Here is a list of all class members with links to the classes they belong to:
- s -
- sanityCheck()
: pappso::Enzyme
- savePdf()
: pappso::MassSpectrumWidget
- SavGolParams()
: pappso::SavGolParams
- scanNumBegin
: pappso::TimsXicStructure
- scanNumber2SpectrumIndex()
: pappso::MsRunReader
- scanNumEnd
: pappso::TimsXicStructure
- selectMsRunReader()
: pappso::TimsMsFileReader
, pappso::XyMsFileReader
- serializeMsRun()
: pappso::MsRunXicExtractorDisk
- set()
: pappso::GrpMapPeptideToGroup
- setAccession()
: pappso::Protein
- setAccumulationTime()
: pappso::TimsFrameBase
- setArea()
: pappso::TracePeak
- setAxisLabelX()
: pappso::BasePlotWidget
- setAxisLabelY()
: pappso::BasePlotWidget
- setBins()
: pappso::MassSpectrumCombiner
- setChargeMinimalFractionalPart()
: pappso::MassSpecTracePlotWidget
- setChargeStateEnvelopePeakSpan()
: pappso::MassSpecTracePlotWidget
- setColorMapPlotConfig()
: pappso::BaseColorMapPlotWidget
- setCurrentIndex()
: pappso::PrecisionWidget
- setDaltonValueChanged()
: pappso::PrecisionWidget
- setDecimalPlaces()
: pappso::MassDataCombinerInterface
- 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
- setFilterResampleKeepXRange()
: pappso::MassDataCombinerInterface
- setFocus()
: pappso::BasePlotWidget
- setFocusSignal()
: pappso::BasePlotWidget
- setGraphData()
: pappso::BaseTracePlotWidget
- setGroupNumber()
: pappso::GrpGroup
, pappso::GrpPeptide
, pappso::GrpPeptideSet
, pappso::GrpProtein
, pappso::GrpSubGroup
- setGrpPeptide()
: pappso::GrpExperiment
- setInputParameters()
: pappso::XtandemOutputSaxHandler
- 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
- setMs1FilterCstSPtr()
: pappso::TimsData
, pappso::TimsMsRunReaderMs2
, pappso::TimsMsRunReaderMs2Selected
- setMs1MeanFilter()
: pappso::MsRunRetentionTime< T >
- setMs1Precision()
: pappso::MassSpectrumWidget
- setMs2BuiltinCentroid()
: pappso::TimsData
, pappso::TimsMsRunReaderMs2
- setMs2FilterCstSPtr()
: pappso::TimsData
, pappso::TimsMsRunReaderMs2
, pappso::TimsMsRunReaderMs2Selected
- setMs2FilterSuite()
: pappso::TandemWrapperRun
- setMs2MeanFilter()
: pappso::MsRunRetentionTime< T >
- setMs2MedianFilter()
: pappso::MsRunRetentionTime< T >
- setMs2Precision()
: pappso::MassSpectrumWidget
- setMsLevel()
: pappso::MassSpectrumWidget
, pappso::QualifiedMassSpectrum
- setMsMsType()
: pappso::TimsFrameBase
- setMsRunId()
: pappso::MassSpectrumId
- setMzCalibration()
: pappso::TimsFrameBase
- setMzFormat()
: pappso::MsRunId
- setMzRangeChanged()
: pappso::QCPSpectrum
- setName()
: pappso::QCPXic
, pappso::XicWidget
- setNativeId()
: pappso::MassSpectrumId
- setNeedMsLevelPeakList()
: pappso::SpectrumCollectionHandlerInterface
- setNeutralLossMass()
: pappso::XtandemSpectrumProcess
- setNeutralLossWindowDalton()
: pappso::XtandemSpectrumProcess
- setNmostIntense()
: pappso::XtandemSpectrumProcess
- setNodesToProcessCount()
: pappso::MsRunDataSetTreeNodeVisitorInterface
- setOboPsiModTerm()
: pappso::FilterOboPsiModSink
, pappso::FilterOboPsiModTermAccession
, pappso::FilterOboPsiModTermDiffMono
, pappso::FilterOboPsiModTermLabel
, pappso::FilterOboPsiModTermName
, pappso::OboPsiModHandlerInterface
- setParameterValue()
: 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
- setPlottingColor()
: pappso::BaseColorMapPlotWidget
, pappso::BasePlotWidget
- setPpmValueChanged()
: pappso::PrecisionWidget
- setPrecision()
: pappso::PrecisionWidget
- setPrecursorNativeId()
: pappso::QualifiedMassSpectrum
- setPrecursorSpectrumIndex()
: pappso::QualifiedMassSpectrum
- setPreferedFileReaderType()
: pappso::MsFileAccessor
- setProtCter()
: pappso::PeptideFixedModificationBuilder
, pappso::PeptideVariableModificationBuilder
- setProtElse()
: pappso::PeptideFixedModificationBuilder
, pappso::PeptideVariableModificationBuilder
- setProtNter()
: pappso::PeptideFixedModificationBuilder
, pappso::PeptideVariableModificationBuilder
- setQualifiedMassSpectrum()
: pappso::MassSpectrumWidget
, pappso::MsRunDataSetTreeNode
, pappso::MsRunReaderScanNumberMultiMap
, pappso::MsRunSimpleStatistics
, pappso::MsRunXicExtractorInterface::MsRunXicExtractorReadPoints
, pappso::MzxmlOutput::Translater
, pappso::SpectrumCollectionHandlerInterface
, RetentionTimeReader
- setRank()
: pappso::GrpPeptide
, pappso::GrpProtein
- setReadAhead()
: pappso::MzxmlOutput
, pappso::SpectrumCollectionHandlerInterface
- setRefineSpectrumModel()
: pappso::XtandemSpectrumProcess
- setRemoveIsotope()
: pappso::XtandemSpectrumProcess
- setRemoveNonInformativeSubgroups()
: pappso::GrpExperiment
- setResValueChanged()
: pappso::PrecisionWidget
- setRetentionTimeInMinutes()
: pappso::XicWidget
- setRetentionTimeInSeconds()
: pappso::XicWidget
- setRightBoundary()
: pappso::TracePeak
- setRtInSeconds()
: pappso::QualifiedMassSpectrum
- setRtRangeChanged()
: pappso::QCPXic
- setRunId()
: pappso::MsRunId
- setSampleName()
: pappso::MsRunId
- setSequence()
: pappso::FastaHandlerInterface
, 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
- setSpectrum()
: pappso::MsRunSlice
- setSpectrumIndex()
: pappso::MassSpectrumId
- setSpectrumP()
: pappso::QCPSpectrum
- setSubGroupNumber()
: pappso::GrpProtein
, pappso::GrpSubGroup
- setTakeOnlyFirstWildcard()
: pappso::Enzyme
- setTandemBinaryPath()
: pappso::TandemWrapperRun
- setTicStart()
: pappso::TraceDetectionMoulon
- setTicStop()
: pappso::TraceDetectionMoulon
- setTime()
: pappso::TimsFrameBase
- setTimsCalibration()
: pappso::TimsFrameBase
- setTmpDir()
: pappso::MsRunXicExtractorFactory
- setTracePeak()
: pappso::TraceDetectionSinkInterface
- setTriangleSlope()
: pappso::FilterTriangle
- setupWidget()
: pappso::BasePlotWidget
- setVisibleMassDelta()
: pappso::MassSpectrumWidget
- setXicExtractMethod()
: pappso::MsRunXicExtractorInterface
, pappso::TimsXicExtractorInterface
- setXmlId()
: pappso::MsRunId
- setXrefOrigin()
: pappso::AaModification
- sgcoeff()
: pappso::FilterSavitzkyGolay
- shouldIstop()
: pappso::TandemWrapperRun
- shouldStop()
: pappso::MsRunDataSetTreeNodeVisitorInterface
, pappso::SpectrumCollectionHandlerInterface
- showTracers()
: pappso::BasePlotWidget
- SimplePeakArea()
: ralab::base::ms::SimplePeakArea< TReal >
- SimplePicker()
: ralab::base::ms::SimplePicker< TReal >
- simplepicker_
: ralab::base::ms::PeakPicker< TReal, TIntegrator >
- size()
: 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
- sizetListDataFormatRegExp
: pappso::Utils
- smoothedintensity_
: ralab::base::ms::PeakPicker< TReal, TIntegrator >
- smoothwith_
: ralab::base::ms::PeakPicker< TReal, TIntegrator >
- sortByRetentionTime()
: pappso::Xic
- sortMz()
: pappso::MassSpectrum
- sortX()
: pappso::Trace
- sortY()
: pappso::Trace
- spaceKeyReleaseEvent()
: pappso::BasePlotWidget
- spectrum_index
: pappso::MsRunXicExtractorInterface::MsRunXicExtractorPoints
- spectrumIndex
: pappso::RtPoint
- spectrumListHasSize()
: pappso::SpectrumCollectionHandlerInterface
- spectrumListSize()
: pappso::MsRunReader
, pappso::PwizMsRunReader
, pappso::TimsMsRunReader
, pappso::TimsMsRunReaderMs2
, pappso::TimsMsRunReaderMs2Selected
, pappso::XyMsRunReader
- splitMzStringToDoubleVectorWithSpaces()
: pappso::Utils
- splitSizetStringToSizetVectorWithSpaces()
: pappso::Utils
- startDocument()
: pappso::XtandemInputSaxHandler
, pappso::XtandemOutputSaxHandler
, pappso::XtandemPresetSaxHandler
- startDragPoint
: pappso::BasePlotContext
- startElement()
: pappso::XtandemInputSaxHandler
, pappso::XtandemOutputSaxHandler
, pappso::XtandemPresetSaxHandler
- startElement_note()
: pappso::XtandemInputSaxHandler
, pappso::XtandemOutputSaxHandler
, pappso::XtandemPresetSaxHandler
- startGrouping()
: pappso::GrpExperiment
, pappso::GrpGroupingMonitor
, pappso::GrpGroupingMonitorInterface
- startNumberingAllGroups()
: pappso::GrpGroupingMonitor
, pappso::GrpGroupingMonitorInterface
- startRemovingNonInformativeSubGroupsInAllGroups()
: pappso::GrpGroupingMonitor
, pappso::GrpGroupingMonitorInterface
- stopGrouping()
: pappso::GrpGroupingMonitor
, pappso::GrpGroupingMonitorInterface
- stopRemovingNonInformativeSubGroupsInAllGroups()
: pappso::GrpGroupingMonitor
, pappso::GrpGroupingMonitorInterface
- storeSlices()
: pappso::MsRunXicExtractorDisk
, pappso::MsRunXicExtractorDiskBuffer
- strip()
: pappso::GrpProtein
- sumAndRemove()
: pappso::FilterTriangle
- sumY()
: pappso::Trace
- sw_
: ralab::base::ms::PeakPicker< TReal, TIntegrator >