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

### - s -

- sanityCheck() : pappso::Enzyme
- savePdf() : pappso::MassSpectrumWidget
- SavGolParams() : pappso::SavGolParams
- scanNumBeginRangeCorrection() : pappso::XicCoordTims
- scanNumber2SpectrumIndex() : pappso::MsRunReader
- ScoreValues() : pappso::specglob::ScoreValues
- SelectionPolygon() : pappso::SelectionPolygon
- SelectionPolygonSpec() : pappso::SelectionPolygonSpec
- selectMsRunReader() : pappso::BafAsciiFileReader, pappso::TimsMsFileReader, pappso::XyMsFileReader
- SelfSpectrum() : pappso::specself::SelfSpectrum
- serializeMsRun() : pappso::MsRunXicExtractorDisk
- set() : pappso::GrpMapPeptideToGroup, pappso::specglob::ScoreValues
- set1D() : pappso::SelectionPolygon
- set2D() : pappso::SelectionPolygon
- setAccession() : pappso::Protein
- setAcqDurationInMilliseconds() : pappso::TimsFrameBase
- setAlignedRetentionTimeVector() : pappso::MsRunRetentionTime< T >
- setArea() : pappso::TracePeak
- setAxisLabelX() : pappso::BasePlotWidget
- setAxisLabelY() : pappso::BasePlotWidget
- setBeginMassDelta() : pappso::specglob::PeptideModel
- setBinningType() : pappso::MzIntegrationParams
- setBins() : pappso::MassSpectrumCombiner
- setBinSizeDivisor() : pappso::MzIntegrationParams
- setChargeMinimalFractionalPart() : pappso::MassSpecTracePlotWidget
- setChargeStateEnvelopePeakSpan() : pappso::MassSpecTracePlotWidget
- setColorMapPlotConfig() : pappso::BaseColorMapPlotWidget
- setCurrentIndex() : pappso::PrecisionWidget
- setDaltonValueChanged() : pappso::PrecisionWidget
- setDataKindX() : pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRect, pappso::IntegrationScopeRhomb
- setDataKindY() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRect, pappso::IntegrationScopeRhomb
- setDecimalPlaces() : pappso::MassDataCombinerInterface, pappso::MzIntegrationParams
- setDescription() : pappso::Protein
- setDetectionThresholdOnMaxmin() : pappso::TraceDetectionZivy
- setDetectionThresholdOnMinmax() : pappso::TraceDetectionZivy
- setDiffFormula() : pappso::AaModification
- setDtInMilliSeconds() : pappso::QualifiedMassSpectrum
- setDynamicRange() : pappso::XtandemSpectrumProcess
- setEmptyMassSpectrum() : pappso::QualifiedMassSpectrum
- setExcludeParent() : pappso::XtandemSpectrumProcess
- setExcludeParentNeutralLoss() : pappso::XtandemSpectrumProcess
- setFileName() : pappso::MsRunId
- setFilterMorphoMaxMin() : pappso::TraceDetectionZivy
- setFilterMorphoMean() : pappso::TraceDetectionMoulon, pappso::TraceDetectionZivy
- setFilterMorphoMinMax() : pappso::TraceDetectionZivy
- setFocus() : pappso::BasePlotWidget
- setFocusSignal() : pappso::BasePlotWidget
- setGlobalLocaleToCurrentOs() : pappso::PwizMsRunReader
- setGlobalLocaleToEnglish() : pappso::PwizMsRunReader
- setGraphData() : pappso::BaseTracePlotWidget
- setGreatestMz() : pappso::MzIntegrationParams
- setGroupNumber() : pappso::GrpGroup, pappso::GrpPeptide, pappso::GrpPeptideSet, pappso::GrpProtein, pappso::GrpSubGroup
- setGrpPeptide() : pappso::GrpExperiment
- setHeight() : pappso::IntegrationScopeRect
- setInputParameters() : pappso::WrapTandemResults
- setInternalCterModification() : pappso::Peptide
- setInternalNterModification() : pappso::Peptide
- setIonList() : pappso::MassSpectrumWidget
- setIonScore() : pappso::XtandemSpectrumProcess
- setLeftBoundary() : pappso::TracePeak
- setMassSpectrumCstSPtr() : pappso::MassSpectrumWidget
- setMassSpectrumId() : pappso::QualifiedMassSpectrum
- setMassSpectrumSPtr() : pappso::QualifiedMassSpectrum
- setMaximumIsotopeNumber() : pappso::MassSpectrumWidget
- setMaximumIsotopeRank() : pappso::MassSpectrumWidget
- setMaxNumberMod() : pappso::PeptideVariableModificationBuilder
- setMaxPeptideVariantListSize() : pappso::Enzyme
- setMaxXicElement() : pappso::TracePeak
- setMinimumMz() : pappso::XtandemSpectrumProcess
- setMinNumberMod() : pappso::PeptideVariableModificationBuilder
- setMiscleavage() : pappso::Enzyme
- setModificationCounter() : pappso::PeptideVariableModificationBuilder
- setModificationPattern() : pappso::PeptideModificatorBase
- setMonoThread() : pappso::MsRunReader, pappso::TimsDdaPrecursors
- setMs1FilterCstSPtr() : pappso::TimsDdaPrecursors, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected
- setMs1MeanFilter() : pappso::MsRunRetentionTime< T >
- setMs1Precision() : pappso::MassSpectrumWidget
- setMs2BuiltinCentroid() : pappso::TimsDdaPrecursors, pappso::TimsMsRunReaderMs2
- setMs2FilterCstSPtr() : pappso::TimsDdaPrecursors, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected
- setMs2MeanFilter() : pappso::MsRunRetentionTime< T >
- setMs2MedianFilter() : pappso::MsRunRetentionTime< T >
- setMs2Precision() : pappso::MassSpectrumWidget
- setMsDataFormat() : pappso::MsRunId
- setMsLevel() : pappso::MassSpectrumWidget, pappso::QualifiedMassSpectrum
- setMsLevels() : pappso::MsRunReadConfig
- setMsMsType() : pappso::TimsFrameBase
- setMsRunId() : pappso::MassSpectrumId
- setMsRunXicExtractorFactoryType() : pappso::MsRunXicExtractorFactory
- setMzCalibration() : pappso::TimsFrameBase
- setMzCalibrationInterfaceSPtr() : pappso::TimsFrameBase
- setMzRangeChanged() : pappso::QCPSpectrum
- setMzTarget() : pappso::OboChooserWidget
- setName() : pappso::QCPXic, pappso::XicWidget
- setNativeId() : pappso::MassSpectrumId
- setNeedMsLevelPeakList() : pappso::SpectrumCollectionHandlerInterface
- setNeedPeakList() : pappso::MsRunReadConfig
- setNeutralLossMass() : pappso::XtandemSpectrumProcess
- setNeutralLossWindowDalton() : pappso::XtandemSpectrumProcess
- setNmostIntense() : pappso::XtandemSpectrumProcess
- setNodesToProcessCount() : pappso::MsRunDataSetTreeNodeVisitorInterface
- setOboPsiModTerm() : pappso::FilterOboPsiModSink, pappso::FilterOboPsiModTermAccession, pappso::FilterOboPsiModTermDiffMono, pappso::FilterOboPsiModTermLabel, pappso::FilterOboPsiModTermName, pappso::OboListModel::OboPsiModHandler, pappso::OboPsiModHandlerInterface
- setOrigAndLastMaxZValue() : pappso::ColorMapPlotConfig
- setOrigAndLastMinZValue() : pappso::ColorMapPlotConfig
- setOrigMaxZValue() : pappso::ColorMapPlotConfig
- setOrigMinZValue() : pappso::ColorMapPlotConfig
- setParameterValue() : pappso::MsRunReadConfig, pappso::QualifiedMassSpectrum
- setParent() : pappso::MsRunDataSetTreeNode
- setPen() : pappso::BasePlotWidget
- setPeptide() : pappso::EnzymeProductInterface, pappso::PeptideBuilder, pappso::PeptideMethioninRemove, pappso::PeptideModificatorPipeline, pappso::PeptideSemiEnzyme, pappso::PeptideSizeFilter
- setPeptideCharge() : pappso::MassSpectrumWidget
- setPeptideSp() : pappso::MassSpectrumWidget, pappso::PeptideFixedModificationBuilder, pappso::PeptideModificatorInterface, pappso::PeptideModificatorPipeline, pappso::PeptideModificatorTee, pappso::PeptideVariableModificationBuilder, pappso::PeptideVariableModificationReplacement
- setPeptideSpectrumCharge() : pappso::PsmFeatures
- setPlottingColor() : pappso::BaseColorMapPlotWidget, pappso::BasePlotWidget
- setPoint() : pappso::IntegrationScope, pappso::SelectionPolygon
- setPostExtractionTraceFilterCstSPtr() : pappso::MsRunXicExtractorInterface
- setPpmValueChanged() : pappso::PrecisionWidget
- setPrecision() : pappso::MzIntegrationParams, pappso::OboChooserWidget, pappso::PrecisionWidget
- setPrecursorMass() : pappso::specself::SelfSpectrum
- setPrecursorNativeId() : pappso::QualifiedMassSpectrum
- setPrecursorSpectrumIndex() : pappso::QualifiedMassSpectrum
- setPreferredFileReaderType() : pappso::MsFileAccessor
- setProtCter() : pappso::PeptideFixedModificationBuilder, pappso::PeptideVariableModificationBuilder
- setProtElse() : pappso::PeptideFixedModificationBuilder, pappso::PeptideVariableModificationBuilder
- setProtNter() : pappso::PeptideFixedModificationBuilder, pappso::PeptideVariableModificationBuilder
- setQualifiedMassSpectrum() : pappso::MassSpectrumWidget, pappso::MsRunDataSetTreeNode, pappso::MsRunQualifiedSpectrumLoader, pappso::MsRunReaderRetentionTimeLine, pappso::MsRunReaderScanNumberMultiMap, pappso::MsRunReaderTicChromatogram, pappso::MsRunSimpleStatistics, pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints, pappso::MzxmlOutput::Translater, pappso::SpectrumCollectionHandlerInterface
- setRank() : pappso::GrpPeptide, pappso::GrpProtein
- setReadAhead() : pappso::MzxmlOutput, pappso::SpectrumCollectionHandlerInterface
- setRefineSpectrumModel() : pappso::XtandemSpectrumProcess
- setRemoveIsotope() : pappso::XtandemSpectrumProcess
- setRemoveNonInformativeSubgroups() : pappso::GrpExperiment
- setRemoveZeroValDataPoints() : pappso::MzIntegrationParams
- setResValueChanged() : pappso::PrecisionWidget
- setRetentionTimeAroundTarget() : pappso::MsRunXicExtractorInterface
- setRetentionTimeEndInSeconds() : pappso::MsRunReadConfig
- setRetentionTimeInMinutes() : pappso::XicWidget
- setRetentionTimeInSeconds() : pappso::XicWidget
- setRetentionTimeStartInSeconds() : pappso::MsRunReadConfig
- setRightBoundary() : pappso::TracePeak
- setRtInSeconds() : pappso::QualifiedMassSpectrum, pappso::TimsFrameBase
- setRtRangeChanged() : pappso::QCPXic
- setRunId() : pappso::MsRunId
- setSampleName() : pappso::MsRunId
- setSelectedMsRunId() : pappso::MsFileAccessor
- setSequence() : pappso::FastaHandlerInterface, pappso::FastaSeqHandler, pappso::Protein
- setSink() : pappso::PeptideBuilder, pappso::PeptideFixedModificationBuilder, pappso::PeptideMethioninRemove, pappso::PeptideModificatorPipeline, pappso::PeptideSemiEnzyme, pappso::PeptideSinkInterface, pappso::PeptideSizeFilter, pappso::PeptideSpSinkInterface, pappso::PeptideVariableModificationBuilder
- setSize() : pappso::MsRunSlice
- setSliceNumber() : pappso::MsRunSlice
- setSmallestMz() : pappso::MzIntegrationParams
- setSpectrum() : pappso::MsRunSlice
- setSpectrumIndex() : pappso::MassSpectrumId
- setSpectrumP() : pappso::QCPSpectrum
- setStatus() : pappso::UiMonitorInterface, pappso::UiMonitorText, pappso::UiMonitorVoid
- setSubGroupNumber() : pappso::GrpProtein, pappso::GrpSubGroup
- setSwitchValue() : pappso::SwitchWidget
- setTakeOnlyFirstWildcard() : pappso::Enzyme
- setTandemBinaryPath() : pappso::TandemWrapperRun
- setText() : pappso::HttpButton
- setTicStart() : pappso::TraceDetectionMoulon
- setTicStop() : pappso::TraceDetectionMoulon
- setTimsCalibration() : pappso::TimsFrameBase
- setTitle() : pappso::UiMonitorInterface, pappso::UiMonitorText, pappso::UiMonitorVoid
- setTmpDir() : pappso::MsRunXicExtractorFactory
- setTotalSteps() : pappso::UiMonitorInterface, pappso::UiMonitorText, pappso::UiMonitorTextPercent, pappso::UiMonitorVoid
- setTracePeak() : pappso::TraceDetectionSinkInterface, pappso::TracePeakList
- setTriangleSlope() : pappso::FilterTriangle
- setupWidget() : pappso::BasePlotWidget
- setVariableModification() : pappso::specself::SelfSpectrum, pappso::specself::SelfSpectrumDataPoint
- setVisibleMassDelta() : pappso::MassSpectrumWidget
- setWidth() : pappso::IntegrationScope
- setXicExtractMethod() : pappso::MsRunXicExtractorInterface
- setXmlId() : pappso::MsRunId
- setXrefOrigin() : pappso::AaModification
- sgcoeff() : pappso::FilterSavitzkyGolay
- shouldIstop() : pappso::UiMonitorInterface, pappso::UiMonitorText, pappso::UiMonitorVoid
- shouldStop() : pappso::MsRunDataSetTreeNodeVisitorInterface, pappso::SpectrumCollectionHandlerInterface
- showTracers() : pappso::BasePlotWidget
- similarity() : pappso::CosineSimilarity
- size() : pappso::FastaFileIndexer, pappso::FilterOboPsiModSink, pappso::GrpMapPeptideToSubGroupSet, pappso::GrpPeptideSet, pappso::GrpSubGroupSet, pappso::MsRunDataSetTree, pappso::MsRunDataSetTreeNode, pappso::MsRunSlice, pappso::Peptide, pappso::PeptideFragment, pappso::PeptideFragmentIon, pappso::PeptideFragmentIonListBase, pappso::PeptideInterface, pappso::PeptideIsotopeSpectrumMatch, pappso::PeptideNaturalIsotope, pappso::PeptideNaturalIsotopeList, pappso::PeptideSpectrumMatch, pappso::Protein, pappso::QualifiedMassSpectrum, pappso::spectree::Bucket, pappso::spectree::BucketClustering
- sort() : pappso::Trace
- sortByRetentionTime() : pappso::Xic
- sortMz() : pappso::MassSpectrum
- sortX() : pappso::Trace
- sortY() : pappso::Trace
- spaceKeyReleaseEvent() : pappso::BasePlotWidget
- SpectralAlignment() : pappso::specglob::SpectralAlignment
- SpecTree() : pappso::spectree::SpecTree
- spectrumListHasSize() : pappso::MsRunQualifiedSpectrumLoader, pappso::SpectrumCollectionHandlerInterface
- spectrumListSize() : pappso::BafAsciiMsRunReader, pappso::MsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, pappso::XyMsRunReader
- SpecXtractInterface() : pappso::spectree::SpecXtractInterface
- SpecXtractMap() : pappso::spectree::SpecXtractMap
- splitMzStringToDoubleVectorWithSpaces() : pappso::Utils
- splitSizetStringToSizetVectorWithSpaces() : pappso::Utils
- startGrouping() : pappso::GrpExperiment, pappso::GrpGroupingMonitor, pappso::GrpGroupingMonitorInterface
- startLinearRead() : pappso::TimsBinDec
- startNumberingAllGroups() : pappso::GrpGroupingMonitor, pappso::GrpGroupingMonitorInterface
- startRemovingNonInformativeSubGroupsInAllGroups() : pappso::GrpGroupingMonitor, pappso::GrpGroupingMonitorInterface
- stopGrouping() : pappso::GrpGroupingMonitor, pappso::GrpGroupingMonitorInterface
- stopRemovingNonInformativeSubGroupsInAllGroups() : pappso::GrpGroupingMonitor, pappso::GrpGroupingMonitorInterface
- storeObservedIdentityBetween() : pappso::IonMobilityGrid
- storeSlices() : pappso::MsRunXicExtractorDisk, pappso::MsRunXicExtractorDiskBuffer
- strip() : pappso::GrpProtein
- sumAndRemove() : pappso::FilterTriangle
- sumY() : pappso::Trace
- SwitchWidget() : pappso::SwitchWidget