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Here is a list of all functions with links to the classes they belong to:

### - r -

- raise() : pappso::PappsoException
- range() : pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRect, pappso::IntegrationScopeRhomb, pappso::SelectionPolygon
- rangeX() : pappso::SelectionPolygon
- rangeY() : pappso::SelectionPolygon
- rawReaderSpectrumCollectionByMsLevel() : pappso::TimsDdaPrecursors
- rbegin() : pappso::Peptide
- read() : pappso::cbor::psm::SageReader, pappso::XmlStreamReaderInterface
- read_msrun_peptide_observations() : pappso::masschroq::JsonInput
- read_note() : pappso::XtandemPresetReader
- read_peptide_list() : pappso::masschroq::JsonInput
- read_protein_list() : pappso::masschroq::JsonInput
- readAction() : pappso::masschroq::JsonInput
- readAlignmentMethodSp() : pappso::masschroq::JsonInput
- readAnalysisCollectionItem() : pappso::cbor::psm::MzIdentMlReader
- readAnalysisData() : pappso::cbor::psm::MzIdentMlReader
- readAnalysisProtocolCollection() : pappso::cbor::psm::MzIdentMlReader
- readAnalysisSoftware() : pappso::cbor::psm::MzIdentMlReader
- readArray() : pappso::cbor::CborStreamReader
- readBinaryDataArray() : pappso::cbor::mzcbor::MzmlConvert
- readBinaryDataArrayList() : pappso::cbor::mzcbor::MzmlConvert
- readCbor() : pappso::cbor::mzcbor::ConvertToMzml, pappso::cbor::mzcbor::MzcborBuildIndexReader, pappso::cbor::mzcbor::MzcborIndexReader, pappso::cbor::mzcbor::MzcborReaderBase, pappso::cbor::psm::PsmFileReaderBase
- readCborArray() : pappso::cbor::CborStreamReader
- readCborMap() : pappso::cbor::CborStreamReader
- readCvParam() : pappso::cbor::psm::MzIdentMlReader
- readDataCollectionItem() : pappso::cbor::psm::MzIdentMlReader
- readDBSequence() : pappso::cbor::psm::MzIdentMlReader
- readFile() : pappso::XmlStreamReaderInterface
- readInformations() : pappso::cbor::psm::PsmFileReaderBase
- readInputs() : pappso::cbor::psm::MzIdentMlReader
- readIntensity() : pappso::TimsDataFastMap
- readJson() : pappso::cbor::psm::SageFileReader
- readLog() : pappso::cbor::psm::PsmFileReaderBase
- readMap() : pappso::cbor::psm::PsmProteinMap
- readMsrun() : pappso::cbor::mzcbor::MzcborBuildIndexReader, pappso::cbor::mzcbor::MzcborReaderBase, pappso::cbor::mzcbor::MzcborSpectrumCollectionReader
- readMzDataFiles() : pappso::masschroq::JsonInput
- readParameterMap() : pappso::cbor::psm::PsmFileReaderBase
- readPeptide() : pappso::cbor::psm::MzIdentMlReader
- readPeptideEvidence() : pappso::cbor::psm::MzIdentMlReader
- readProjectParameters() : pappso::masschroq::JsonInput
- readProteinMap() : pappso::cbor::psm::PsmCbor2Json, pappso::cbor::psm::PsmFileReaderBase
- readPsm() : pappso::cbor::psm::PsmFileReaderBase
- readPsmFile() : pappso::cbor::psm::PsmFileReaderBase
- readPsmProteinRef() : pappso::cbor::psm::PsmFileReaderBase
- readQuantificationMethodSp() : pappso::masschroq::JsonInput
- readReferenceableParamGroupList() : pappso::cbor::mzcbor::MzcborReaderBase
- readRoot() : pappso::cbor::mzcbor::ConvertToMzml, pappso::cbor::mzcbor::MzcborIndexReader, pappso::cbor::mzcbor::MzcborReaderBase, pappso::cbor::psm::PsmFileReaderBase
- readSample() : pappso::cbor::psm::PsmFileAppend, pappso::cbor::psm::PsmFileReaderBase
- readScan() : pappso::cbor::mzcbor::MzcborSpectrumCollectionReader, pappso::cbor::psm::PsmFileReaderBase, pappso::cbor::psm::PsmFileScanProcess
- readScanCvParams() : pappso::cbor::mzcbor::Spectrum
- readSearchDatabase() : pappso::cbor::psm::MzIdentMlReader
- readSequenceCollectionItem() : pappso::cbor::psm::MzIdentMlReader
- readSpectraData() : pappso::cbor::psm::MzIdentMlReader
- readSpectrum() : pappso::cbor::mzcbor::MzcborBuildIndexReader, pappso::cbor::mzcbor::MzcborSpectrumCollectionReader
- readSpectrumCollection() : pappso::BafAsciiMsRunReader, pappso::MsRunReader, pappso::MzcborMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, pappso::XyMsRunReader
- readSpectrumCollection2() : pappso::BafAsciiMsRunReader, pappso::MsRunReader, pappso::MzcborMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, pappso::XyMsRunReader
- readSpectrumCollectionByMsLevel() : pappso::BafAsciiMsRunReader, pappso::MsRunReader, pappso::MzcborMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::XyMsRunReader
- readSpectrumCollectionWithMsrunReadConfig() : pappso::MzcborMsRunReader, pappso::PwizMsRunReader
- readSpectrumIdentification() : pappso::cbor::psm::MzIdentMlReader
- readSpectrumIdentificationItem() : pappso::cbor::psm::MzIdentMlReader
- readSpectrumIdentificationResult() : pappso::cbor::psm::MzIdentMlReader
- readSpectrumListAndLeave() : pappso::cbor::mzcbor::MzcborBuildIndexReader, pappso::cbor::mzcbor::MzcborSpectrumCollectionReader
- readStream() : pappso::cbor::mzcbor::MzmlConvert, pappso::cbor::psm::MzIdentMlReader, pappso::WrapTandemInput, pappso::WrapTandemResults, pappso::XmlStreamReaderInterface, pappso::XtandemPresetReader
- readTandemPresetFile() : pappso::TandemWrapperRun
- readTimsFrame() : pappso::TimsFrameRawDataChunck
- readTsvFile() : pappso::cbor::psm::SageReader
- readUserParam() : pappso::cbor::psm::MzIdentMlReader
- readyReadStandardError() : pappso::TandemWrapperRun
- readyReadStandardOutput() : pappso::TandemWrapperRun
- realft() : pappso::FilterSavitzkyGolay
- recGenerateModel() : pappso::AaStringCodec
- reconstructTrace() : pappso::FilterLowIntensitySignalRemoval
- recordDragDirections() : pappso::BasePlotContext
- recordLine() : pappso::cbor::psm::SageTsvHandler
- recursiveDepletion() : pappso::PeptideNaturalIsotopeAverage
- redrawPlotBackground() : pappso::BasePlotWidget
- reduce() : pappso::cbor::psm::PsmProteinMap
- refreshBaseContext() : pappso::MassSpecTracePlotWidget
- registerJsConstructor() : pappso::BasePlotContext, pappso::DataPointJs, pappso::MassSpecTracePlotContext, pappso::MassSpectrumCombiner, pappso::MassSpectrumJs, pappso::MassSpectrumMinusCombiner, pappso::MassSpectrumPlusCombiner, pappso::MzIntegrationParams, pappso::QPointFJs, pappso::TraceJs
- releaseDevice() : pappso::BafAsciiMsRunReader, pappso::MsRunReader, pappso::MzcborMsRunReader, pappso::PwizMsRunReader, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderMs2, pappso::XyMsRunReader
- remove() : pappso::GrpMapPeptideToSubGroupSet, pappso::GrpSubGroupSet
- removeAaModification() : pappso::Aa, pappso::Peptide
- removeAllButInternalModification() : pappso::Aa
- removeArtefactualSpike() : pappso::TimsDataFastMap
- removeBracketsForAlignedAA() : pappso::specglob::PeptideModel
- removeBucketsWithinCartIdRange() : pappso::spectree::BucketClustering
- removeCterAminoAcid() : pappso::Peptide
- removeDataSetQualMassSpectraOutsideDtOrRtRange() : pappso::MsRunDataSetTree
- removeDataSetTreeNodesOutsideDtOrRtRange() : pappso::MsRunDataSetTree
- removeFirstNonInformativeSubGroup() : pappso::GrpGroup
- removeNonInformativeSubGroups() : pappso::GrpExperiment, pappso::GrpGroup
- removeNterAminoAcid() : pappso::Peptide
- removeTraceInExclusionMargin() : pappso::FilterMzExclusion
- removeTranslationStop() : pappso::Protein
- removeUnsupportedMasses() : pappso::specpeptidoms::SpOMSSpectrum
- removeZeroValDataPointsChanged() : pappso::MzIntegrationParams
- removeZeroYDataPoints() : pappso::Trace
- removingNonInformativeSubGroupsInGroup() : pappso::GrpGroupingMonitor, pappso::GrpGroupingMonitorInterface
- rend() : pappso::Peptide
- replaceAaModification() : pappso::Aa, pappso::Peptide
- replaceAaModificationOnAminoAcid() : pappso::Peptide
- replaceLeucineIsoleucine() : pappso::AaBase, pappso::Peptide
- replaceModificationsAtPosition() : pappso::PeptideVariableModificationReplacement
- replaceWildcards() : pappso::Enzyme
- replotAll() : pappso::XicWidget
- replotWithAxesRanges() : pappso::BasePlotWidget
- replotWithAxisRangeX() : pappso::BasePlotWidget
- replotWithAxisRangeY() : pappso::BasePlotWidget
- reportSimilarity() : pappso::spectree::SpecXtractInterface, pappso::spectree::SpecXtractMap
- rescale() : pappso::MassSpectrumWidget, pappso::QCPSpectrum, pappso::QCPXic, pappso::XicWidget
- rescaleOneRange() : pappso::XicWidget
- reserve() : pappso::specpeptidoms::Scenario
- reset() : pappso::DataPoint, pappso::DataPointJs, pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRect, pappso::IntegrationScopeRhomb, pappso::MsRunReadConfig, pappso::MzIntegrationParams, pappso::specpeptidoms::Alignment, pappso::specpeptidoms::PeptideModel, pappso::XicCoord, pappso::XicCoordTims, pappso::XtandemHyperscoreBis
- resetAxesRangeHistory() : pappso::BasePlotWidget
- resetDeconvolutionData() : pappso::MassSpecTracePlotContext
- resetLocationSaver() : pappso::specpeptidoms::LocationSaver
- resetPoints() : pappso::SelectionPolygon
- resetScenario() : pappso::specpeptidoms::Scenario
- resetSelectionRectangle() : pappso::BasePlotWidget
- resolvingPowerComputationSignal() : pappso::MassSpecTracePlotWidget
- ResPrecision() : pappso::ResPrecision
- restoreAxesRangeHistory() : pappso::BasePlotWidget
- restorePreviousAxesRangeHistory() : pappso::BasePlotWidget
- reverse() : pappso::Peptide, pappso::Protein
- reverseFindDiffMz() : pappso::specglob::ExperimentalSpectrum
- rotate() : pappso::Peptide
- roundToDecimal32bitsAsLongLongInt() : pappso::Utils
- roundToDecimals() : pappso::Utils
- rowCount() : pappso::OboListModel
- rtChanged() : pappso::XicWidget
- rtChangeEvent() : pappso::XicWidget
- rtrim() : pappso::specglob::SpectralAlignment
- run() : pappso::TandemWrapperRun
- runFilter() : pappso::FilterSavitzkyGolay
- runTandem() : pappso::TandemWrapperRun