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

### - a -

- Aa() : pappso::Aa
- AaBase() : pappso::AaBase
- AaCode() : pappso::AaCode
- AaModification() : pappso::AaModification
- AaStringCodec() : pappso::AaStringCodec
- AaStringCodeMassMatching() : pappso::AaStringCodeMassMatching
- accept() : pappso::BafAsciiMsRunReader, pappso::MsRunDataSetTree, pappso::MsRunDataSetTreeNode, pappso::MsRunReader, pappso::PwizMsRunReader, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, pappso::XyMsRunReader
- acceptMsLevel() : pappso::MsRunReadConfig
- acceptRetentionTimeInSeconds() : pappso::MsRunReadConfig
- accumulateIntensity() : pappso::TimsDataFastMap
- acquireDevice() : pappso::BafAsciiMsRunReader, pappso::MsRunReader, pappso::PwizMsRunReader, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::XyMsRunReader
- acquireSlices() : pappso::MsRunXicExtractorDisk
- add() : pappso::GrpMapPeptideToSubGroupSet, pappso::GrpSubGroupSet
- addAa() : pappso::PeptideFixedModificationBuilder, pappso::PeptideVariableModificationBuilder
- addAaModification() : pappso::Aa, pappso::AaCode, pappso::Peptide
- addAaModificationOnAllAminoAcid() : pappso::Peptide
- addAll() : pappso::GrpPeptideSet, pappso::GrpSubGroupSet
- addColorMap() : pappso::BaseColorMapPlotWidget
- addDataPointRefByExclusion() : pappso::FilterChargeDeconvolution
- addDataPointToList() : pappso::FilterChargeDeconvolution
- addDataSetQualMassSpectraInsideDtRtRange() : pappso::MsRunDataSetTree
- addDataSetTreeNodesInsideDtRtRange() : pappso::MsRunDataSetTree
- addExclusionMap() : pappso::FilterRemoveC13
- addFilterFromString() : pappso::FilterSuiteString
- addFixedAaModification() : pappso::PeptideBuilder
- addFixedCterModificationString() : pappso::PeptideModificatorPipeline
- addFixedModificationString() : pappso::PeptideModificatorPipeline
- addFixedNterModificationString() : pappso::PeptideModificatorPipeline
- addGroup() : pappso::GrpGroup
- addInGroup() : pappso::TimsDiaSlices::MsMsWindowGroupList
- addItemCart() : pappso::spectree::BucketClustering
- addition() : pappso::XicCoord, pappso::XicCoordTims
- addLabeledModificationString() : pappso::PeptideModificatorPipeline
- addMassDelta() : pappso::QCPSpectrum
- addMassSpectrum() : pappso::MsRunDataSetTree
- addModificator() : pappso::PeptideModificatorTee
- addMs1IsotopePattern() : pappso::QCPSpectrum
- addMsMsEvent() : pappso::QCPXic, pappso::XicWidget
- addNewNode() : pappso::spectree::SpecTree
- addPeakIonIsotopeMatch() : pappso::QCPSpectrum
- addPeptideAsSeamark() : pappso::MsRunRetentionTime< T >
- addPoint() : pappso::IntegrationScopeRhomb
- addPostGroupingGrpProteinSpRemoval() : pappso::GrpExperiment
- addPotentialCterModificationString() : pappso::PeptideModificatorPipeline
- addPotentialModificationString() : pappso::PeptideModificatorPipeline
- addPotentialNterModificationString() : pappso::PeptideModificatorPipeline
- addPreGroupingGrpProteinSpRemoval() : pappso::GrpExperiment
- addSubGroupSp() : pappso::GrpExperiment, pappso::GrpGroup
- addTrace() : pappso::BaseTracePlotWidget
- addXicP() : pappso::QCPXic
- addXicPeakList() : pappso::QCPXic, pappso::XicWidget
- addXicSp() : pappso::XicWidget
- align() : pappso::MsRunRetentionTime< T >, pappso::specglob::SpectralAlignment
- allLayerNamesToString() : pappso::BasePlotWidget
- almostEqual() : pappso::Utils
- append() : pappso::Trace
- appendPrecursorIonData() : pappso::QualifiedMassSpectrum
- appendSliceInBuffer() : pappso::MsRunXicExtractorDiskBuffer
- appendSliceOnDisk() : pappso::MsRunXicExtractorDisk
- appendText() : pappso::UiMonitorInterface, pappso::UiMonitorText, pappso::UiMonitorVoid
- appendToFile() : pappso::Utils
- appendToStream() : pappso::MsRunSlice
- assignResidualMass2Cter() : pappso::specglob::PeptideModel
- asSortedList() : pappso::spectree::BucketClustering
- atRetentionTime() : pappso::Xic
- axisDoubleClickHandler() : pappso::BasePlotWidget, pappso::BaseTracePlotWidget
- axisPan() : pappso::BasePlotWidget, pappso::BaseTracePlotWidget
- axisReframe() : pappso::BasePlotWidget, pappso::BaseTracePlotWidget
- axisRescale() : pappso::BasePlotWidget, pappso::BaseTracePlotWidget
- axisScale() : pappso::BaseColorMapPlotWidget
- axisZoom() : pappso::BasePlotWidget, pappso::BaseTracePlotWidget