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

### - c -

- calculateDragDeltas() : pappso::BasePlotWidget
- calculateMassFromChemicalComponents() : pappso::AaModification
- CborOutputStream() : pappso::masschroq::CborOutputStream
- CborScanMapBase() : pappso::cbor::psm::CborScanMapBase
- CborStreamReader() : pappso::cbor::CborStreamReader
- CborStreamReaderInterface() : pappso::cbor::CborStreamReaderInterface
- CborStreamWriter() : pappso::cbor::CborStreamWriter
- check() : pappso::GrpGroup, pappso::GrpMapPeptideToSubGroupSet
- checkForAaModification() : pappso::specglob::PeptideModel
- checkForAaModificationP() : pappso::specglob::PeptideModel
- checkForMutation() : pappso::specglob::PeptideModel
- checkForMutations() : pappso::specglob::PeptideModel
- checkInf() : pappso::cbor::psm::PsmFeaturesScan
- checkNativeId() : pappso::PwizMsRunReader
- checkScanNum() : pappso::TimsFrameBase
- checkSequenceDiversity() : pappso::specpeptidoms::SemiGlobalAlignment
- checkXtandemVersion() : pappso::TandemWrapperRun
- ChemicalFormula() : pappso::ChemicalFormula
- chronoIntervalDebugString() : pappso::Utils
- chronoTimePointDebugString() : pappso::Utils
- clear() : pappso::GrpMapPeptideToGroup, pappso::masschroq::PeptideMeasurementsBase, pappso::MsRunQualifiedSpectrumLoader, pappso::MsRunSlice, pappso::QCPXic, pappso::specpeptidoms::Scenario, pappso::spectree::SpecXtractMap, pappso::TimsDataFastMap, pappso::TraceJs, pappso::XicWidget
- clearData() : pappso::MassSpectrumWidget, pappso::QCPSpectrum
- clearGraphData() : pappso::BaseTracePlotWidget
- clearMeasurements() : pappso::masschroq::MsRunPeptideList
- clearScanBuffer() : pappso::cbor::psm::PsmFileScanProcess
- clearTerm() : pappso::OboPsiModTerm
- clearXicPeakBorders() : pappso::QCPXic, pappso::XicWidget
- clicked() : pappso::XicWidget
- clone() : pappso::BasePlotContext, pappso::CubicSplineModel, pappso::ExceptionInterrupted, pappso::ExceptionNotFound, pappso::ExceptionNotImplemented, pappso::ExceptionNotPossible, pappso::ExceptionNotRecognized, pappso::ExceptionOutOfRange, pappso::MassSpecTracePlotContext, pappso::MzIntegrationParams, pappso::PappsoException, pappso::XtandemError
- cloneElement() : pappso::XmlStreamReaderInterface
- cloneMassSpectrumSPtr() : pappso::QualifiedMassSpectrum
- cloneNode() : pappso::XmlStreamReaderInterface
- cloneStartElement() : pappso::XmlStreamReaderInterface
- close() : pappso::cbor::CborStreamReaderInterface, pappso::cbor::mzcbor::ConvertToMzml, pappso::cbor::mzcbor::MzcborIndexReader, pappso::cbor::mzcbor::MzcborReaderBase, pappso::cbor::psm::PsmCbor2Json, pappso::cbor::psm::PsmFileAppend, pappso::cbor::psm::PsmFileScanProcessAndCopy, pappso::FastaFileIndexer, pappso::FastaFileIndexerInterface, pappso::masschroq::CborOutputStream, pappso::MgfOutput, pappso::MzxmlOutput
- closeLinearRead() : pappso::TimsBinDec
- code() : pappso::AaStringCodec
- codeLlc() : pappso::AaStringCodec
- codeOnlyContains() : pappso::AaStringCodec
- collectPeptideMs2RetentionTime() : pappso::masschroq::MsRunPeptideList
- collectPeptidePeakRetentionTime() : pappso::masschroq::MsRunPeptideList
- ColorMapPlotConfig() : pappso::ColorMapPlotConfig
- combine() : pappso::MassDataCombinerInterface, pappso::MassSpectrumMinusCombiner, pappso::MassSpectrumPlusCombiner, pappso::TraceMinusCombiner, pappso::TracePlusCombiner
- combineScansInTofIndexIntensityMap() : pappso::TimsFrame, pappso::TimsFrameBase
- combineScansToTraceWithDowngradedMzResolution() : pappso::TimsFrame, pappso::TimsFrameBase
- combineScansToTraceWithDowngradedMzResolution2() : pappso::TimsFrame, pappso::TimsFrameBase
- comma() : pappso::cbor::JsonStreamWriter
- computeBestChargeOfDataPoint() : pappso::FilterChargeDeconvolution
- computeCondition() : pappso::specpeptidoms::SpOMSSpectrum
- computeConsensusRetentionTime() : pappso::masschroq::Peptide
- computeCorrections() : pappso::IonMobilityGrid
- computeIsotopeDeconvolution() : pappso::FilterChargeDeconvolution
- computeIsotopeMassList() : pappso::MassSpectrumWidget
- computeIsotopologues() : pappso::masschroq::JsonInput, pappso::masschroq::Peptide, pappso::masschroq::PeptideBase
- computeMinMaxCoordinates() : pappso::SelectionPolygon
- computePeptideCodeFragments() : pappso::ProteinIntegerCode
- computeResolvingPower() : pappso::MassSpecTracePlotWidget
- computeSeamarks() : pappso::MsRunRetentionTime< T >
- computeSignaToNoiseRatio() : pappso::LocalSignalToNoiseEstimator
- computeTicChromatogram() : pappso::TimsFramesMsRunReader
- computeXtandemHyperscore() : pappso::XtandemHyperscoreBis
- contains() : pappso::GrpPeptideSet, pappso::GrpSubGroupSet, pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRect, pappso::IntegrationScopeRhomb, pappso::masschroq::MsRunGroup, pappso::MzRange, pappso::PeptideSpectrumMatch, pappso::SelectionPolygon
- containsAll() : pappso::GrpPeptideSet
- ContainsAny() : ContainsAny
- containsAny() : pappso::GrpGroup, pappso::GrpPeptideSet
- containsRt() : pappso::TracePeak
- containsX() : pappso::Trace
- convertOrginalMsData2mzXmlData() : pappso::TandemWrapperRun
- convertTo1D() : pappso::SelectionPolygon
- convertToLocalFileOrDie() : pappso::cbor::psm::SageReader
- ConvertToMzml() : pappso::cbor::mzcbor::ConvertToMzml
- convlv() : pappso::FilterSavitzkyGolay
- convolution() : pappso::ProteinIntegerCode, pappso::ProteinPresenceAbsenceMatrix
- convolutionKernel() : pappso::ProteinIntegerCode, pappso::ProteinPresenceAbsenceMatrix
- copyAndLzfDecompress() : pappso::TimsFrameType1
- copyDeep() : pappso::specglob::PeptideModel
- copyPoint() : pappso::SelectionPolygon
- correctAlign() : pappso::specpeptidoms::SemiGlobalAlignment
- CorrectionTree() : pappso::specpeptidoms::CorrectionTree
- correctNewTimeValues() : pappso::MsRunRetentionTime< T >
- correctPeakIndexes() : pappso::specpeptidoms::SpOMSSpectrum
- CosineSimilarity() : pappso::CosineSimilarity
- count() : pappso::UiMonitorInterface, pappso::UiMonitorText, pappso::UiMonitorTextPercent, pappso::UiMonitorVoid
- countMatchedIonComplementPairs() : pappso::PsmFeatures
- countModificationOnAa() : pappso::Peptide
- countPlus() : pappso::GrpProtein
- countTotalMatchedIons() : pappso::PeptideSpectrumMatch
- craftLineParserRegExp() : pappso::BafAsciiMsRunReader
- craftLineParserRegExpPattern() : pappso::BafAsciiMsRunReader
- createAllAncillaryItems() : pappso::BasePlotWidget
- createArbitraryBins() : pappso::MzIntegrationParams
- createBins() : pappso::MzIntegrationParams
- createDataBasedBins() : pappso::MzIntegrationParams
- createDataBasedBinsOld() : pappso::MzIntegrationParams
- createInstance() : pappso::AaModification
- createInstanceC13N15LabelledAminoAcid() : pappso::AaModification
- createInstanceMutation() : pappso::AaModification
- createSymetricPeakList() : pappso::specglob::ExperimentalSpectrum
- CubicSplineModel() : pappso::CubicSplineModel
- cumulateScan() : pappso::TimsFrame, pappso::TimsFrameType1
- cumulateScan2() : pappso::TimsFrame, pappso::TimsFrameType1
- cumulateScanIntensities() : pappso::TimsFrame, pappso::TimsFrameBase
- cumulateScanRangeIntensities() : pappso::TimsFrame, pappso::TimsFrameBase
- cumulateScansToTrace() : pappso::TimsFrame, pappso::TimsFrameBase
- currentProteinRefListContainsDecoy() : pappso::cbor::psm::PsmFileReaderBase
- currentProteinRefListContainsTarget() : pappso::cbor::psm::PsmFileReaderBase
- currentXaxisRangeIndices() : pappso::BaseColorMapPlotWidget
- currentYaxisRangeIndices() : pappso::BaseColorMapPlotWidget