- s -

safeParse_() : MzMLFile
sameNrOfMSFilesPerFraction() : ExperimentalDesign
Sample() : Sample
sample_stddev() : mean_and_stddev
sample_variance() : mean_and_stddev
SampleSection() : ExperimentalDesign::SampleSection
SampleVisualizer() : SampleVisualizer
sanityCheck_() : TOPPASScene
save_() : XMLFile
saveAll_() : MetaDataBrowser
saveAsImage() : Plot1DWidget , PlotWidget
saveCurrentLayer() : PlotCanvas
saveCurrentPipelineAs() : TOPPASBase
saveFeatureCompoundInfoAsTSV() : SiriusMSFile
saveFile() : INIFileEditorWindow
saveFileAs() : INIFileEditorWindow
saveIDs_() : SpectraIDViewTab
saveIfChanged() : TOPPASScene
SaveImageDialog() : SaveImageDialog
saveLayerAll() : TOPPViewBase
saveLayerVisible() : TOPPViewBase
saveMe() : TOPPASScene
savePipeline() : TOPPASBase
savePipelineAs() : TOPPASBase
savePipelineResourceFile() : TOPPASBase
savePreferences() : TOPPASBase , TOPPViewBase
saveToClipboard() : TOPPASBase
saveToFile() : LayerStoreData , LayerStoreDataConsensusMapAll , LayerStoreDataConsensusMapVisible , LayerStoreDataFeatureMapAll , LayerStoreDataFeatureMapVisible , LayerStoreDataIdentAll , LayerStoreDataIdentVisible , LayerStoreDataPeakMapAll , LayerStoreDataPeakMapVisible
SavitzkyGolayFilter() : SavitzkyGolayFilter
scale_() : AxisPainter
scaleBy() : RangeBase , RangeManager< RangeBases >
scaledIntensity_() : Plot3DOpenGLCanvas
scaledInversMZ_() : Plot3DOpenGLCanvas
scaledInversRT_() : Plot3DOpenGLCanvas
scaledMZ_() : Plot3DOpenGLCanvas
scaledRT_() : Plot3DOpenGLCanvas
ScanEvent() : Ms2SpectrumStats::ScanEvent
ScanWindow() : ScanWindow
ScanWindowVisualizer() : ScanWindowVisualizer
score() : DiaPrescore
score_with_isotopes() : DIAScoring
scoreAllChromatograms_() : OpenSwathWorkflow
scoreAndFilterPeakGroups_() : FLASHDeconvAlgorithm
scoreAssay_() : ConfidenceScoring
ScoredProcessingResult() : ScoredProcessingResult
scoreFeature_() : ConfidenceScoring
scoreHullpoints() : MasstraceCorrelator
scoreIdentification_() : MRMFeatureFinderScoring
scoreIsotopePattern_() : DIAScoring
scoreMap() : ConfidenceScoring
scoreMZ_() : FeatureFindingMetabo
scoreMZByExpectedMean_() : FeatureFindingMetabo
scoreMZByExpectedRange_() : FeatureFindingMetabo
scorePeakgroups() : MRMFeatureFinderScoring
scoreRT_() : FeatureFindingMetabo
scoreSpectra() : TargetedSpectraExtractor
ScoreType() : ScoreType
search() : SimpleSearchEngineAlgorithm
searchAndShow_() : DIATreeTab , SpectraTreeTab
SearchEngineBase() : SearchEngineBase
searchMass_() : AccurateMassSearchEngine
searchModification() : ModificationsDB
searchModifications() : ModificationsDB
searchModificationsByDiffMonoMass() : ModificationsDB
searchModificationsByDiffMonoMassSorted() : ModificationsDB
searchModificationsFast() : ModificationsDB
searchNextCell_() : HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator
SearchParameters() : ProteinIdentification::SearchParameters
searchPrefix() : StringListUtils
searchSpectrum() : TargetedSpectraExtractor
searchSuffix() : StringListUtils
seed() : RandomShuffler
SeedListGenerator() : SeedListGenerator
seekGToSavedPosition() : FuzzyStringComparator::InputLine
select() : MSSpectrum
selectAll() : Annotations1DContainer
selectChromHelper_() : MRMTransitionGroupPicker
selectCompoundsForBatch_() : OpenSwathWorkflow
selected() : ParamTree
selectFeaturesFromCandidates_() : FeatureFinderAlgorithmMetaboIdent
selectionChanged() : ParamTree
selectionCopied() : TOPPASScene
selectItemAt() : Annotations1DContainer
selectMRMFeature() : MRMFeatureSelector
SelectorParameters() : MRMFeatureSelector::SelectorParameters
selectSpectra() : TargetedSpectraExtractor
selectSwathTransitions() : OpenSwathHelper
selectSwathTransitionsPasef() : OpenSwathHelper
SemanticValidator() : SemanticValidator
sendClipboardContent() : TOPPASBase
sendCursorStatus() : PlotCanvas , PlotWidget , TOPPASWidget
sendStatus() : BaseVisualizerGUI
sendStatusMessage() : PlotCanvas , PlotWidget , TOPPASWidget
seqTypeSwitch_() : TheoreticalSpectrumGenerationDialog
sequence() : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_
SequenceIdentity_() : DecoyGenerator
sequenceMatches() : FASTAFile::FASTAEntry
SequestInfile() : SequestInfile
SequestOutfile() : SequestOutfile
set() : Date , DateTime , GlobalExceptionHandler , FilterList , IsotopeDistribution , MzTabBoolean , MzTabDouble , MzTabDoubleList , MzTabInteger , MzTabIntegerList , MzTabModificationList , MzTabParameterList , MzTabString , MzTabStringList , NASequence , RecentFilesMenu , TOPPASVertex::TOPPASFilenames
set2DData() : MSExperiment
set_chromatogram_flag() : LayerDataPeak
set_high_bound() : _Region< __K, _Val, _SubVal, _Acc, _Cmp >
set_low_bound() : _Region< __K, _Val, _SubVal, _Acc, _Cmp >
setAAAfter() : PeptideEvidence
setAABefore() : PeptideEvidence
setAbsChargeRange() : PeakGroup
setAbsolute() : FineIsotopePatternGenerator
setAcceptableAbsolute() : FuzzyStringComparator
setAcceptableRelative() : FuzzyStringComparator
setAccession() : CVMappingTerm , CVTerm , MzTabParameter , ProteinHit
setAccessionAttribute() : SemanticValidator
setAccuracy() : MassAnalyzer
setAcquisitionInfo() : ChromatogramSettings , SpectrumSettings
setAcquisitionMode() : IonDetector
setActionMode() : TOPPASScene
setActivationEnergy() : Precursor
setActivationMethod() : DeconvolvedSpectrum
setActivationMethods() : Precursor
setActive() : ChargePair , DataFilters
setADCSamplingFrequency() : IonDetector
setAdditionalContextMenu() : PlotCanvas
setAddress() : ContactPerson
setAdductBase() : MassExplainer
setAllowChildren() : CVMappingTerm
setAllowedThreads() : TOPPASScene
setAllowIsotopeError() : XTandemInfile
setAllowShortNumbers() : AxisWidget
setAlwaysAppendData() : PeakFileOptions
setAmount() : Adduct
setAnalysisResults() : PeptideHit
setArea() : Area< N_DIM >
setAtBottomRow() : TableView
setAtomicNumber() : Element
setAverageMass() : ResidueModification
setAverageWeight() : Element , Residue
setAveragine() : FLASHDeconvAlgorithm
setAvgMass() : Ribonucleotide
setAvgPPMError() : PeakGroup
setAxisBounds() : AxisWidget
setBackboneBasicityLeft() : Residue
setBackboneBasicityRight() : Residue
setBaselossFormula() : Ribonucleotide
setBaseName() : PeptideIdentification
setBlacklistItems() : FilterableList
setBlind() : InspectInfile
setCalculatedMassToCharge() : IdentificationHit
setCalculatedMZ() : AccurateMassSearchResult
setCallbacks() : ExternalProcess , ExternalProcessMBox
setCanvas_() : PlotWidget
setCastValue_() : AbsoluteQuantitationMethodFile , MRMFeaturePickerFile
setCentroidSD() : MassTrace
setChanged() : TOPPASScene
setCharge() : AccurateMassSearchResult , Adduct , BaseFeature , ChargePair , EmpiricalFormula , FeatureHandle , FeatureHypothesis , IdentificationHit , PeptideHit , Precursor
setChargeIsotopeCosine() : PeakGroup
setChargeScore() : PeakGroup
setChargeSNR() : PeakGroup
setChargeState() : PeptideCompound , TraMLProduct , LightCompound
setChecksum() : SourceFile
setCheckTermValueTypes() : SemanticValidator
setCheckUnits() : SemanticValidator
setChromatogramAnnotation() : LayerDataChrom
setChromatogramProcessingFunc() : MSDataTransformingConsumer
setChromatograms() : MSExperiment
setChromatogramType() : ChromatogramSettings
setChromData() : LayerDataChrom
setCleavageSite() : XTandemInfile
setClipboard() : TOPPASScene
setCode() : Ribonucleotide
setCoefficientLimits() : MZTrafoModel
setCoefficients() : MZTrafoModel
setColor() : Annotation1DCaret< DataPoint > , Annotation1DPeakItem< DataPoint > , ColorSelector , TOPPASEdge
setColumn() : HPLC
setColumnBounds() : LPWrapper
setColumnHeaders() : ConsensusMap
setColumnName() : LPWrapper
setColumnType() : LPWrapper
setCombinationsLogic() : CVMappingRule
setCometID() : DigestionEnzymeProtein
setComment() : ChromatogramSettings , ExperimentalSettings , HPLC , Sample , SpectrumSettings
setCommentRows() : MzTab , MzTabM
setCommonName() : SpectralMatch
setCompletionTime() : DataProcessing
setCompomer() : ChargePair
setComponentName() : AbsoluteQuantitationMethod
setCompoundRef() : IncludeExcludeTarget , ReactionMonitoringTransition
setCompounds() : TargetedExperiment
setCompression() : MSNumpressCoder::NumpressConfig , PeakFileOptions
setConcentration() : Sample
setConcentrationUnits() : AbsoluteQuantitationMethod
setConfig() : MzMLSqliteHandler , SqMassFile
setConfigurations() : IncludeExcludeTarget
setContactInfo() : ContactPerson
setContacts() : ExperimentalSettings , TargetedExperiment
setConvexHulls() : Feature
setCorrectionFactor() : DBSuitability::SuitabilityData
setCorrelationCoefficient() : AbsoluteQuantitationMethod
setCoverage() : ProteinHit
setCreationDate() : Identification
setCTermGain() : DigestionEnzymeProtein
setCTerminalModification() : AASequence
setCTerminalModificationByDiffMonoMass() : AASequence
setCurrentIndex() : LayerData1DBase
setCurrentLayer() : LayerStack
setCurrentLayerParameters() : PlotCanvas
setCurrentLayerPeakPenStyle() : Plot1DCanvas
setCurrentProcessingStep() : IdentificationData
setCustomizations() : Instrument
setCutOff() : BaseModel
setCutsAfterRegEx() : DigestionEnzymeRNA
setCutsBeforeRegEx() : DigestionEnzymeRNA
setCVIdentifierRef() : CVMappingTerm , CVTerm
setCVLabel() : MzTabParameter
setCVReferences() : CVMappings
setCVs() : TargetedExperiment
setCVTerms() : CVMappingRule , CVTermList , CVTermListInterface
setCWD() : InputFile , InputFileList
setData() : FeatureFinderAlgorithm , FeatureFinderAlgorithmPicked , BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value >
setDatabase() : SequestInfile
setDataPoints() : TransformationDescription
setDataProcessing() : ChromatogramSettings , ConsensusMap , FeatureMap , MetaInfoDescription , SpectrumSettings
setDate() : DateTime
setDateTime() : ExperimentalSettings , ProteinIdentification
setDb() : InspectInfile
setDecoyTransitionType() : ReactionMonitoringTransition
setDefaultParametersFilename() : XTandemInfile
setDefaultParams_() : IsobaricChannelExtractor , IsobaricQuantifier , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTEighteenPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
setDefaults() : Param
setDelayInSeconds() : FileWatcher
setDescription() : MetaInfoRegistry , ProteinHit , TOPPASScene
setDetectingTransition() : ReactionMonitoringTransition , LightTransition
setDFSColor() : TOPPASVertex
setDiffAverageMass() : ResidueModification
setDiffFormula() : ResidueModification
setDiffMonoMass() : ResidueModification
setDimMinMax() : DIntervalBase< D >
setDirectory() : OutputDirectory
setDrawInterestingMZs() : Plot1DCanvas
setDrawMode() : Plot1DCanvas
setDrawMode1D() : TOPPViewBase
setDriftTime() : MSSpectrum , Precursor , PeptideCompound , LightCompound
setDriftTimeArray() : OSSpectrum
setDriftTimeUnit() : Mobilogram , MSSpectrum , Precursor
setDriftTimeWindowLowerOffset() : Precursor
setDriftTimeWindowUpperOffset() : Precursor
setEdgeScore() : ChargePair
setEditorData() : ListEditorDelegate , ParamEditorDelegate
setElement() : IMSAlphabet , LPWrapper
setElementIndex() : ChargePair
setElementPath() : CVMappingRule
setEmail() : ContactPerson
setEmpiricalFormula() : AccurateMassSearchResult
setEmptyRows() : MzTab , MzTabM
setEnd() : PeptideEvidence
setEnzyme() : EnzymaticDigestion , InspectInfile , ProteaseDigestion , RNaseDigestion , SequestInfile
setExcludeTargets() : TargetedExperiment
setExpectedSize() : FullSwathFileConsumer , IMSDataConsumer , MSDataAggregatingConsumer , MSDataCachedConsumer , MSDataChainingConsumer , MSDataSqlConsumer , MSDataStoringConsumer , MSDataTransformingConsumer , MSDataWritingConsumer , NoopMSDataConsumer
setExperimentalMassToCharge() : IdentificationHit
setExperimentalSettings() : FullSwathFileConsumer , IMSDataConsumer , MSDataAggregatingConsumer , MSDataCachedConsumer , MSDataChainingConsumer , MSDataSqlConsumer , MSDataStoringConsumer , MSDataTransformingConsumer , MSDataWritingConsumer , NoopMSDataConsumer , NoopMSDataWritingConsumer
setExperimentalSettingsFunc() : MSDataTransformingConsumer
setExperimentLabel() : PeptideIdentification
setExperimentType() : ConsensusMap
setExportDecoys() : MascotRemoteQuery
setFactor() : SpectrumCheapDPCorr
setFeatOptions() : FileHandler
setFeature() : FeatureEditDialog
setFeatureName() : AbsoluteQuantitationMethod
setFeatures() : ConsensusFeature
setFile() : GlobalExceptionHandler
setFileFormatFilter() : InputFile , TOPPASInputFileDialog
setFilename() : InputFile
setFileName() : ListEditorDelegate
setFilenames() : InputFileList , TOPPASInputFileListVertex
setFileSize() : SourceFile
setFileType() : SourceFile
setFillData() : PeakFileOptions
setFilters() : PlotCanvas
setFilters_() : FLASHDeconvAlgorithm
setFinalMSExponent() : MassAnalyzer
setFirstColumn() : FuzzyStringComparator
setFirstName() : ContactPerson
setFitterParam() : EmgScoring
setFivePrimeGain() : DigestionEnzymeRNA
setFivePrimeMod() : NASequence
setFixedModification() : ModificationDefinition
setFlags() : Annotation1DTextItem
setFloatDataArrays() : Mobilogram , MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
setFlux() : HPLC
setForceMQCompatability() : PeakFileOptions
setForceTPPCompatability() : PeakFileOptions
setFormula() : Adduct , Residue , ResidueModification , Ribonucleotide
setFoundAdduct() : AccurateMassSearchResult
setFoundMass() : AccurateMassSearchResult
setFoundPrecursorCharge() : SpectralMatch
setFoundPrecursorMass() : SpectralMatch
setFractionIdentifier() : ExperimentalSettings
setFragmentMassErrorUnit() : XTandemInfile
setFragmentMassTolerance() : XTandemInfile
setFreeText() : PythonModuleRequirement
setFromParam() : RecentFilesMenu
setFullId() : ResidueModification
setFullName() : ResidueModification
setFunction() : GlobalExceptionHandler
setGradient() : HPLC
setGravityAxis() : Gravitator
setHeaderExportName() : TableView
setHeaders() : TableView , TreeView
setHigherScoreBetter() : PeptideIdentification , ProteinIdentification
setHits() : SpectrumIdentification , PeptideIdentification , ProteinIdentification
setHoverPos() : TOPPASEdge
setHPLC() : ExperimentalSettings
setHTMLCode() : Ribonucleotide
setHullPoints() : ConvexHull2D
setID() : Compomer
setId() : IdentificationHit , ResidueModification
setIdentifier() : Acquisition , CVMappingRule , CVReference , DocumentIdentifier , PeptideIdentification , ProteinIdentification
setIdentifyingTransition() : ReactionMonitoringTransition , LightTransition
setIMUnit() : IMDataConverter
setInchiString() : SpectralMatch
setIncludeTargets() : TargetedExperiment
setIndex() : PeakGroup
setIndividualIntensities() : AccurateMassSearchResult
setInf() : MzTabDouble , MzTabInteger
setInferenceEngine() : ProteinIdentification
setInferenceEngineVersion() : ProteinIdentification
setInitialParameters() : GammaDistributionFitter , GaussFitter , GumbelDistributionFitter , GumbelMaxLikelihoodFitter
setInitialParameters_() : EGHTraceFitter , EmgFitter1D , GaussTraceFitter
setInitialParametersMOM_() : EmgFitter1D
setInletType() : IonSource
setInputFilename() : XTandemInfile
setInputOutputCombo_() : ToolsDialog
setInstitution() : ContactPerson
setInstrument() : ExperimentalSettings , HPLC , InspectInfile
setInstruments() : TargetedExperiment
setInstrumentSettings() : ChromatogramSettings , SpectrumSettings
setIntegerDataArrays() : Mobilogram , MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
setIntensity() : ChromatogramPeak , MobilityPeak1D , MobilityPeak2D , Peak1D , Peak2D
setIntensity32Bit() : PeakFileOptions
setIntensityArray() : Chromatogram , Spectrum , OSChromatogram , OSSpectrum
setIntensityAsGravity() : Gravitator
setIntensityMode() : PlotCanvas , PlotWidget , TOPPViewBase
setIntensityRange() : FeatureFileOptions , PeakFileOptions
setIntermediateProducts() : ReactionMonitoringTransition
setInternalChars_() : Colorizer
setInterpolationMode() : MultiGradient , MultiGradientSelector
setInterpolationStep() : InterpolationModel
setInterpretations() : IncludeExcludeTarget
setInterProtein_() : XFDRAlgorithm
setIntraProtein_() : XFDRAlgorithm
setInvalid() : QTCluster
setInverseOrientation() : AxisWidget
setIonCutoffPercentage() : SequestInfile
setIonDetectors() : Instrument
setIonizationMethod() : IonSource
setIonLadderVisible() : Plot1DCanvas
setIonOptics() : Instrument
setIonSeriesWeights() : SequestInfile
setIonSources() : Instrument
setISName() : AbsoluteQuantitationMethod
setIsolationWidth() : MassAnalyzer
setIsolationWindowLowerOffset() : Precursor , Product
setIsolationWindowUpperOffset() : Precursor , Product
setIsotopeCosine() : PeakGroup
setIsotopeDaDistance() : PeakGroup
setIsotopeDistribution() : Element , IMSElement
setIsotopesSimScore() : AccurateMassSearchResult
setIsRepeatable() : CVMappingTerm
setItems() : FilterableList , ListFilterDialog
setKey() : TOPPASInputFileListVertex
setLabel() : MassTrace , PlotCanvas
setLastName() : ContactPerson
setLayerFlag() : PlotCanvas
setLayerName() : PlotCanvas
setLeftSplitter() : HistogramDialog , HistogramWidget
setLegend() : AxisWidget , HistogramDialog , HistogramWidget
setLevel() : LogStream , LogStreamBuf
setLibraryIntensity() : ReactionMonitoringTransition , LightTransition
setLine() : GlobalExceptionHandler
setList() : ListTable , ListEditor
setListRestrictions() : ListEditor
setLLOD() : AbsoluteQuantitationMethod
setLLOQ() : AbsoluteQuantitationMethod
setLoadConvexHull() : FeatureFileOptions
setLoadDetail() : MzMLHandler , MzXMLHandler , XMLHandler
setLoadedFilePath() : DocumentIdentifier
setLoadedFileType() : DocumentIdentifier
setLoadSubordinates() : FeatureFileOptions
setLogDestination() : FuzzyStringComparator
setLogger() : ProgressLogger
setLogLevel() : LogConfigHandler
setLogMode() : HistogramDialog , HistogramWidget
setLogProb() : Adduct
setLogScale() : AxisWidget
setLogType() : ProgressLogger
setLossFormulas() : Residue
setLossNames() : Residue
setLowMassIons() : Residue
setMagneticFieldStrength() : MassAnalyzer
setMandatoryExportColumns() : TableView
setMapIndex() : FeatureHandle::FeatureHandleMutable_ , FeatureHandle
setMapper() : Plot1DWidget , Plot2DWidget , Plot3DWidget , PlotCanvas , PlotWidget
setMapping() : LinearInterpolation< Key, Value >
setMapping_0() : BilinearInterpolation< Key, Value >
setMapping_1() : BilinearInterpolation< Key, Value >
setMappingRules() : CVMappings
setMargin() : AxisWidget
setMass() : Sample
setMassAnalyzers() : Instrument
setMassDiff() : ChargePair
setMasstraceIntensities() : AccurateMassSearchResult
setMassTypeFragment() : SequestInfile
setMassTypeParent() : SequestInfile
setMatchedWhitelist() : FuzzyStringComparator
setMatchingHMDBids() : AccurateMassSearchResult
setMatchingIndex() : AccurateMassSearchResult
setMatchingScore() : SpectralMatch
setMatchingSpectrumIndex() : SpectralMatch
setMatchPeakAllowedError() : SequestInfile
setMatchPeakCount() : SequestInfile
setMatchPeakTolerance() : SequestInfile
setMatrix() : Matrix< Value > , NeedlemanWunsch
setMax() : DIntervalBase< D > , RangeBase
setMaxAAACount() : ACTrie
setMaxAAPerModPerPeptide() : SequestInfile
setMaxCharge() : Tagger
setMaxDataPoolSize() : PeakFileOptions
setMaxFloat() : Param
setMaxFloat_() : TOPPBase
setMaxInt() : Param
setMaxInt_() : TOPPBase
setMaxIntensity() : RangeIntensity
setMaxInternalCleavageSites() : SequestInfile
setMaxIsotope() : CoarseIsotopePatternGenerator
setMaxIsotopeIndex() : FLASHDeconvHelperStructs::PrecalculatedAveragine
setMaxLength() : LogWindow
setMaxMMCount() : ACTrie
setMaxMobility() : RangeMobility
setMaxModifications() : ModificationDefinitionsSet
setMaxModsPerPeptide() : SequestInfile
setMaxMZ() : RangeMZ
setMaxNumberOfThreads() : TOPPBase
setMaxOccurrences() : ModificationDefinition
setMaxPrecursorCharge() : XTandemInfile
setMaxPTMsize() : InspectInfile
setMaxRT() : RangeRT
setMaxValidEValue() : XTandemInfile
setMaxX() : DIntervalBase< D >
setMaxY() : DIntervalBase< D >
setMean() : BasicStatistics< RealT >
setMergeLayers() : TOPPViewOpenDialog
setMessage() : GlobalExceptionHandler
setMetaData() : MzTab , MzTabM
setMetadataOnly() : FeatureFileOptions , PeakFileOptions
setMetaValue() : IdentificationData , MetaInfoInterface , MRMFeatureFilter
setMethodOfCombination() : AcquisitionInfo
setMin() : DIntervalBase< D > , RangeBase
setMinFloat() : Param
setMinFloat_() : TOPPBase
setMinimumSize_() : IMSIsotopeDistribution
setMinInt() : Param
setMinInt_() : TOPPBase
setMinIntensity() : RangeIntensity
setMinMax() : DIntervalBase< D >
setMinMaxOfRange() : Plot1DGoToDialog , Plot2DGoToDialog
setMinMobility() : RangeMobility
setMinMZ() : RangeMZ
setMinRT() : RangeRT
setMinX() : DIntervalBase< D >
setMinY() : DIntervalBase< D >
setMirrorModeActive() : Plot1DCanvas
setMissedCleavages() : EnzymaticDigestion
setMobility() : MobilityPeak1D , MobilityPeak2D
setMobilityData() : LayerDataIonMobility
setModel() : Instrument
setModelData() : ListEditorDelegate , ParamEditorDelegate
setModification() : AASequence , ModificationDefinition , Residue
setModificationByDiffMonoMass() : AASequence , Residue
setModificationDefinitionsSet() : OMSSAXMLFile
setModificationIdentifier() : MzTabModification
setModifications() : ModificationDefinitionsSet , PepNovoInfile , ProteinHit , XTandemInfile
setModificationsPerPeptide() : InspectInfile
setModified() : ParamEditor
setMonoisotopicMass() : PeakGroup
setMonoMass() : ResidueModification , Ribonucleotide
setMonoWeight() : Element , Residue
setMS1Map() : MRMFeatureFinderScoring
setMSData() : FeatureFinderAlgorithmMetaboIdent , FeatureFinderIdentificationAlgorithm
setMSDataConsumer() : MzMLHandler , MzXMLHandler
setMSFile() : MzTabSpectraRef
setMSFileSection() : ExperimentalDesign
setMSGFID() : DigestionEnzymeProtein
setMSLevel() : MSSpectrum
setMSLevels() : PeakFileOptions
setMSmallMoleculeEvidenceSectionRows() : MzTabM
setMSmallMoleculeFeatureSectionRows() : MzTabM
setMSmallMoleculeSectionRows() : MzTabM
setMulticharge() : InspectInfile
setMZ() : MobilityPeak2D , Peak1D , Peak2D , PeptideIdentification , Product , TraMLProduct
setMz32Bit() : PeakFileOptions
setMZArray() : Spectrum , OSSpectrum
setMZErrorPPM() : AccurateMassSearchResult
setMZRange() : FeatureFileOptions , PeakFileOptions
setName() : ContactPerson , CVReference , CVTerm , DefaultParamHandler , DigestionEnzyme , Element , GlobalExceptionHandler , IMSElement , IncludeExcludeTarget , Instrument , IdentificationHit , LayerDataBase , MetaInfoDescription , ModelDescription< D > , MSChromatogram , MSSpectrum , MzTabParameter , ReactionMonitoringTransition , Residue , ResidueModification , Ribonucleotide , Sample , Software
setNameAttribute() : SemanticValidator
setNameOfFile() : SourceFile
setNameSuffix() : LayerDataBase
setNaN() : MzTabDouble , MzTabInteger
setNativeID() : ChromatogramSettings , ReactionMonitoringTransition , SpectrumSettings
setNativeIDType() : SourceFile
setNativeIDTypeAccession() : SourceFile
setNeutralLossAverageMasses() : ResidueModification
setNeutralLossDiffFormulas() : ResidueModification
setNeutralLossesForIons() : SequestInfile
setNeutralLossMonoMasses() : ResidueModification
setNewCode() : Ribonucleotide
setNoiseSuppression() : XTandemInfile
setNominalMass() : IMSIsotopeDistribution
setNormalizedIntensityValues() : ConsensusMapNormalizerAlgorithmQuantile
setNormalizeXcorr() : SequestInfile
setNPoints() : AbsoluteQuantitationMethod
setNrMS1Spectra() : SwathQC
setNTermGain() : DigestionEnzymeProtein
setNTerminalModification() : AASequence
setNTerminalModificationByDiffMonoMass() : AASequence
setNTermLossFormulas() : Residue
setNTermLossNames() : Residue
setNucleicAcidSectionRows() : MzTab
setNucleotideReadingFrame() : SequestInfile
setNull() : MzTabBoolean , MzTabDouble , MzTabDoubleList , MzTabInteger , MzTabIntegerList , MzTabModification , MzTabModificationList , MzTabParameter , MzTabParameterList , MzTabSpectraRef , MzTabString , MzTabStringList
setNumber() : Sample
setNumberOfMissedCleavages() : XTandemInfile
setNumberOfThreads() : XTandemInfile
setNumpressConfigurationFloatDataArray() : PeakFileOptions
setNumpressConfigurationIntensity() : PeakFileOptions
setNumpressConfigurationMassTime() : PeakFileOptions
setObjective() : LPWrapper
setObjectiveSense() : LPWrapper
setObservedIntensity() : AccurateMassSearchResult
setObservedMZ() : AccurateMassSearchResult
setObservedPrecursorMass() : SpectralMatch
setObservedPrecursorRT() : SpectralMatch
setObservedRT() : AccurateMassSearchResult
setObservedSpectrumIndex() : SpectralMatch
setObservedSpectrumNativeID() : SpectralMatch
setOffset() : BiGaussModel , EmgModel , ExtendedIsotopeModel , GaussModel , InterpolationModel , IsotopeModel , LinearInterpolation< Key, Value >
setOffset_0() : BilinearInterpolation< Key, Value >
setOffset_1() : BilinearInterpolation< Key, Value >
setOligonucleotideSectionRows() : MzTab
setOMSSAID() : DigestionEnzymeProtein
setOnDiscPeakData() : LayerDataChrom , LayerDataPeak
setOneLetterCode() : Residue
setOpenMPNumThreads() : OpenMSBuildInfo
setOptions() : FeatureXMLFile , FileHandler , IndexedMzMLFileLoader , ConsensusXMLHandler , FeatureXMLHandler , MzDataHandler , MzMLHandler , MzXMLHandler , MzDataFile , MzMLFile , MzXMLFile
setOrder() : IonDetector , IonSource , MassAnalyzer
setOrganism() : Sample
setOrigin() : ResidueModification , Ribonucleotide
setOriginalSpectrum() : DeconvolvedSpectrum
setOriginAnnotationMode_() : IDRipper
setOSMSectionRows() : MzTab
setOutDir() : TOPPASScene
setOutputFilename() : XTandemInfile
setOutputFolderName() : TOPPASOutputVertex
setOutputLines() : SequestInfile
setOutputResults() : XTandemInfile
setOverallQuality() : Feature
setPairValue_() : MRMFeatureQCFile
setParam() : TOPPViewPrefDialog , ModelDescription< D > , TOPPASToolVertex
setParameters() : DefaultParamHandler
setParameters_() : QTClusterFinder
setParseUnknownScores() : PepXMLFile
setPartialSequence() : SequestInfile
setPassThreshold() : IdentificationHit
setPathToFile() : SourceFile
setPeakAnnotations() : PeptideHit
setPeakData() : LayerDataPeak
setPeakGroups() : DeconvolvedSpectrum
setPeakMassTolerance() : InspectInfile , SequestInfile
setPen() : Annotations1DContainer
setPenalty() : NeedlemanWunsch
setPeptideEvidence_() : XQuestResultXMLHandler
setPeptideEvidences() : PeptideHit
setPeptideGroupLabel() : Peptide
setPeptideIdentifications() : BaseFeature , SpectrumSettings
setPeptideIds() : IPeptideIds , LayerDataFeature , LayerDataIdent
setPeptideMassUnit() : SequestInfile
setPeptideRef() : IncludeExcludeTarget , ReactionMonitoringTransition
setPeptides() : TargetedExperiment
setPeptideScoresForMap_() : IDScoreGetterSetter
setPeptideScoresFromMap_() : IDScoreGetterSetter
setPeptideSectionRows() : MzTab
setPercentage() : Gradient
setPipelineRunning() : TOPPASScene
setPka() : Residue
setPkb() : Residue
setPkc() : Residue
setPlotWidget() : PlotCanvas
setPluginPath() : TVToolDiscovery
setPolarity() : InstrumentSettings , IonSource
setPos() : ChromatogramPeak , MobilityPeak1D , Peak1D
setPosition() : Annotation1DCaret< DataPoint > , Annotation1DPeakItem< DataPoint > , Annotation1DTextItem , Annotation1DVerticalLineItem , ChromatogramPeak , FASTAFile , MobilityPeak1D , MobilityPeak2D , Peak1D , Peak2D
setPositionsAndParameters() : MzTabModification
setPossibleChargeStates() : Precursor
setPrechosenItems() : ListFilterDialog
setPrecision() : Weights
setPrecursor() : ChromatogramSettings , DeconvolvedSpectrum
setPrecursorAdduct() : SpectralMatch
setPrecursorCVTermList() : IncludeExcludeTarget , ReactionMonitoringTransition
setPrecursorErrorType() : XTandemInfile
setPrecursorIntensity() : DeconvolvedSpectrum
setPrecursorMassErrorUnit() : XTandemInfile
setPrecursorMassTolerance() : InspectInfile , SequestInfile
setPrecursorMassToleranceMinus() : XTandemInfile
setPrecursorMassTolerancePlus() : XTandemInfile
setPrecursorMZ() : IncludeExcludeTarget , ReactionMonitoringTransition
setPrecursorMZSelectedIon() : PeakFileOptions
setPrecursorPeakGroup() : DeconvolvedSpectrum
setPrecursors() : SpectrumSettings
setPrecursorScanNumber() : DeconvolvedSpectrum
setPrediction() : IncludeExcludeTarget , ReactionMonitoringTransition
setPreferredFixedModifications() : PepXMLFile
setPreferredVariableModifications() : PepXMLFile
setPrefix() : LogStream
setPresenceAndScanEventNumber_() : Ms2SpectrumStats
setPressure() : HPLC
setPrimaryID() : BaseFeature
setPrimaryIdentifier() : SpectralMatch
setPrimaryMSRunPath() : ConsensusMap , FeatureMap , ProteinIdentification
setPrintDuplicateReferences() : SequestInfile
setProcessingActions() : DataProcessing
setProduct() : ChromatogramSettings , ReactionMonitoringTransition
setProductCVTermList() : IncludeExcludeTarget
setProductMZ() : IncludeExcludeTarget , ReactionMonitoringTransition
setProducts() : SpectrumSettings
setProgress() : GUIProgressLoggerImpl , ProgressLogger::ProgressLoggerImpl , ProgressLogger
setProtein() : OSWData
setProteinAccession() : PeptideEvidence
setProteinIdentifications() : ConsensusMap , ExperimentalSettings , FeatureMap
setProteinMassFilter() : SequestInfile
setProteins() : TargetedExperiment
setProteinSectionRows() : MzTab
setPSIID() : DigestionEnzymeProtein
setPSIMODAccession() : ResidueModification
setPSMSectionRows() : MzTab
setPublications() : TargetedExperiment
setQuality() : BaseFeature , Feature
setQuantifyingTransition() : ReactionMonitoringTransition , LightTransition
setQuantMethod() : MassTrace
setQuantMethods() : AbsoluteQuantitation
setQuery() : ACTrieState
setQueryMass() : AccurateMassSearchResult
setQuerySpectra() : MascotRemoteQuery
setQvalue() : PeakGroup
setRange() : DimBase , DimIM , DimINT , DimMZ , DimRT , MRMFeatureFilter , Plot1DGoToDialog , Plot2DGoToDialog
setRank() : IdentificationHit , PeptideHit , ProteinHit
setRANSACParams() : MZTrafoModel
setRANSACSeed() : MZTrafoModel
setRatios() : ConsensusFeature
setRecycling() : TOPPASVertex
setReference() : FeatureGroupingAlgorithmUnlabeled , MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering
setReflectronState() : MassAnalyzer
setRegEx() : DigestionEnzyme
setRegExDescription() : DigestionEnzyme
setRemovePrecursorNearPeaks() : SequestInfile
setRepAbsCharge() : PeakGroup
setRequiredModules() : PythonModuleRequirement
setRequirementLevel() : CVMappingRule
setResidueSets() : Residue
setResiduesInUpperCase() : SequestInfile
setResolution() : IonDetector , MassAnalyzer
setResolutionMethod() : MassAnalyzer
setResolutionType() : MassAnalyzer
setRestrictions() : ListEditorDelegate
setRetentionTime() : IncludeExcludeTarget , ReactionMonitoringTransition
setRichText() : Annotation1DCaret< DataPoint >
setRightSplitter() : HistogramDialog , HistogramWidget
setRoundMasses() : CoarseIsotopePatternGenerator
setRowBounds() : LPWrapper
setRowName() : LPWrapper
setRT() : ChromatogramPeak , Mobilogram , MSSpectrum , Peak2D , PeptideIdentification , RetentionTime
setRTRange() : FeatureFileOptions , PeakFileOptions
setRunID() : OSWData
setSample() : ExperimentalSettings
setSamples() : BiGaussModel , EmgModel , ExtendedIsotopeModel , GaussModel , InterpolationModel , IsotopeModel
setSampleSection() : ExperimentalDesign
setSaveFileName() : TOPPASScene
setScale() : EuclideanSimilarity , LinearInterpolation< Key, Value >
setScale_0() : BilinearInterpolation< Key, Value >
setScale_1() : BilinearInterpolation< Key, Value >
setScalingFactor() : InterpolationModel
setScanDirection() : MassAnalyzer
setScanEventNumber_() : Ms2SpectrumStats
setScanLaw() : MassAnalyzer
setScanMode() : InstrumentSettings
setScanNumber() : PeakGroup
setScanRate() : MassAnalyzer
setScanRegExp_() : SpectrumLookup
setScanTime() : MassAnalyzer
setScanWindows() : InstrumentSettings
setScopePath() : CVMappingRule
setScore() : FeatureHypothesis , PeptideHit , ProteinHit
setScore_() : IDScoreGetterSetter
setScoreAndMoveIfTarget_() : IDScoreGetterSetter
setScoreHigherWorse_() : IDScoreGetterSetter
setScoreHigherWorseAndMoveIfTarget_() : IDScoreGetterSetter
setScores() : MRMFeature
setScores_() : IDScoreGetterSetter
setScoresAndRemoveDecoys_() : IDScoreGetterSetter
setScoresHigherWorse_() : IDScoreGetterSetter
setScoresHigherWorseAndRemoveDecoys_() : IDScoreGetterSetter
setScoreType() : PeptideIdentification , ProteinIdentification
setScoreType_() : IDScoreGetterSetter
setScoreTypeAndSettings_() : BayesianProteinInferenceAlgorithm
setSearchEngine() : ProteinIdentification
setSearchEngineVersion() : ProteinIdentification
setSearchParameters() : ProteinIdentification
setSecondaryIdentifier() : SpectralMatch
setSectionDescription() : Param
setSeed() : DecoyGenerator , RANSAC< TModelType > , UniqueIdGenerator
setSeeds() : FeatureFinderAlgorithm , FeatureFinderAlgorithmPicked
setSelected() : Annotation1DItem
setSelectedPen() : Annotations1DContainer
setSemiCleavage() : XTandemInfile
setSeparator() : MzTabStringList
setSequence() : IMSElement , NASequence , PeptideHit , ProteinHit
setSequenceHeaderFilter() : SequestInfile
setShowFragmentIons() : SequestInfile
setSideChainBasicity() : Residue
setSignificanceThreshold() : PeptideIdentification , ProteinIdentification
setSingleMass() : Adduct
setSize() : SaveImageDialog
setSizeOnly() : FeatureFileOptions , FeatureXMLHandler
setSizeRatio_() : SaveImageDialog
setSkipXMLChecks() : IndexedMzMLHandler , MzMLSpectrumDecoder , OnDiscMSExperiment , PeakFileOptions
setSmallMoleculeSectionRows() : MzTab
setSMILESString() : SpectralMatch
setSmoothedIntensities() : MassTrace
setSNR() : PeakGroup
setSoftware() : DataProcessing , Instrument , TargetedExperiment
setSortChromatogramsByRT() : PeakFileOptions
setSortSpectraByMZ() : PeakFileOptions
setSourceClassification() : ResidueModification
setSourceFeatureIndex() : AccurateMassSearchResult
setSourceFile() : ChromatogramSettings , SpectrumSettings
setSourceFiles() : ExperimentalSettings , TargetedExperiment
setSourceOutParam() : TOPPASEdge
setSourceVertex() : TOPPASEdge
setSpecificity() : EnzymaticDigestion
setSpecRef() : MzTabSpectraRef
setSpecRefFile() : MzTabSpectraRef
setSpectra() : InspectInfile , MSExperiment
setSpectraDataRef() : SpectrumMetaDataLookup
setSpectraProcessingFunc() : MSDataTransformingConsumer
setSpectrumIdentifications() : Identification
setSpectrumReference() : PeptideIdentification
setSqlRunID() : MSExperiment
setSqlSourceFile() : OSWData
setStandardEnzymeInfo_() : SequestInfile
setStart() : PeptideEvidence
setState() : Sample
setStatus() : MetaDataBrowser
setStrictFlag() : MRMFeatureFinderScoring
setStringDataArrays() : Mobilogram , MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
setSubordinates() : Feature
setSubsamples() : Sample
setSum() : BasicStatistics< RealT >
setSumFormula() : SpectralMatch
setSymbol() : Element
setSynonyms() : DigestionEnzyme , Residue , ResidueModification
setTabText() : EnhancedTabBar
setTabWidth() : FuzzyStringComparator
setTag() : SemanticValidator
setTagCount() : InspectInfile
setTargetCVTerms() : TargetedExperiment
setTargetDummyType() : FLASHDeconvAlgorithm , PeakGroup
setTargeted() : PeakGroup
setTargetInParam() : TOPPASEdge
setTargetMasses() : FLASHDeconvAlgorithm
setTargetMetaValue() : TargetedExperiment
setTargetVertex() : TOPPASEdge
setTaxon() : XTandemInfile
setTaxonomyFilename() : XTandemInfile
setTemperature() : HPLC
setTermName() : CVMappingTerm
setTermSpecificity() : ResidueModification , Ribonucleotide
setText() : Annotation1DItem
setTextBox() : Plot1DCanvas
setTextOffset() : Annotation1DVerticalLineItem
setThreeLetterCode() : Residue
setThreePrimeGain() : DigestionEnzymeRNA
setThreePrimeMod() : NASequence
setThreshold() : ClusterHierarchical , FineIsotopePatternGenerator
setTickLevel() : AxisWidget
setTicks() : Annotation1DDistanceItem
setTime() : DateTime
setTimeArray() : Chromatogram , OSChromatogram
setTitle() : PythonModuleRequirement
setToEnd_() : MatchedIterator< CONT_T, TRAIT, CONST_T >
setTOFTotalPathLength() : MassAnalyzer
setTool_() : ToolsDialog
setToolDescriptions() : ToolDescriptionHandler
setTopoNr() : TOPPASOutputVertex , TOPPASToolVertex , TOPPASVertex
setTopoSortMarked() : TOPPASVertex
setToString() : FuzzyStringComparator::InputLine
setTotalProbability() : FineIsotopePatternGenerator
setTransformationModel() : AbsoluteQuantitationMethod
setTransformationModelParams() : AbsoluteQuantitationMethod
setTransitionGroupID() : MRMTransitionGroup< ChromatogramType, TransitionType >
setTransitions() : TargetedExperiment
setType() : ListEditorDelegate , IonDetector , MassAnalyzer , SpectrumSettings
setTypeName() : ListEditorDelegate , ListEditor
setULOD() : AbsoluteQuantitationMethod
setULOQ() : AbsoluteQuantitationMethod
setUnassignedPeptideIdentifications() : ConsensusMap , FeatureMap
setUniModRecordId() : ResidueModification
setUniqueId() : UniqueIdInterface
setUnit() : CVTerm , DataValue , MetaInfoRegistry
setUnitAccessionAttribute() : SemanticValidator
setUnitNameAttribute() : SemanticValidator
setUnitType() : DataValue
setup() : SimpleSVM
setURL() : ContactPerson
setUrl() : NetworkGetRequest
setUsePPM() : CalibrationData
setUseTerm() : CVMappingTerm
setUseTermName() : CVMappingTerm
setValidFormats_() : TOPPBase
setValidStrings() : Param
setValidStrings_() : TOPPBase
setValue() : CVTerm , DistanceMatrix< Value > , Matrix< Value > , MetaInfo , MzTabParameter , Param
setValueAttribute() : SemanticValidator
setValueFromFile() : DigestionEnzyme , DigestionEnzymeProtein , DigestionEnzymeRNA
setValueQuick() : DistanceMatrix< Value >
setVariance() : BasicStatistics< RealT >
setVendor() : Instrument
setVerbose() : TVToolDiscovery
setVerboseLevel() : FuzzyStringComparator
setVersion() : Software
setVisibleArea() : PlotCanvas
setVisibleArea1D() : TVIdentificationViewController
setVisibleAreaX() : PlotCanvas
setVisibleAreaY() : PlotCanvas
setVolume() : Sample
setWhitelist() : FuzzyStringComparator
setWidgetsfromFDDefaultParam_() : FLASHDeconvTabWidget
setWidth() : BaseFeature , FeatureHandle
setWriteIndex() : PeakFileOptions
setWriteSupplementalData() : PeakFileOptions
setX() : DPosition< D, TCoordinateType >
setXLabel() : Plot3DOpenGLCanvas
setXTandemID() : DigestionEnzymeProtein
setY() : DPosition< D, TCoordinateType >
setYLabel() : Plot3DOpenGLCanvas
setZLabel() : Plot3DOpenGLCanvas
setZoomScan() : InstrumentSettings
shape() : TOPPASEdge , TOPPASVertex
shared_xerces_ptr() : shared_xerces_ptr< T >
shift() : RangeBase
shiftedIonsToString() : RNPxlFragmentAnnotationHelper
shiftedToPHFA() : RNPxlFragmentAnnotationHelper
shortDimensionName() : MobilityPeak2D , Peak2D
shortDimensionNameIM() : MobilityPeak2D
shortDimensionNameMZ() : MobilityPeak2D , Peak2D
shortDimensionNameRT() : Peak2D
shortDimensionUnit() : MobilityPeak2D , Peak2D
shortDimensionUnitIM() : MobilityPeak2D
shortDimensionUnitMZ() : MobilityPeak2D , Peak2D
shortDimensionUnitRT() : Peak2D
show() : EnhancedTabBar
showAboutDialog() : FLASHDeconvWizardBase , QApplicationTOPP , SwathWizardBase , TOPPASBase
showAllHits_() : MetaDataBrowser
showAsWindow_() : TOPPASBase
showChromatograms() : TVDIATreeTabController
showChromatogramsAsNew1D() : DataSelectionTabs , Plot2DCanvas , Plot2DWidget , SpectraTreeTab , TVDIATreeTabController , TVSpectraViewController
showChromatogramsInCanvas_() : TVDIATreeTabController
showContextMenu() : HistogramWidget
showCurrentLayerPreferences() : Plot1DCanvas , Plot2DCanvas , Plot3DCanvas , PlotCanvas
showCurrentPeaksAs2D() : Plot1DCanvas , Plot1DWidget , Plot3DCanvas , Plot3DWidget , TOPPViewBase
showCurrentPeaksAs3D() : Plot1DCanvas , Plot1DWidget , Plot2DCanvas , Plot2DWidget , TOPPViewBase
showCurrentPeaksAsDIA() : Plot1DCanvas , Plot1DWidget , TOPPViewBase
showCurrentPeaksAsIonMobility() : Plot1DCanvas , Plot1DWidget , Plot2DCanvas , Plot2DWidget , TOPPViewBase
showCursorStatus() : TOPPASBase , TOPPViewBase
showDetails_() : MetaDataBrowser
showDocumentation() : ParamEditor
showFileDialog() : InputFile , InputFileList , OutputDirectory , TOPPASOutputFilesDialog
showFileDialog_() : PythonSelector
showFilesDialog() : TOPPASInputFileListVertex
showGoToDialog() : Plot1DWidget , Plot2DWidget , Plot3DWidget , PlotWidget , TOPPViewBase
showGridLines() : PlotCanvas
showIntensityDistribution() : PlotWidget
showIOMappingDialog() : TOPPASEdge
showLegend() : AxisWidget , Plot1DWidget , Plot3DCanvas , Plot3DWidget , PlotWidget
showMetaData() : PlotCanvas
showMetaDistribution() : PlotWidget
showPipelineFinishedLogMessage() : TOPPASBase
showPlotWidgetInWindow() : TOPPViewBase
showPreferences() : TOPPViewBase
showProjections() : Plot2DCanvas
showProjections_() : Plot2DWidget
showRange() : Plot2DGoToDialog
showSpectrumAlignmentDialog() : TOPPViewBase
showSpectrumAsNew1D() : DataSelectionTabs , Plot2DCanvas , Plot2DWidget , SpectraTreeTab , TVIdentificationViewController , TVSpectraViewController
showSpectrumBrowser() : TOPPViewBase
showSpectrumGenerationDialog() : TOPPViewBase
showSpectrumMetaData() : SpectraTreeTab , TOPPViewBase
showSplitters() : HistogramWidget
showStatistics() : PlotWidget
showStatusMessage() : TOPPASBase , TOPPViewBase
showTOPPDialog() : TOPPViewBase
showTOPPDialog_() : TOPPViewBase
showURL() : TOPPASBase
showWindow() : TOPPViewBase
shufflePeptide() : MRMDecoy
shufflePeptides() : DecoyGenerator
SignalToNoiseEstimator() : SignalToNoiseEstimator< Container >
SignalToNoiseEstimatorMeanIterative() : SignalToNoiseEstimatorMeanIterative< Container >
SignalToNoiseEstimatorMedian() : SignalToNoiseEstimatorMedian< Container >
SignalToNoiseEstimatorMedianRapid() : SignalToNoiseEstimatorMedianRapid
SignalToNoiseOpenMS() : SignalToNoiseOpenMS< ContainerT >
simpleExtractChromatograms_() : OpenSwathCalibrationWorkflow
simpleFindBestFeature() : OpenSwathHelper
SimplePeak() : SimpleTSGXLMS::SimplePeak
SimpleSearchEngineAlgorithm() : SimpleSearchEngineAlgorithm
SimpleSVM() : SimpleSVM
SimpleTSGXLMS() : SimpleTSGXLMS
simplify() : String
simpson_() : PeakIntegrator
simulateNoReRanking() : DBSuitability::SuitabilityData
SingleLinkage() : SingleLinkage
SiriusExportAlgorithm() : SiriusExportAlgorithm
SiriusTargetDecoySpectra() : SiriusFragmentAnnotation::SiriusTargetDecoySpectra
size() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , AASequence , CalibrationData , ConsensusFeature , ConstRefVector< ContainerT > , DataFilters , DeconvolvedSpectrum , DPosition< D, TCoordinateType > , ExposedVector< VectorElement > , FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector > , FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern , HashGrid< Cluster > , IMSAlphabet , IMSIsotopeDistribution , Weights , IsotopeDistribution , KDTreeFeatureMaps , Histogram< ValueType, BinSizeType > , Mobilogram , MRMFeatureOpenMS , MRMTransitionGroup< ChromatogramType, TransitionType > , MSExperiment , MultiGradient , MultiplexFilteredMSExperiment , MultiplexFilteredPeak , NASequence , OnDiscMSExperiment , Param::ParamNode , Param , PeakGroup , QCBase::SpectraMap , QTCluster , SplineInterpolatedPeaks , StringView , TOPPASVertex::TOPPASFilenames , TransitionGroupOpenMS< SpectrumT, TransitionT > , IMRMFeature , ITransitionGroup , MockMRMFeature , MockTransitionGroup
sizeHint() : ColorSelector
sizeProfile() : MultiplexFilteredPeak
SizeUnderflow() : SizeUnderflow
smartFileNames_() : TOPPASToolVertex
smoothData() : ElutionPeakDetection , LowessSmoothing
snapShot_() : StopWatch
snapToGrid() : TOPPASScene
Software() : Software
SoftwareVisualizer() : SoftwareVisualizer
solve() : BSpline2d , LPWrapper , NonNegativeLeastSquaresSolver
solveNNLS_() : IsobaricIsotopeCorrector
SolverParam() : LPWrapper::SolverParam
somethingHasChanged() : TOPPASEdge , TOPPASVertex
sort() : DeconvolvedSpectrum , ROCCurve , MSSpectrum , PeakGroup , PeptideIdentification , ProteinIdentification
sort_() : ExperimentalDesign , IsotopeDistribution
sortByComparator() : ConstRefVector< ContainerT >
sortByIntensity() : ConsensusMap , ConstRefVector< ContainerT > , FeatureMap , IsotopeDistribution , Mobilogram , MSChromatogram , MSSpectrum
sortByIonMobility() : MSSpectrum
sortByMaps() : ConsensusMap
sortByMass() : IsotopeDistribution
sortByMZ() : ConsensusMap , FeatureMap
sortByNames() : IMSAlphabet
sortByOverallQuality() : FeatureMap
sortByPosition() : ConsensusMap , ConstRefVector< ContainerT > , FeatureMap , Mobilogram , MSChromatogram , MSSpectrum
sortByPositionPresorted() : MSSpectrum
sortByPrecursorInt() : MetaboTargetedAssay
sortByQscore() : DeconvolvedSpectrum
sortByQuality() : ConsensusMap
sortByRank() : PeptideIdentification
sortByRT() : CalibrationData , ConsensusMap , FeatureMap
sortBySize() : ConsensusMap
sortByUnique_() : ProteinInference
sortByValues() : IMSAlphabet
sortChromatograms() : MSExperiment
SortExtractionCoordinatesByMZ() : ChromatogramExtractorAlgorithm::ExtractionCoordinates
SortExtractionCoordinatesReverseByMZ() : ChromatogramExtractorAlgorithm::ExtractionCoordinates
sortPeptideIdentifications() : BaseFeature
sortPeptideIdentificationsByMapIndex() : ConsensusMap
sortPSM_() : MzTabFile
sortSpectra() : MSExperiment
sortSpectrumByMZ() : SpectrumAddition
sortTransitionsByName() : TargetedExperiment
sortTransitionsByProductMZ() : TargetedExperiment
SourceFile() : SourceFile
SourceFileVisualizer() : SourceFileVisualizer
sourceHasChanged() : TOPPASEdge
spatiallyGreaterEqual() : DPosition< D, TCoordinateType >
spatiallyLessEqual() : DPosition< D, TCoordinateType >
SpecArrayFile() : SpecArrayFile
SpectraDistance_() : SpectraMerger::SpectraDistance_
SpectraIDViewTab() : SpectraIDViewTab
SpectralMatch() : SpectralMatch
SpectraMap() : QCBase::SpectraMap
SpectraMerger() : SpectraMerger
spectrastAnnotationExtract() : TransitionTSVFile
spectrastRTExtract() : TransitionTSVFile
SpectraSTSimilarityScore() : SpectraSTSimilarityScore
SpectraTreeTab() : SpectraTreeTab
Spectrum() : Spectrum
SpectrumAccessOpenMS() : SpectrumAccessOpenMS
SpectrumAccessOpenMSCached() : SpectrumAccessOpenMSCached
SpectrumAccessOpenMSInMemory() : SpectrumAccessOpenMSInMemory
SpectrumAccessQuadMZTransforming() : SpectrumAccessQuadMZTransforming
SpectrumAccessSqMass() : SpectrumAccessSqMass
SpectrumAccessTransforming() : SpectrumAccessTransforming
SpectrumAlignment() : SpectrumAlignment
SpectrumAlignmentDialog() : SpectrumAlignmentDialog
SpectrumAlignmentScore() : SpectrumAlignmentScore
SpectrumAnnotator() : SpectrumAnnotator
SpectrumCheapDPCorr() : SpectrumCheapDPCorr
spectrumContextMenu_() : SpectraTreeTab
SpectrumCount() : SpectrumCount
spectrumDeselected() : SpectraIDViewTab
spectrumDoubleClicked() : SpectraTreeTab
SpectrumIdentification() : SpectrumIdentification
SpectrumLookup() : SpectrumLookup
SpectrumMeta() : SpectrumMeta
SpectrumMetaData() : SpectrumMetaDataLookup::SpectrumMetaData
SpectrumMetaDataLookup() : SpectrumMetaDataLookup
SpectrumPrecursorComparator() : SpectrumPrecursorComparator
spectrumSearchText_() : DIATreeTab , SpectraTreeTab
spectrumSelected() : SpectraIDViewTab , SpectraTreeTab
SpectrumSettings() : SpectrumSettings
SpectrumSettingsVisualizer() : SpectrumSettingsVisualizer
SplineInterpolatedPeaks() : SplineInterpolatedPeaks
SplinePackage() : SplinePackage
split() : ConsensusMap , String
split_quoted() : String
splitByFAIMSCV() : IMDataConverter
splitByMiddle() : XQuestResultXMLHandler
splitByNth() : XQuestResultXMLHandler
splitExperimentByIonMobility() : IMDataConverter
splitModificationBySpecifiedAA() : MascotXMLHandler
splitTransitionGroupsDetection_() : MRMFeatureFinderScoring
splitTransitionGroupsIdentification_() : MRMFeatureFinderScoring
SqliteConnector() : SqliteConnector
SqlOperationFailed() : SqlOperationFailed
SqMassFile() : SqMassFile
sqrt2pi() : BasicStatistics< RealT >
SqrtScaler() : SqrtScaler
squared_difference_counted() : squared_difference_counted< _Tp, _Dist >
StablePairFinder() : StablePairFinder
stairsInterpolation() : MultiGradientSelector
standard_stddev() : mean_and_stddev
standard_variance() : mean_and_stddev
start() : FakeProcess , StopWatch
start_vertex() : IDBoostGraph::dfs_ccsplit_visitor
startElement() : CVMappingFile , IdXMLFile , ConsensusXMLHandler , FeatureXMLHandler , MascotXMLHandler , MzDataHandler , MzIdentMLHandler , MzMLHandler , MzMLValidator , MzXMLHandler , ParamXMLHandler , PTMXMLHandler , SemanticValidator , ToolDescriptionHandler , TraMLHandler , UnimodXMLHandler , XMLHandler , XQuestResultXMLHandler , OMSSAXMLFile , PepXMLFile , PepXMLFileMascot , ProtXMLFile , QcMLFile , TransformationXMLFile , XTandemXMLFile
startPos() : TOPPASEdge
startProgress() : GUIProgressLoggerImpl , ProgressLogger::ProgressLoggerImpl , ProgressLogger
static_for_each_base_() : RangeManager< RangeBases >
Statistics() : PeptideAndProteinQuant::Statistics
statistics_() : FeatureFinderIdentificationAlgorithm
stddev() : mean_and_stddev
SteinScottImproveScore() : SteinScottImproveScore
stepMaster_() : ACTrie
stepSpawn_() : ACTrie
stop() : StopWatch
store() : AbsoluteQuantitationMethodFile , AcquisitionInfoVisualizer , AcquisitionVisualizer , BaseVisualizerGUI , CachedmzML , ConsensusXMLFile , ContactPersonVisualizer , CsvFile , DataProcessingVisualizer , DocumentIdentifierVisualizer , DTA2DFile , DTAFile , EDTAFile , ExperimentalSettingsVisualizer , FASTAFile , FeatureXMLFile , GNPSMetaValueFile , GNPSMGFFile , GNPSQuantificationFile , GradientVisualizer , HPLCVisualizer , IBSpectraFile , IdXMLFile , IndexedMzMLFileLoader , InspectInfile , InstrumentSettingsVisualizer , InstrumentVisualizer , OMSFileStore , IonDetectorVisualizer , IonSourceVisualizer , KroenikFile , MascotGenericFile , MassAnalyzerVisualizer , MetaInfoDescriptionVisualizer , MetaInfoVisualizer , MRMFeatureQCFile , MsInspectFile , MSPFile , MSPGenericFile , MzDataFile , MzIdentMLFile , MzMLFile , MzQCFile , MzTabFile , MzTabMFile , MzXMLFile , OMSFile , ParamCTDFile , ParamCWLFile , ParamEditor , ParamJSONFile , ParamXMLFile , PepNovoInfile , PeptideHitVisualizer , PeptideIdentificationVisualizer , PepXMLFile , PercolatorInfile , PrecursorVisualizer , ProductVisualizer , ProteinHitVisualizer , ProteinIdentificationVisualizer , ProtXMLFile , PTMXMLFile , QcMLFile , SampleVisualizer , ScanWindowVisualizer , SequestInfile , SiriusMSFile , SoftwareVisualizer , SourceFileVisualizer , SpecArrayFile , SpectrumSettingsVisualizer , SqMassFile , TextFile , ToolDescriptionFile , TOPPASResources , TOPPASScene , TraMLFile , TransformationXMLFile , XMassFile , XQuestResultXMLFile , CSVWriter , DataMatrix , IDataFrameWriter
storeAdducts_() : OMSFileStore
storeAppliedProcessingStep_() : OMSFileStore
storeBaseFeature_() : OMSFileStore
storeBuffer() : MzMLFile
storeConsensusColumnHeaders_() : OMSFileStore
storeConsensusFeatures() : FileHandler
storeConsensusFeatures_() : OMSFileStore
storeCVTerm_() : OMSFileStore
storeDataProcessing_() : OMSFileStore
storeDBSearchParams_() : OMSFileStore
storeElements_() : ElementDB
storeExperiment() : FileHandler
storeFeatureAndSubordinates_() : OMSFileStore
storeFeatures() : FileHandler
storeFeatures_() : OMSFileStore
storeFullCM() : LayerStoreDataConsensusMapAll
storeFullData() : LayerData1DChrom , LayerData1DIonMobility , LayerData1DPeak , LayerDataBase , LayerDataChrom , LayerDataConsensus , LayerDataFeature , LayerDataIdent , LayerDataIonMobility , LayerDataPeak
storeFullExperiment() : LayerStoreDataPeakMapAll
storeFullFM() : LayerStoreDataFeatureMapAll
storeFullIdent() : LayerStoreDataIdentAll
storeIdentifications() : FileHandler
storeIdentifiedCompounds_() : OMSFileStore
storeIdentifiedSequences_() : OMSFileStore
storeInformationFromDeconvolvedSpectrum() : MassFeatureTrace
storeINI_() : ToolsDialog , TOPPASToolConfigDialog
storeInputFiles_() : OMSFileStore
storeISO() : MSstatsFile
storeIsotopes_() : ElementDB
storeJSON() : SwathQC
storeLFQ() : MSstatsFile , TriqlerFile
storeMapMetaData_() : OMSFileStore
storeMetaInfo_() : OMSFileStore
storeMetaInfos_() : OMSFileStore
storeObservationMatches_() : OMSFileStore
storeObservations_() : OMSFileStore
storeOriginalRT_() : MapAlignmentTransformer
storeParentGroupSets_() : OMSFileStore
storeParentMatches_() : OMSFileStore
storeParentSequences_() : OMSFileStore
storePeptideReliabilityColumn() : MzTabFile
storePeptideUriColumn() : MzTabFile
storeProcessingSoftwares_() : OMSFileStore
storeProcessingSteps_() : OMSFileStore
storeProteinGoTerms() : MzTabFile
storeProteinReliabilityColumn() : MzTabFile
storeProteinUriColumn() : MzTabFile
storePSMReliabilityColumn() : MzTabFile
storePSMUriColumn() : MzTabFile
storeQC() : FileHandler
storeRecursive_() : ParamEditor
storeRotationAndZoom() : Plot3DOpenGLCanvas
storeScoredProcessingResults_() : OMSFileStore
storeScoreTypes_() : OMSFileStore
storeSmallMoleculeReliabilityColumn() : MzTabFile
storeSmallMoleculeUriColumn() : MzTabFile
storeSpectraMSP() : TargetedSpectraExtractor
storeSpectrum() : FileHandler
storeSpectrum_() : FIAMSDataProcessor
storeTIC() : DTA2DFile
storeTransformations() : FileHandler
storeTransitions() : FileHandler
storeVersionAndDate_() : OMSFileStore
storeVisibleChromatogram() : LayerStoreDataPeakMapVisible
storeVisibleCM() : LayerStoreDataConsensusMapVisible
storeVisibleData() : LayerData1DChrom , LayerData1DIonMobility , LayerData1DPeak , LayerDataBase , LayerDataChrom , LayerDataConsensus , LayerDataFeature , LayerDataIdent , LayerDataIonMobility , LayerDataPeak
storeVisibleExperiment() : LayerStoreDataPeakMapVisible
storeVisibleFM() : LayerStoreDataFeatureMapVisible
storeVisibleIdent() : LayerStoreDataIdentVisible
storeVisibleSpectrum() : LayerStoreDataPeakMapVisible
StreamElement_() : FuzzyStringComparator::StreamElement_
streamEnd() : Bzip2Ifstream , GzipIfstream
StreamHandler() : StreamHandler
StreamStruct() : LogStreamBuf::StreamStruct
String() : String
stringListToIsotopeCorrectionMatrix_() : IsobaricQuantitationMethod
StringListUtils() : StringListUtils
StringManager() : StringManager
stringSimdDecoder_() : Base64
stringSimdEncoder_() : Base64
StringView() : StringView
stripExtension() : FileHandler
subset() : MRMTransitionGroup< ChromatogramType, TransitionType >
subsetDependent() : MRMTransitionGroup< ChromatogramType, TransitionType >
substitute() : String
substr() : String , StringView
suffix() : Param::ParamNode , String
sum() : BasicStatistics< RealT >
sumIntensity_() : MSstatsFile , TriqlerFile
Summary() : Summary
SummaryStatistics() : SummaryStatistics< T >
supportMax() : LinearInterpolation< Key, Value >
supportMax_0() : BilinearInterpolation< Key, Value >
supportMax_1() : BilinearInterpolation< Key, Value >
supportMin() : LinearInterpolation< Key, Value >
supportMin_0() : BilinearInterpolation< Key, Value >
supportMin_1() : BilinearInterpolation< Key, Value >
SVOutStream() : SVOutStream
swap() : ConsensusMap , ConstRefVector< ContainerT > , DocumentIdentifier , DPosition< D, TCoordinateType > , FeatureMap , Gravitator , IdentificationData , Weights , unique_xerces_ptr< T > , MetaInfoInterface , Mobilogram , MSExperiment , PeakGroup , UniqueIdIndexer< T > , UniqueIdInterface
swapDimensions() : DRange< D >
swapExtension() : FileHandler
swapFeaturesOnly() : FeatureMap
SwathLibraryStats() : SwathLibraryStats
SwathMap() : SwathMap
SwathMapMassCorrection() : SwathMapMassCorrection
SwathQC() : SwathQC
SwathTabWidget() : SwathTabWidget
SwathWizardBase() : SwathWizardBase
switchBackScoreType() : IDScoreSwitcherAlgorithm
switchKR() : MRMDecoy
switchOrientation_() : SpectraIDViewTab
switchScores() : IDScoreSwitcherAlgorithm
switchToGeneralScoreType() : IDScoreSwitcherAlgorithm
switchToScoreType() : IDScoreSwitcherAlgorithm
sync() : LogStreamBuf
sync_() : RecentFilesMenu
synchronizePeakAnnotations() : LayerData1DPeak
syncLF_() : LogStreamBuf