorInterface |
pappso::UiMonitorText |
pappso::UiMonitorTextPercent |
pappso::UiMonitorVoid |
pappso::Utils |
std::vector< T > | STL class
pappso::FilterSuite | Apply a suite of filters from a vector
pappso::Trace | A simple container of DataPoint instances
pappso::MassSpectrum | Class to represent a mass spectrum
pappso::Xic |
pappso::TracePeakList |
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::XtandemHyperscore |
pappso::XtandemHyperscoreBis |
pappso::XtandemSpectrumProcess |