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

### - g -

- generateCodeMassFromModel() : pappso::AaStringCodec
- generateLlcCodeListByMaxPeptideSize() : pappso::AaStringCodec
- generateLlcCodeListUpToMaxPeptideSize() : pappso::AaStringCodec
- generateTheoreticalPeaks() : pappso::specglob::PeptideModel
- get() : pappso::specglob::ScoreValues
- getAa() : pappso::AaCode, pappso::Peptide
- getAaCode() : pappso::AaCode, pappso::AaStringCodec
- getAaCodeFromMass() : pappso::AaStringCodeMassMatching
- getAaCodeFromMassList() : pappso::AaStringCodeMassMatching
- getAaCodeFromMassWearingModification() : pappso::AaStringCodeMassMatching
- getAaMass() : pappso::AaBase
- getAaPositionList() : pappso::Peptide
- getAaSequenceCoverage() : pappso::PsmFeatures
- getAccession() : pappso::AaModification, pappso::GrpProtein, pappso::Protein
- getAlignedRetentionTimeVector() : pappso::MsRunRetentionTime< T >
- getAminoAcidChar() : pappso::AaBase
- getAminoAcidCharList() : pappso::AaBase
- getArea() : pappso::TracePeak
- getBackRetentionTimeReference() : pappso::MsRunRetentionTime< T >
- getBestPeakIterator() : pappso::PeptideIsotopeSpectrumMatch, pappso::PeptideSpectrumMatch
- getBestRealignScore() : pappso::specglob::SpectralAlignment
- getBetterPeptideModel() : pappso::specglob::PostTreatment
- getBinningType() : pappso::MzIntegrationParams
- getBins() : pappso::MassSpectrumCombiner
- getBinSizeDivisor() : pappso::MzIntegrationParams
- getBottomMostPoint() : pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRect, pappso::IntegrationScopeRhomb, pappso::SelectionPolygon
- getBottomMostPoints() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getByIntensityRatio() : pappso::PeptideNaturalIsotopeList
- getByIsotopeNumber() : pappso::PeptideNaturalIsotopeList
- getCartList() : pappso::spectree::Bucket
- getCharge() : pappso::PeakIonMatch, pappso::PeptideNaturalIsotopeAverage, pappso::XicPeptideFragmentIonNaturalIsotope, pappso::XicPeptideInterface
- getChargeMinimalFractionalPart() : pappso::MassSpecTracePlotWidget
- getChargeStateEnvelopePeakSpan() : pappso::MassSpecTracePlotWidget
- getChEBIUrl() : pappso::HttpButton
- getCIDionList() : pappso::PeptideFragmentIonListBase
- getClosestPrecursorIdByMz() : pappso::TimsDdaPrecursors
- getCoefficientOfDetermination() : pappso::LinearRegression
- getColorMapPlotConfig() : pappso::BaseColorMapPlotWidget
- getCombinedMs2ScansByGlobalSliceIndex() : pappso::TimsDiaSlices
- getCombinedMs2ScansByPrecursorId() : pappso::TimsDdaPrecursors
- getCommonDeltaRt() : pappso::MsRunRetentionTime< T >
- getCommonSeamarksDeltaRt() : pappso::MsRunRetentionTime< T >
- getComplementPairsAaSequenceCoverage() : pappso::PsmFeatures
- getCompletePeptideIonName() : pappso::PeptideFragmentIon
- getComponents() : pappso::PeptideNaturalIsotopeAverage
- getCompressedSize() : pappso::TimsFrameRawDataChunck
- getConstAa() : pappso::Peptide
- getContext() : pappso::BasePlotWidget
- getCount() : pappso::GrpProtein
- getCountNote() : pappso::XtandemPresetReader
- getCountSharedPeaks() : pappso::specglob::PeptideModel
- getDaltonInstance() : pappso::PrecisionFactory
- getDataKindX() : pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRect, pappso::IntegrationScopeRhomb
- getDataKindY() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRect, pappso::IntegrationScopeRhomb
- getDecimalPlaces() : pappso::MassDataCombinerInterface, pappso::MzIntegrationParams
- getDeltaMass() : pappso::PeptideRawFragmentMasses
- getDescription() : pappso::FastaSeqHandler, pappso::GrpProtein, pappso::Protein
- getDetectionThresholdOnMaxmin() : pappso::TraceDetectionZivy
- getDetectionThresholdOnMinmax() : pappso::TraceDetectionZivy
- getDriftTimeInMilliseconds() : pappso::TimsFrameBase
- getDtInMilliSeconds() : pappso::QualifiedMassSpectrum
- getDynamicRange() : pappso::FilterRescaleY, pappso::XtandemSpectrumProcess
- getETDionList() : pappso::PeptideFragmentIonListBase
- getExcludeParent() : pappso::XtandemSpectrumProcess
- getExcludeParentNeutralLoss() : pappso::XtandemSpectrumProcess
- getExperimentalSpectrumCsp() : pappso::specglob::SpectralAlignment
- getExperimentalSpectrumDataPoint() : pappso::specglob::SpectralAlignment
- getFileFormat() : pappso::BafAsciiFileReader, pappso::MsFileAccessor, pappso::MsFileReader, pappso::PwizMsFileReader, pappso::TimsMsFileReader, pappso::XyMsFileReader
- getFileName() : pappso::MsFileAccessor, pappso::MsRunId
- getFileReaderType() : pappso::MsFileAccessor
- getFilterMorphoMedian() : pappso::FilterMorphoBackground
- getFilterMorphoMinMax() : pappso::FilterMorphoBackground
- getFirst() : pappso::FilterOboPsiModSink
- getFirstAccession() : pappso::GrpSubGroup
- getFormula() : pappso::PeptideInterface
- getFrameCount() : pappso::TimsData
- getFrameId() : pappso::TimsFrameRawDataChunck
- getFrameIdByGlobalSliceIndex() : pappso::TimsDiaSlices
- getFrameIdDescrList() : pappso::TimsData
- getFrameLength() : pappso::TimsFrameRawDataChunck
- getFrameNumberOfScans() : pappso::TimsFrameRawDataChunck
- getFrameSliceRangeByGlobalSliceIndex() : pappso::TimsDiaSlices
- getFrontRetentionTimeReference() : pappso::MsRunRetentionTime< T >
- getGlobalScanIndexByScanCoordinates() : pappso::TimsData
- getGlobalSliceIndexBeginByFrameId() : pappso::TimsDiaSlices
- getGreatestMz() : pappso::MzIntegrationParams
- getGroupingId() : pappso::GrpGroup, pappso::GrpPeptide, pappso::GrpProtein, pappso::GrpSubGroup
- getGroupList() : pappso::GrpMapPeptideToGroup
- getGroupNumber() : pappso::GrpGroup, pappso::GrpPeptide, pappso::GrpProtein, pappso::GrpSubGroup
- getGrpGroupSpList() : pappso::GrpExperiment
- getGrpPeptideList() : pappso::GrpPeptideSet
- getGrpPeptideSet() : pappso::GrpGroup
- getGrpProteinList() : pappso::GrpSubGroup
- getGrpProteinSp() : pappso::GrpExperiment
- getGrpProteinSpList() : pappso::GrpExperiment
- getGrpSubGroupSpList() : pappso::GrpGroup
- getHalfWindowSize() : pappso::FilterLocalMaximum, pappso::FilterMorphoAntiSpike, pappso::FilterMorphoWindowBase
- getHeight() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRect, pappso::IntegrationScopeRhomb
- getHyperscore() : pappso::XtandemHyperscore, pappso::XtandemHyperscoreBis
- getId() : pappso::spectree::Bucket, pappso::spectree::ItemCart, pappso::TimsFrameBase
- getIndexNodeMap() : pappso::MsRunDataSetTree
- getInnermostRangeX() : pappso::BasePlotWidget
- getInnermostRangeY() : pappso::BasePlotWidget
- getInstance() : pappso::AaModification, pappso::MsRunXicExtractorFactory, pappso::MzCalibrationStore
- getInstanceCustomizedMod() : pappso::AaModification
- getInstanceInsertionAccessionByAaLetter() : pappso::AaModification
- getInstanceMutation() : pappso::AaModification
- getInstanceRemovalAccessionByAaLetter() : pappso::AaModification
- getInstanceXtandemMod() : pappso::AaModification
- getIntensityAxisP() : pappso::XicWidget
- getIntensityExperimentalPeaks() : pappso::specglob::PeptideModel
- getIntensityOfMatchedIon() : pappso::PsmFeatures
- getIntensityRatio() : pappso::PeptideNaturalIsotope, pappso::PeptideNaturalIsotopeAverage
- getIntensityRatioPerIsotopeNumber() : pappso::PeptideNaturalIsotopeList
- getIntensitySharedPeaks() : pappso::specglob::PeptideModel
- getIntercept() : pappso::LinearRegression
- getInternalCterModification() : pappso::Aa, pappso::Peptide
- getInternalNterModification() : pappso::Aa, pappso::Peptide
- getIonIsotopeLinearRegression() : pappso::PsmFeatures
- getIonIsotopeRatioScore() : pappso::IonIsotopeRatioScore
- getIonList() : pappso::PeptideFragmentIonListBase
- getIonMobilityTraceByTofIndexRange() : pappso::TimsFrameBase
- getIonMobTraceList() : pappso::TimsFrameMobilityTraces
- getIonPairPrecursorMassDelta() : pappso::PsmFeatures
- getIonScore() : pappso::XtandemSpectrumProcess
- getIonTypeCountArray() : pappso::PeptideSpectrumMatch
- getIsotopeMap() : pappso::PeptideNaturalIsotope
- getIsotopeNumber() : pappso::PeptideNaturalIsotope, pappso::PeptideNaturalIsotopeAverage
- getIsotopeRank() : pappso::PeptideNaturalIsotopeAverage
- getItemCartCount() : pappso::spectree::BucketClustering
- getItemList() : pappso::spectree::ItemCart
- getLastMs1FrameIdByMs2FrameId() : pappso::TimsDiaSlices
- getLeftBoundary() : pappso::TracePeak
- getLeftMostBottomPoint() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getLeftMostPoint() : pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb, pappso::SelectionPolygon
- getLeftMostPoints() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getLeftMostTopPoint() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getLetter() : pappso::AaBase
- getLexicalOrderedString() : pappso::Utils
- getLiAbsoluteString() : pappso::Peptide
- getLimitMax() : pappso::AaStringCodec
- getMapCorrectionsStart() : pappso::IonMobilityGrid
- getMapDiferrencesStart() : pappso::IonMobilityGrid
- getMapFrame2WindowGroupPtr() : pappso::TimsDiaSlices
- getMapSimilarities() : pappso::spectree::SpecXtractMap
- getMass() : pappso::Aa, pappso::AaBase, pappso::AaCode, pappso::AaModification, pappso::AaStringCodec, pappso::Ion, pappso::Peptide, pappso::PeptideFragment, pappso::PeptideFragmentIon, pappso::PeptideNaturalIsotope, pappso::Protein, pappso::specglob::PeptideModel
- getMassDelta() : pappso::specglob::PeptideModel
- getMassList() : pappso::specglob::ExperimentalSpectrum, pappso::specglob::PeptideSpectrum
- getMassSpectrumCstSPtr() : pappso::QualifiedMassSpectrum, pappso::TimsData, pappso::TimsFrameBase
- getMassSpectrumCstSPtrByGlobalScanIndex() : pappso::TimsData
- getMassSpectrumCstSPtrByRawIndex() : pappso::TimsData
- getMassSpectrumId() : pappso::QualifiedMassSpectrum
- getMassSpectrumSPtr() : pappso::QualifiedMassSpectrum, pappso::TimsFrame, pappso::TimsFrameBase, pappso::TimsFrameType1
- getMatchedIons() : pappso::XtandemHyperscore, pappso::XtandemHyperscoreBis
- getMatchedMzDiffMean() : pappso::PsmFeatures
- getMatchedMzDiffSd() : pappso::PsmFeatures
- getMatchPrecursorIdByKo() : pappso::TimsDdaPrecursors
- getMatrix() : pappso::specglob::SpectralAlignment, pappso::specself::SelfSpectrum
- getMaxConsecutiveIon() : pappso::PsmFeatures
- getMaxHalfEdgeWindows() : pappso::FilterMorphoMax
- getMaximumRawMassIndex() : pappso::TimsFrameBase
- getMaxIntensityMatchedIonComplementPairPrecursorMassDelta() : pappso::PsmFeatures
- getMaxIntensityPeakIonMatch() : pappso::PsmFeatures
- getMaxMinHalfEdgeWindows() : pappso::FilterMorphoMaxMin, pappso::TraceDetectionZivy
- getMaxPosIterator() : pappso::specglob::SpectralAlignment
- getMaxScore() : pappso::specglob::SpectralAlignment
- getMaxXicElement() : pappso::TracePeak
- getMeanHalfEdgeWindows() : pappso::FilterMorphoMean
- getMemoryBuffer() : pappso::TimsFrameRawDataChunck
- getMinHalfEdgeWindows() : pappso::FilterMorphoMin
- getMinimumMz() : pappso::XtandemSpectrumProcess
- getMinMaxHalfEdgeWindows() : pappso::FilterMorphoMinMax, pappso::TraceDetectionZivy
- getMiscleavage() : pappso::Enzyme
- getMobilityScan() : pappso::TimsFrame, pappso::TimsFrameBase
- getModificationList() : pappso::Aa
- getModificationPositionList() : pappso::Peptide, pappso::PeptideModificatorBase
- getMorpheusScore() : pappso::MorpheusScore
- getMostIntensePeakBetween() : pappso::QCPSpectrum
- getMs1MeanFilter() : pappso::MsRunRetentionTime< T >
- getMs1QualifiedSpectrumByGlobalSliceIndex() : pappso::TimsDiaSlices
- getMs1RetentionTimeVector() : pappso::MsRunRetentionTime< T >
- getMs2BuiltinCentroid() : pappso::TimsDdaPrecursors
- getMs2FiltersOptions() : pappso::XtandemPresetReader
- getMs2FilterSuiteString() : pappso::TandemWrapperRun
- getMs2MeanFilter() : pappso::MsRunRetentionTime< T >
- getMs2MedianFilter() : pappso::MsRunRetentionTime< T >
- getMs2QualifiedSpectrumByGlobalSliceIndex() : pappso::TimsDiaSlices
- getMsDataFormat() : pappso::MsRunId
- getMsLevel() : pappso::QualifiedMassSpectrum, pappso::TimsFrameBase
- getMsLevelByGlobalScanIndex() : pappso::TimsData
- getMsLevelBySpectrumIndex() : pappso::TimsData
- getMsLevelCount() : pappso::MsRunSimpleStatistics
- getMsLevels() : pappso::MsRunReadConfig
- getMsLevelsAsString() : pappso::MsRunReadConfig
- getMsMsWindowByGlobalSliceIndex() : pappso::TimsDiaSlices
- getMsMsWindowGroupList() : pappso::TimsDiaSlices
- getMsPointDistance() : pappso::Xic
- getMsRunId() : pappso::MsRunReader, pappso::MsRunRetentionTime< T >, pappso::MsRunXicExtractorInterface
- getMsRunIdCstSPtr() : pappso::MassSpectrumId
- getMsRunIds() : pappso::BafAsciiFileReader, pappso::MsFileAccessor, pappso::MsFileReader, pappso::PwizMsFileReader, pappso::TimsMsFileReader, pappso::XyMsFileReader
- getMsRunReaderSPtr() : pappso::MsRunRetentionTime< T >, pappso::MsRunXicExtractorInterface
- getMsRunReaderSPtrByRunId() : pappso::MsFileAccessor
- getMz() : pappso::Ion, pappso::MzRange, pappso::PeptideNaturalIsotopeAverage, pappso::QualifiedXic, pappso::specglob::PeptideModel
- getMzCalibrationInterfaceSPtr() : pappso::TimsFrameBase
- getMzFromTofIndex() : pappso::MzCalibrationInterface, pappso::MzCalibrationModel1, pappso::MzCalibrationModel1Cached
- getMzList() : pappso::TimsFrameMobilityTraces
- getMzSortedPrecursorDataChargeValuesAsString() : pappso::QualifiedMassSpectrum
- getMzSortedPrecursorDataMzValuesAsString() : pappso::QualifiedMassSpectrum
- getMzTarget() : pappso::OboListWidget
- getName() : pappso::AaModification, pappso::PeptideFragmentIon, pappso::PeptideInterface, pappso::XicWidget
- getNativeId() : pappso::MassSpectrumId
- getNearestPeakBetween() : pappso::QCPSpectrum
- getNeutralLossMass() : pappso::XtandemSpectrumProcess
- getNeutralLossWindowDalton() : pappso::XtandemSpectrumProcess
- getNmostIntense() : pappso::XtandemSpectrumProcess
- getNominal() : pappso::PrecisionBase
- getNrmsd() : pappso::LinearRegression
- getNumberOfAtom() : pappso::Aa, pappso::AaBase, pappso::AaModification, pappso::AtomNumberInterface, pappso::Peptide, pappso::PeptideFragment, pappso::PeptideFragmentIon, pappso::PeptideNaturalIsotope
- getNumberOfCorrectedValues() : pappso::MsRunRetentionTime< T >
- getNumberOfIsotope() : pappso::Aa, pappso::AaBase, pappso::AaModification, pappso::AtomNumberInterface, pappso::Peptide, pappso::PeptideFragment, pappso::PeptideFragmentIon, pappso::PeptideNaturalIsotope
- getNumberOfMatchedIons() : pappso::PsmFeatures
- getNumberOfModification() : pappso::Aa, pappso::Peptide
- getNumberOfNeutralPhosphoLoss() : pappso::PeptideFragmentIon
- getNumberOfPoints() : pappso::FilterGreatestY, pappso::FilterGreatestYperWindow
- getNumberOfThreads() : pappso::XtandemPresetReader
- getOboPsiModTerm() : pappso::OboListModel, pappso::OboTermForm
- getOboPsiModTermFileFormat() : pappso::MsFileAccessor
- getOboPsiModTermList() : pappso::FilterOboPsiModSink
- getOboPsiModTermNativeIDFormat() : pappso::MsFileAccessor, pappso::PwizMsRunReader
- getOboPsiModTermSelected() : pappso::OboChooserWidget
- getOlsUrl() : pappso::HttpButton
- getOne() : pappso::FilterOboPsiModSink
- getOneOverK0Transformation() : pappso::TimsFrameBase
- getOrigColorMapPlotConfig() : pappso::BaseColorMapPlotWidget
- getOriginalMsDataFileName() : pappso::WrapTandemInput
- getOriginalPeptideModel() : pappso::specglob::PostTreatment
- getOriginalTandemOutputFileName() : pappso::WrapTandemInput
- getOriginalTandemPresetFileName() : pappso::WrapTandemInput
- getOutermostRangeX() : pappso::BasePlotWidget
- getOutermostRangeY() : pappso::BasePlotWidget
- getParam() : pappso::XicCoord, pappso::XicCoordTims
- getParameters() : pappso::FilterSavitzkyGolay
- getParameterValue() : pappso::MsRunReadConfig, pappso::QualifiedMassSpectrum
- getParent() : pappso::MsRunDataSetTreeNode
- getPeak() : pappso::PeakIonMatch
- getPeakIonIsotopeMatchList() : pappso::PeptideIsotopeSpectrumMatch
- getPeakIonPairs() : pappso::PsmFeatures
- getPen() : pappso::BasePlotWidget
- getPeptideCodedFragment() : pappso::ProteinIntegerCode
- getPeptideFragmentIonList() : pappso::PeptideFragmentIonListBase
- getPeptideFragmentIonSp() : pappso::PeakIonMatch, pappso::PeptideFragmentIonListBase, pappso::XicPeptideFragmentIon, pappso::XicPeptideFragmentIonNaturalIsotope
- getPeptideFragmentList() : pappso::PeptideFragmentIonListBase
- getPeptideFragmentSp() : pappso::PeptideFragmentIon
- getPeptideInterfaceSp() : pappso::PeptideNaturalIsotopeAverage, pappso::PeptideNaturalIsotopeList
- getPeptideIonColor() : pappso::PeptideFragmentIon
- getPeptideIonDirection() : pappso::PeakIonMatch, pappso::PeptideFragment, pappso::PeptideFragmentIon
- getPeptideIonDirectionName() : pappso::PeptideFragment
- getPeptideIonName() : pappso::PeptideFragmentIon
- getPeptideIonType() : pappso::PeakIonMatch, pappso::PeptideFragmentIon
- getPeptideNaturalIsotopeAverageSp() : pappso::PeakIonIsotopeMatch, pappso::XicPeptideFragmentIonNaturalIsotope
- getPeptideSet() : pappso::GrpSubGroup
- getPeptideSp() : pappso::PeptideFragment, pappso::PeptideFragmentIonListBase, pappso::specglob::PeptideSpectrum
- getPeptideSpectraCsp() : pappso::specglob::SpectralAlignment
- getPercentage() : pappso::FilterCeilingAmplitudePercentage, pappso::FilterFloorAmplitudePercentage
- getPhosphorylationNumber() : pappso::PeptideFragmentIonListBase
- getPlottingColor() : pappso::BaseColorMapPlotWidget, pappso::BasePlotWidget
- getPoint() : pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb, pappso::SelectionPolygon
- getPoints() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb, pappso::SelectionPolygon
- getPpmInstance() : pappso::PrecisionFactory
- getPrecision() : pappso::MzIntegrationParams, pappso::PeptideNaturalIsotopeAverage, pappso::PrecisionWidget
- getPrecisionPtr() : pappso::AaStringCodeMassMatching, pappso::OboListWidget
- getPrecisionPtrFractionInstance() : pappso::PrecisionFactory
- getPrecisionPtrInstance() : pappso::PrecisionFactory
- getPrecursorCharge() : pappso::QualifiedMassSpectrum
- getPrecursorDataChargeValuesAsString() : pappso::QualifiedMassSpectrum
- getPrecursorDataMzValuesAsString() : pappso::QualifiedMassSpectrum
- getPrecursorIntensity() : pappso::QualifiedMassSpectrum
- getPrecursorIonData() : pappso::QualifiedMassSpectrum
- getPrecursorIonDataSortedWithMz() : pappso::QualifiedMassSpectrum
- getPrecursorMass() : pappso::QualifiedMassSpectrum, pappso::specglob::ExperimentalSpectrum
- getPrecursorMz() : pappso::QualifiedMassSpectrum
- getPrecursorMzDelta() : pappso::specglob::SpectralAlignment
- getPrecursorNativeId() : pappso::QualifiedMassSpectrum
- getPrecursorsByMzRtCharge() : pappso::TimsDdaPrecursors
- getPrecursorScanNumber() : pappso::MzxmlOutput
- getPrecursorsIDFromMzRt() : pappso::TimsMsRunReaderMs2
- getPrecursorSpectrumIndex() : pappso::QualifiedMassSpectrum
- getpreferredFileReaderType() : pappso::MsFileAccessor
- getPresenceAbsenceMatrix() : pappso::ProteinPresenceAbsenceMatrix
- getProteinSp() : pappso::ProteinIntegerCode
- getPubMedUrl() : pappso::HttpButton
- getPwizSpectrumPtr() : pappso::PwizMsRunReader
- getQfileLinear() : pappso::TimsBinDec
- getQfileRandom() : pappso::TimsBinDec
- getQRegExpRecognitionSite() : pappso::Enzyme
- getQualifiedMassSpectrum() : pappso::MsRunDataSetTreeNode, pappso::specglob::ExperimentalSpectrum
- getQualifiedMassSpectrumByGlobalScanIndex() : pappso::TimsData
- getQualifiedMassSpectrumByRawIndex() : pappso::TimsData
- getQualifiedMassSpectrumList() : pappso::MsRunQualifiedSpectrumLoader
- getQualifiedMs1MassSpectrumBySpectrumDescr() : pappso::TimsDdaPrecursors
- getQualifiedMs2MassSpectrumBySpectrumDescr() : pappso::TimsDdaPrecursors
- getQuantileThreshold() : pappso::FilterQuantileBasedRemoveY
- getRange() : pappso::BasePlotWidget
- getRangeX() : pappso::BasePlotWidget
- getRangeY() : pappso::BasePlotWidget
- getRank() : pappso::GrpPeptide, pappso::GrpProtein
- getRawIndexFromCoordinate() : pappso::TimsData
- getRawMsBySpectrumIndex() : pappso::TimsData
- getRawTraceSPtr() : pappso::TimsFrame, pappso::TimsFrameType1
- getRawValuePairList() : pappso::TimsFrame, pappso::TimsFrameType1
- getRefineSpectrumModel() : pappso::XtandemSpectrumProcess
- getRemoveIsotope() : pappso::XtandemSpectrumProcess
- getRESIDUrl() : pappso::HttpButton
- getResInstance() : pappso::PrecisionFactory
- getRetentionTimeEndInSeconds() : pappso::MsRunReadConfig
- getRetentionTimeFromSecondsToLocal() : pappso::QCPXic
- getRetentionTimeLine() : pappso::MsRunReader, pappso::MsRunReaderRetentionTimeLine, pappso::TimsData, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderMs2
- getRetentionTimeLineInSeconds() : pappso::TimsData
- getRetentionTimeStartInSeconds() : pappso::MsRunReadConfig
- getRhombHorizontalSize() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getRhombVerticalSize() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getRightBoundary() : pappso::TracePeak
- getRightMostBottomPoint() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getRightMostPoint() : pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb, pappso::SelectionPolygon
- getRightMostPoints() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getRightMostTopPoint() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getRmsd() : pappso::LinearRegression
- getRootNodes() : pappso::MsRunDataSetTree
- getRtAxisP() : pappso::XicWidget
- getRtInMinutes() : pappso::QualifiedMassSpectrum
- getRtInSeconds() : pappso::QualifiedMassSpectrum, pappso::TimsFrameBase
- getRunId() : pappso::MsRunId
- getSampleName() : pappso::MsRunId
- getScaleFactorY() : pappso::FilterScaleFactorY
- getScanByGlobalScanIndex() : pappso::TimsData
- getScanCoordinateFromRawIndex() : pappso::TimsData
- getScanCoordinatesByGlobalScanIndex() : pappso::TimsData
- getScanIndexFromOneOverK0() : pappso::TimsFrameBase
- getScanIndexList() : pappso::TimsFrameMobilityTraces
- getScanIntensityList() : pappso::TimsFrame, pappso::TimsFrameBase, pappso::TimsFrameType1
- getScanNumber() : pappso::MzxmlOutput
- getScanNumberFromNativeId() : pappso::MzxmlOutput
- getScanOffset() : pappso::TimsFrame
- getScanPeakCount() : pappso::TimsFrame, pappso::TimsFrameBase, pappso::TimsFrameType1
- getScanTofIndexList() : pappso::TimsFrame, pappso::TimsFrameBase, pappso::TimsFrameType1
- getScore() : pappso::ProteinPresenceAbsenceMatrix
- getScoreRow() : pappso::specglob::SpectralAlignment
- getSeamarks() : pappso::MsRunRetentionTime< T >
- getSeamarksReferences() : pappso::MsRunRetentionTime< T >
- getSelectedMsRunId() : pappso::MsFileAccessor
- getSeqAaCode() : pappso::ProteinIntegerCode
- getSequence() : pappso::FastaSeqHandler, pappso::GrpPeptide, pappso::Peptide, pappso::PeptideFragment, pappso::PeptideFragmentIon, pappso::PeptideInterface, pappso::PeptideNaturalIsotope, pappso::Protein
- getSequenceByIndex() : pappso::FastaFileIndexer, pappso::FastaFileIndexerInterface
- getSequenceLi() : pappso::PeptideInterface
- getSize() : pappso::AaCode, pappso::LinearRegression
- getSliceNumber() : pappso::MsRunSlice
- getSlope() : pappso::LinearRegression
- getSmallestMz() : pappso::MzIntegrationParams
- getSmoothingHalfEdgeWindows() : pappso::TraceDetectionMoulon, pappso::TraceDetectionZivy
- getSpectrum() : pappso::MsRunSlice
- getSpectrumCount() : pappso::MsRunDataSetTree
- getSpectrumDescrListByFrameId() : pappso::TimsDdaPrecursors
- getSpectrumDescrWithPrecursorId() : pappso::TimsDdaPrecursors
- getSpectrumDescrWithScanCoordinates() : pappso::TimsDdaPrecursors
- getSpectrumFirstNodeIndex() : pappso::spectree::SpecTree
- getSpectrumIndex() : pappso::MassSpectrumId
- getSpectrumIndexFromScanNumber() : pappso::MsRunReaderScanNumberMultiMap
- getSubGroupNumber() : pappso::GrpProtein, pappso::GrpSubGroup
- getSubGroupSet() : pappso::GrpMapPeptideToSubGroupSet
- getSubGroupSpList() : pappso::GrpGroup
- getSwitchValue() : pappso::SwitchWidget
- getSymetricMz() : pappso::specglob::ExperimentalSpectrum
- getTargetMzSum() : pappso::specglob::ExperimentalSpectrum
- getTheoreticalIonMassList() : pappso::specglob::PeptideModel
- getTheoreticalPeakDataPointList() : pappso::specglob::PeptideModel
- getTheoreticalPeakDataPointListToString() : pappso::specglob::PeptideModel
- getThreshold() : pappso::FilterLowIntensitySignalRemoval
- getThresholdX() : pappso::FilterResampleKeepGreater
- getTicChromatogram() : pappso::MsRunReader, pappso::MsRunReaderTicChromatogram, pappso::TimsData, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderMs2
- getTicStart() : pappso::TraceDetectionMoulon
- getTicStop() : pappso::TraceDetectionMoulon
- getTimsBinDecPtr() : pappso::TimsData
- getTimsDataDirectory() : pappso::TimsData
- getTimsDataFastMapInstance() : pappso::TimsDataFastMap
- getTimsDataSPtr() : pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderMs2
- getTimsDdaPrecursorsPtr() : pappso::TimsData
- getTimsDiaSlicesPtr() : pappso::TimsData
- getTimsFrameBaseCstSPtr() : pappso::TimsData
- getTimsFrameBaseCstSPtrCached() : pappso::TimsData
- getTimsFrameCstSPtr() : pappso::TimsData
- getTimsFrameCstSPtrCached() : pappso::TimsData
- getTimsFrameFromRawDataChunck() : pappso::TimsBinDec
- getTimsFrameRecordList() : pappso::TimsData
- getTimsFrameSPtrByOffset() : pappso::TimsBinDec
- getTimsMS1FrameIdsInRtRange() : pappso::TimsData
- getTimsMS2FrameIdsInRtRange() : pappso::TimsData
- getTofFromTofIndex() : pappso::MzCalibrationInterface
- getTofIndexFromMz() : pappso::MzCalibrationInterface, pappso::MzCalibrationModel1
- getTofIndexList() : pappso::TimsDataFastMap, pappso::TimsFrameMobilityTraces
- getTopMostPoint() : pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRect, pappso::IntegrationScopeRhomb, pappso::SelectionPolygon
- getTopMostPoints() : pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getTotalCount() : pappso::MsRunSimpleStatistics
- getTotalIntensity() : pappso::PsmFeatures
- getTotalIntensityOfMatchedIonComplementPairs() : pappso::PsmFeatures
- getTotalIntensityOfMatchedIons() : pappso::PsmFeatures
- getTotalMatchedIons() : pappso::XtandemHyperscoreBis
- getTotalModificationMass() : pappso::Aa
- getTotalNumberOfFrames() : pappso::TimsData
- getTotalNumberOfScans() : pappso::TimsData, pappso::TimsFrameBase
- getTotalPrecursorCount() : pappso::TimsDdaPrecursors
- getTotalScanCount() : pappso::TimsData
- getTotalSlicesCount() : pappso::TimsDiaSlices
- getTrace() : pappso::specself::SelfSpectrum
- getTraceFromTofIndexIntensityMap() : pappso::TimsFrameBase
- getUnimodUrl() : pappso::HttpButton
- getValue() : pappso::FilterRemoveY
- getValueRangeOnKeyRange() : pappso::BaseTracePlotWidget
- getValuesX() : pappso::BaseTracePlotWidget
- getValuesY() : pappso::BaseTracePlotWidget
- getVersion() : pappso::Utils
- getVoltageTransformation() : pappso::TimsFrameBase
- getWidth() : pappso::IntegrationScope, pappso::IntegrationScopeBase, pappso::IntegrationScopeRhomb
- getWindowGroupPtrByGroupId() : pappso::TimsDiaSlices::MsMsWindowGroupList
- getWindowValue() : pappso::FilterMorphoMax, pappso::FilterMorphoMean, pappso::FilterMorphoMedian, pappso::FilterMorphoMin, pappso::FilterMorphoSum, pappso::FilterMorphoWindowBase
- getXicCoordTimsFromPrecursorId() : pappso::TimsDdaPrecursors
- getXicCstSPtr() : pappso::QualifiedXic, pappso::XicWidget
- getXicFromPwizMSDataFile() : pappso::MsRunXicExtractor
- getXicSPtr() : pappso::QualifiedXic
- getXmlId() : pappso::MsRunId
- getXrefOrigin() : pappso::AaModification
- getXtandemPredictedIonIntensityFactor() : pappso::XtandemHyperscore, pappso::XtandemHyperscoreBis
- getYatX() : pappso::BaseTracePlotWidget
- getYfromX() : pappso::LinearRegression
- GraphicDeviceWidget() : GraphicDeviceWidget
- groupingProtein() : pappso::GrpGroupingMonitor, pappso::GrpGroupingMonitorInterface
- GrpExperiment() : pappso::GrpExperiment, pappso::GrpGroup, pappso::GrpPeptide, pappso::GrpProtein
- GrpGroup() : pappso::GrpGroup, pappso::GrpSubGroupSet
- GrpGroupingMonitor() : pappso::GrpGroupingMonitor
- GrpMapPeptideToGroup() : pappso::GrpMapPeptideToGroup, pappso::GrpPeptideSet
- GrpMapPeptideToSubGroupSet() : pappso::GrpMapPeptideToSubGroupSet, pappso::GrpPeptideSet
- GrpPeptide() : pappso::GrpPeptide
- GrpPeptideSet() : pappso::GrpPeptideSet
- GrpProtein() : pappso::GrpProtein
- GrpSubGroup() : pappso::GrpSubGroup
- GrpSubGroupSet() : pappso::GrpSubGroupSet