Here is a list of all class members with links to the classes they belong to:
- g -
- getAa()
: pappso::Peptide
- getAaMass()
: pappso::AaBase
- getAaPositionList()
: pappso::Peptide
- getAccession()
: pappso::AaModification
, pappso::GrpProtein
, pappso::Protein
- getAlignedRetentionTimeVector()
: pappso::MsRunRetentionTime< T >
- getAminoAcidCharList()
: pappso::AaBase
- getArea()
: pappso::TracePeak
- getBackRetentionTimeReference()
: pappso::MsRunRetentionTime< T >
- getBestPeakIterator()
: pappso::PeptideIsotopeSpectrumMatch
, pappso::PeptideSpectrumMatch
- getBins()
: pappso::MassSpectrumCombiner
- getByIntensityRatio()
: pappso::PeptideNaturalIsotopeList
- getByIsotopeNumber()
: pappso::PeptideNaturalIsotopeList
- getCentroidOptions()
: pappso::XtandemPresetSaxHandler
- getCharge()
: pappso::PeakIonMatch
, pappso::PeptideNaturalIsotopeAverage
, pappso::XicPeptideFragmentIonNaturalIsotope
, pappso::XicPeptideInterface
- getChargeMinimalFractionalPart()
: pappso::MassSpecTracePlotWidget
- getChargeStateEnvelopePeakSpan()
: pappso::MassSpecTracePlotWidget
- getCIDionList()
: pappso::PeptideFragmentIonListBase
- getClosestIdByMz()
: pappso::TimsData
- getCoefficientOfDetermination()
: pappso::LinearRegression
- getColorMapPlotConfig()
: pappso::BaseColorMapPlotWidget
- getCommonDeltaRt()
: pappso::MsRunRetentionTime< T >
- getComponents()
: pappso::PeptideNaturalIsotopeAverage
- getConstAa()
: pappso::Peptide
- getContext()
: pappso::BasePlotWidget
- getCount()
: pappso::GrpProtein
- getDaltonInstance()
: pappso::MassSpectrumCombinerFactory
, pappso::PrecisionFactory
- getDecimalPlaces()
: pappso::MassDataCombinerInterface
- getDeltaMass()
: pappso::PeptideRawFragmentMasses
- getDescription()
: pappso::GrpProtein
, pappso::Protein
- getDetectionThresholdOnMaxmin()
: pappso::TraceDetectionZivy
- getDetectionThresholdOnMinmax()
: pappso::TraceDetectionZivy
- getDriftTime()
: pappso::TimsFrameBase
- getDtInMilliSeconds()
: pappso::QualifiedMassSpectrum
- getDynamicRange()
: pappso::FilterRescaleY
, pappso::XtandemSpectrumProcess
- getETDionList()
: pappso::PeptideFragmentIonListBase
- getExcludeParent()
: pappso::XtandemSpectrumProcess
- getExcludeParentNeutralLoss()
: pappso::XtandemSpectrumProcess
- getFileFormat()
: pappso::MsFileAccessor
, pappso::MsFileReader
, pappso::PwizMsFileReader
, pappso::TimsMsFileReader
, pappso::XyMsFileReader
- getFileName()
: pappso::MsFileAccessor
, pappso::MsRunId
- getFilterMorphoMedian()
: pappso::FilterMorphoBackground
- getFilterMorphoMinMax()
: pappso::FilterMorphoBackground
- getFirst()
: pappso::FilterOboPsiModSink
- getFirstAccession()
: pappso::GrpSubGroup
- getFormula()
: pappso::PeptideInterface
- getFrontRetentionTimeReference()
: pappso::MsRunRetentionTime< T >
- 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
- getHyperscore()
: pappso::XtandemHyperscore
, pappso::XtandemHyperscoreBis
- getId()
: pappso::TimsFrameBase
- getIndexNodeMap()
: pappso::MsRunDataSetTree
- getInnermostRangeX()
: pappso::BasePlotWidget
- getInnermostRangeY()
: pappso::BasePlotWidget
- getInstance()
: pappso::AaModification
, pappso::MsRunXicExtractorFactory
- getInstanceCustomizedMod()
: pappso::AaModification
- getInstanceMutation()
: pappso::AaModification
- getInstanceXtandemMod()
: pappso::AaModification
- getIntensityRatio()
: pappso::PeptideNaturalIsotope
, pappso::PeptideNaturalIsotopeAverage
- getIntensityRatioPerIsotopeNumber()
: pappso::PeptideNaturalIsotopeList
- getIntercept()
: pappso::LinearRegression
- getInternalCterModification()
: pappso::Aa
, pappso::Peptide
- getInternalNterModification()
: pappso::Aa
, pappso::Peptide
- getIonIsotopeRatioScore()
: pappso::IonIsotopeRatioScore
- getIonList()
: pappso::PeptideFragmentIonListBase
- getIonScore()
: pappso::XtandemSpectrumProcess
- getIonTypeCountArray()
: pappso::PeptideSpectrumMatch
- getIsotopeMap()
: pappso::PeptideNaturalIsotope
- getIsotopeNumber()
: pappso::PeptideNaturalIsotope
, pappso::PeptideNaturalIsotopeAverage
- getIsotopeRank()
: pappso::PeptideNaturalIsotopeAverage
- getLeftBoundary()
: pappso::TracePeak
- getLetter()
: pappso::AaBase
- getLexicalOrderedString()
: pappso::Utils
- getLiAbsoluteString()
: pappso::Peptide
- getMass()
: pappso::Aa
, pappso::AaBase
, pappso::AaModification
, pappso::Ion
, pappso::Peptide
, pappso::PeptideFragment
, pappso::PeptideFragmentIon
, pappso::PeptideNaturalIsotope
, pappso::Protein
- getMassSpectrumCstSPtr()
: pappso::QualifiedMassSpectrum
, pappso::TimsData
, pappso::TimsFrame
- getMassSpectrumCstSPtrByRawIndex()
: pappso::TimsData
- getMassSpectrumId()
: pappso::QualifiedMassSpectrum
- getMassSpectrumSPtr()
: pappso::QualifiedMassSpectrum
, pappso::TimsFrame
, pappso::TimsFrameBase
- getMatchedIons()
: pappso::XtandemHyperscore
, pappso::XtandemHyperscoreBis
- getMatchPrecursorIdByKo()
: pappso::TimsData
- getMaxHalfEdgeWindows()
: pappso::FilterMorphoMax
- getMaxMinHalfEdgeWindows()
: pappso::FilterMorphoMaxMin
, pappso::TraceDetectionZivy
- getMaxXicElement()
: pappso::TracePeak
- getMeanHalfEdgeWindows()
: pappso::FilterMorphoMean
- getMids()
: ralab::base::resample::Convert2Dense
- getMinHalfEdgeWindows()
: pappso::FilterMorphoMin
- getMinimumMz()
: pappso::XtandemSpectrumProcess
- getMinMaxHalfEdgeWindows()
: pappso::FilterMorphoMinMax
, pappso::TraceDetectionZivy
- getMiscleavage()
: pappso::Enzyme
- getModificationList()
: pappso::Aa
- getModificationPositionList()
: pappso::Peptide
, pappso::PeptideModificatorBase
- getMorpheusScore()
: pappso::MorpheusScore
- getMs1RetentionTimeVector()
: pappso::MsRunRetentionTime< T >
- getMsLevel()
: pappso::QualifiedMassSpectrum
, pappso::TimsFrameBase
- getMsLevelBySpectrumIndex()
: pappso::TimsData
- getMsLevelCount()
: pappso::MsRunSimpleStatistics
- getMsPointDistance()
: pappso::Xic
- getMsRunId()
: pappso::MsRunReader
, pappso::MsRunXicExtractorInterface
- getMsRunIdCstSPtr()
: pappso::MassSpectrumId
- getMsRunIds()
: pappso::MsFileAccessor
, pappso::MsFileReader
, pappso::PwizMsFileReader
, pappso::TimsMsFileReader
, pappso::XyMsFileReader
- getMsRunReaderSPtr()
: pappso::MsRunRetentionTime< T >
- getMsRunReaderSPtrByRunId()
: pappso::MsFileAccessor
- getMz()
: pappso::Ion
, pappso::MzRange
, pappso::PeptideNaturalIsotopeAverage
, pappso::QualifiedXic
- getMzFormat()
: pappso::MsRunId
- getMzFromTof()
: pappso::TimsFrameBase
- getMzInstance()
: pappso::MassSpectrumCombinerFactory
, pappso::PrecisionFactory
- getMzSortedPrecursorDataChargeValuesAsString()
: pappso::QualifiedMassSpectrum
- getMzSortedPrecursorDataMzValuesAsString()
: pappso::QualifiedMassSpectrum
- getName()
: pappso::AaModification
, pappso::PeptideFragmentIon
, pappso::PeptideInterface
, pappso::XicWidget
- getNativeId()
: pappso::MassSpectrumId
- getNbrPeaks()
: pappso::TimsFrame
, pappso::TimsFrameBase
- getNearestPeakBetween()
: pappso::QCPSpectrum
- getNeutralLossMass()
: pappso::XtandemSpectrumProcess
- getNeutralLossWindowDalton()
: pappso::XtandemSpectrumProcess
- getNmostIntense()
: pappso::XtandemSpectrumProcess
- getNominal()
: pappso::PrecisionBase
- getNrmsd()
: pappso::LinearRegression
- getNToppeaks()
: ralab::base::ms::PeakPicker< TReal, TIntegrator >
- 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
- getNumberOfModification()
: pappso::Aa
, pappso::Peptide
- getNumberOfNeutralPhosphoLoss()
: pappso::PeptideFragmentIon
- getNumberOfPoints()
: pappso::FilterGreatestY
, pappso::FilterGreatestYperWindow
- getNumberOfThreads()
: pappso::XtandemPresetSaxHandler
- getOboPsiModTermList()
: pappso::FilterOboPsiModSink
- getOne()
: pappso::FilterOboPsiModSink
- getOneOverK0Transformation()
: pappso::TimsFrameBase
- getOriginalMsDataFileName()
: pappso::XtandemInputSaxHandler
- getOriginalTandemOutputFileName()
: pappso::XtandemInputSaxHandler
- getOriginalTandemPresetFileName()
: pappso::XtandemInputSaxHandler
- getOutermostRangeX()
: pappso::BasePlotWidget
- getOutermostRangeY()
: pappso::BasePlotWidget
- getParameters()
: pappso::FilterSavitzkyGolay
- getParameterValue()
: pappso::QualifiedMassSpectrum
- getParent()
: pappso::MsRunDataSetTreeNode
- getPeak()
: pappso::PeakIonMatch
- getPeakArea()
: ralab::base::ms::PeakPicker< TReal, TIntegrator >
- getPeakIonIsotopeMatchList()
: pappso::PeptideIsotopeSpectrumMatch
- getPeakMass()
: ralab::base::ms::PeakPicker< TReal, TIntegrator >
- getPen()
: pappso::BasePlotWidget
- 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
- getPhosphorylationNumber()
: pappso::PeptideFragmentIonListBase
- getPlottingColor()
: pappso::BaseColorMapPlotWidget
, pappso::BasePlotWidget
- getPlusCombiner()
: pappso::MassSpectrumCombinerFactory
- getPpmInstance()
: pappso::MassSpectrumCombinerFactory
, pappso::PrecisionFactory
- getPrecision()
: pappso::PeptideNaturalIsotopeAverage
, pappso::PrecisionWidget
- getPrecursorCharge()
: pappso::QualifiedMassSpectrum
- getPrecursorDataChargeValuesAsString()
: pappso::QualifiedMassSpectrum
- getPrecursorDataMzValuesAsString()
: pappso::QualifiedMassSpectrum
- getPrecursorIntensity()
: pappso::QualifiedMassSpectrum
- getPrecursorIonData()
: pappso::QualifiedMassSpectrum
- getPrecursorIonDataSortedWithMz()
: pappso::QualifiedMassSpectrum
- getPrecursorMz()
: pappso::QualifiedMassSpectrum
- getPrecursorNativeId()
: pappso::QualifiedMassSpectrum
- getPrecursorScanNumber()
: pappso::MzxmlOutput
- getPrecursorsFromMzRtCharge()
: pappso::TimsData
- getPrecursorsIDFromMzRt()
: pappso::TimsMsRunReaderMs2
- getPrecursorSpectrumIndex()
: pappso::QualifiedMassSpectrum
- getProblem()
: ralab::base::ms::SimplePicker< TReal >
- getPwizSpectrumPtr()
: pappso::PwizMsRunReader
- getQRegExpRecognitionSite()
: pappso::Enzyme
- getQualifiedMassSpectrum()
: pappso::MsRunDataSetTreeNode
- getQualifiedMassSpectrumByRawIndex()
: pappso::TimsData
- getQualifiedMs1MassSpectrumByPrecursorId()
: pappso::TimsData
- getQualifiedMs2MassSpectrumByPrecursorId()
: pappso::TimsData
- getRange()
: pappso::BasePlotWidget
- getRangeX()
: pappso::BasePlotWidget
- getRangeY()
: pappso::BasePlotWidget
- getRank()
: pappso::GrpPeptide
, pappso::GrpProtein
- getRawIndexFromCoordinate()
: pappso::TimsData
- getRawIndexFromMz()
: pappso::TimsFrameBase
- getRawTraceSPtr()
: pappso::TimsFrame
- getRefineSpectrumModel()
: pappso::XtandemSpectrumProcess
- getRemoveIsotope()
: pappso::XtandemSpectrumProcess
- getResampledIntensity()
: ralab::base::ms::PeakPicker< TReal, TIntegrator >
- getResampledMZ()
: ralab::base::ms::PeakPicker< TReal, TIntegrator >
- getResInstance()
: pappso::MassSpectrumCombinerFactory
, pappso::PrecisionFactory
- getRetentionTimeFromSecondsToLocal()
: pappso::QCPXic
- getRightBoundary()
: pappso::TracePeak
- getRmsd()
: pappso::LinearRegression
- getRootNodes()
: pappso::MsRunDataSetTree
- getRtInMinutes()
: pappso::QualifiedMassSpectrum
- getRtInSeconds()
: pappso::QualifiedMassSpectrum
- getRunId()
: pappso::MsRunId
- getSampleName()
: pappso::MsRunId
- getScaleFactorY()
: pappso::FilterScaleFactorY
- getScanCoordinateFromRawIndex()
: pappso::TimsData
- getScanIndexList()
: pappso::TimsFrame
- getScanIntensities()
: pappso::TimsFrame
- getScanNumber()
: pappso::MzxmlOutput
- getScanNumberFromNativeId()
: pappso::MzxmlOutput
- getScanNumFromOneOverK0()
: pappso::TimsFrameBase
- getScanOffset()
: pappso::TimsFrame
- getSeamarks()
: pappso::MsRunRetentionTime< T >
- getSeamarksReferences()
: pappso::MsRunRetentionTime< T >
- getSequence()
: pappso::GrpPeptide
, pappso::Peptide
, pappso::PeptideFragment
, pappso::PeptideFragmentIon
, pappso::PeptideInterface
, pappso::PeptideNaturalIsotope
, pappso::Protein
- getSequenceByIndex()
: pappso::FastaFileIndexer
, pappso::FastaFileIndexerInterface
- getSequenceLi()
: pappso::PeptideInterface
- getSliceNumber()
: pappso::MsRunSlice
- getSlope()
: pappso::LinearRegression
- getSmoothedIntensity()
: ralab::base::ms::PeakPicker< TReal, TIntegrator >
- getSmoothingHalfEdgeWindows()
: pappso::TraceDetectionMoulon
, pappso::TraceDetectionZivy
- getSpectrum()
: pappso::MsRunSlice
- getSpectrumCount()
: pappso::MsRunDataSetTree
- getSpectrumIndex()
: pappso::MassSpectrumId
- getSpectrumIndexFromScanNumber()
: pappso::MsRunReaderScanNumberMultiMap
- getSubGroupNumber()
: pappso::GrpProtein
, pappso::GrpSubGroup
- getSubGroupSet()
: pappso::GrpMapPeptideToSubGroupSet
- getSubGroupSpList()
: pappso::GrpGroup
- getThresholdX()
: pappso::FilterResampleKeepGreater
- getTicStart()
: pappso::TraceDetectionMoulon
- getTicStop()
: pappso::TraceDetectionMoulon
- getTime()
: pappso::TimsFrameBase
- getTimsFrameBaseCstSPtr()
: pappso::TimsData
- getTimsFrameBaseCstSPtrCached()
: pappso::TimsData
- getTimsFrameCstSPtr()
: pappso::TimsData
- getTimsFrameCstSPtrCached()
: pappso::TimsData
- getTimsFrameSPtrByOffset()
: pappso::TimsBinDec
- getTimsMS1FrameIdRange()
: pappso::TimsData
- getTofFromIndex()
: pappso::TimsFrameBase
- getTotalCount()
: pappso::MsRunSimpleStatistics
- getTotalMatchedIons()
: pappso::XtandemHyperscoreBis
- getTotalNumberOfPrecursors()
: pappso::TimsData
- getTotalNumberOfScans()
: pappso::TimsData
- getTraceFromCumulatedScans()
: pappso::TimsFrame
- getValueRangeOnKeyRange()
: pappso::BaseTracePlotWidget
- getValuesX()
: pappso::BaseTracePlotWidget
- getValuesY()
: pappso::BaseTracePlotWidget
- getVoltageTransformation()
: pappso::TimsFrameBase
- getWindowValue()
: pappso::FilterMorphoMax
, pappso::FilterMorphoMean
, pappso::FilterMorphoMedian
, pappso::FilterMorphoMin
, pappso::FilterMorphoSum
, pappso::FilterMorphoWindowBase
- getXicCstSPtr()
: pappso::MsRunXicExtractor
, pappso::MsRunXicExtractorDisk
, pappso::MsRunXicExtractorInterface
, pappso::QualifiedXic
, pappso::XicWidget
- getXicCstSPtrList()
: pappso::MsRunXicExtractor
, pappso::MsRunXicExtractorDisk
, pappso::MsRunXicExtractorInterface
- getXicFromPwizMSDataFile()
: pappso::MsRunXicExtractor
- getXicSPtr()
: pappso::QualifiedXic
- getXmlId()
: pappso::MsRunId
- 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