- s -

• safeParse_() : MzMLFile
• sameNrOfMSFilesPerFraction() : ExperimentalDesign
• Sample() : Sample
• sample_stddev() : mean_and_stddev
• sample_variance() : mean_and_stddev
• samplePeptideModel1D_() : RawMSSignalSimulation
• samplePeptideModel2D_() : RawMSSignalSimulation
• SampleSection() : ExperimentalDesign::SampleSection
• sampleTheCMarrWavelet_() : IsotopeWaveletTransform< PeakType >
• SampleTreatment() : SampleTreatment
• SampleVisualizer() : SampleVisualizer
• sanityCheck_() : TOPPASScene
• save_() : XMLFile
• saveAll_() : MetaDataBrowser
• saveAsImage() : Spectrum1DWidget , SpectrumWidget
• saveCurrentLayer() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas
• saveCurrentPipelineAs() : TOPPASBase
• saveFile() : INIFileEditorWindow
• saveFileAs() : INIFileEditorWindow
• saveIDs_() : SpectraIdentificationViewWidget
• saveIfChanged() : TOPPASScene
• SaveImageDialog() : SaveImageDialog
• saveLayerAll() : TOPPViewBase
• saveLayerVisible() : TOPPViewBase
• saveMe() : TOPPASScene
• saveModel() : SVMWrapper
• savePipeline() : TOPPASBase
• savePipelineAs() : TOPPASBase
• savePipelineResourceFile() : TOPPASBase
• savePreferences() : TOPPASBase , TOPPViewBase
• savePreprocessedDB_() : PrecursorIonSelectionPreprocessing
• savePreprocessedDBWithRT_() : PrecursorIonSelectionPreprocessing
• saveToClipboard() : TOPPASBase
• SavitzkyGolayFilter() : SavitzkyGolayFilter
• scale_() : AxisPainter
• scaleData() : SVMWrapper
• scaleData_() : SimpleSVM
• scaleDescriptorSet_() : SvmTheoreticalSpectrumGenerator
• scaledIntensity_() : Spectrum3DOpenGLCanvas
• scaledInversMZ_() : Spectrum3DOpenGLCanvas
• scaledInversRT_() : Spectrum3DOpenGLCanvas
• scaledMZ_() : Spectrum3DOpenGLCanvas
• scaledRT_() : Spectrum3DOpenGLCanvas
• Scaler() : Scaler
• scaleSingleFeature_() : SvmTheoreticalSpectrumGenerator
• ScanEvent() : Ms2SpectrumStats::ScanEvent
• ScanWindow() : ScanWindow
• ScanWindowVisualizer() : ScanWindowVisualizer
• score() : DiaPrescore
• score_with_isotopes() : DIAScoring
• scoreAllChromatograms_() : OpenSwathWorkflow
• scoreAssay_() : ConfidenceScoring
• scoreCalculation_() : MapAlignmentAlgorithmSpectrumAlignment
• ScoredProcessingResult() : ScoredProcessingResult
• scoreETDFeatures_() : CompNovoIonScoring
• scoreFeature_() : ConfidenceScoring
• scoreHullpoints() : MasstraceCorrelator
• scoreIdentification_() : MRMFeatureFinderScoring
• scoreIsotopePattern_() : DIAScoring
• scoreIsotopes() : CompNovoIonScoringBase
• scoreIsotopes_() : CompNovoIonScoringBase
• scoreMap() : ConfidenceScoring
• scoreMZ_() : FeatureFindingMetabo
• scoreMZByExpectedMean_() : FeatureFindingMetabo
• scoreMZByExpectedRange_() : FeatureFindingMetabo
• scorePeakgroups() : MRMFeatureFinderScoring
• scoreRT_() : FeatureFindingMetabo
• scoreSpectra() : CompNovoIonScoring , TargetedSpectraExtractor
• scoreSpectrum() : CompNovoIonScoringCID
• scoreThis_() : IsotopeWaveletTransform< PeakType >
• ScoreType() : ScoreType
• scoreWitnessSet_() : CompNovoIonScoring , CompNovoIonScoringBase , CompNovoIonScoringCID
• scoring_() : MapAlignmentAlgorithmSpectrumAlignment
• search() : SimpleSearchEngineAlgorithm
• search_AC_pattern() : MS2Info
• searchAndShow_() : SpectraViewWidget
• searchInScan_() : TwoDOptimization
• searchMass_() : AccurateMassSearchEngine
• searchModifications() : ModificationsDB
• searchModificationsByDiffMonoMass() : ModificationsDB
• searchModificationsFast() : ModificationsDB
• searchNextCell_() : HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator
• SearchParameters() : ProteinIdentification::SearchParameters
• searchPrefix() : StringListUtils
• searchSuffix() : StringListUtils
• SeedListGenerator() : SeedListGenerator
• seekGToSavedPosition() : FuzzyStringComparator::InputLine
• select() : MSSpectrum
• selectAll() : Annotations1DContainer
• selectChromHelper_() : MRMTransitionGroupPicker
• selectCompoundsForBatch_() : OpenSwathWorkflow
• selected() : ParamTree
• selectFragments() : MRMFragmentSelection
• selectionChanged() : ParamTree
• selectionCopied() : TOPPASScene
• selectItemAt() : Annotations1DContainer
• selectMRMFeature() : MRMFeatureSelector
• SelectorParameters() : MRMFeatureSelector::SelectorParameters
• selectPivotIons_() : CompNovoIdentificationBase
• selectSpectra() : TargetedSpectraExtractor
• selectSwathTransitions() : OpenSwathHelper
• SemanticValidator() : SemanticValidator
• sendClipboardContent() : TOPPASBase
• sendCursorStatus() : SpectrumCanvas , SpectrumWidget , TOPPASWidget
• sendStatus() : BaseVisualizerGUI
• sendStatusMessage() : SpectrumCanvas , SpectrumWidget , TOPPASWidget
• sequence() : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_
• SequenceIdentity_() : DecoyGenerator
• sequenceMatches() : FASTAFile::FASTAEntry
• SequestInfile() : SequestInfile
• SequestOutfile() : SequestOutfile
• set() : CentroidData , Date , DateTime , GlobalExceptionHandler , FilterList , IsotopeDistribution , MzTabBoolean , MzTabDouble , MzTabDoubleList , MzTabInteger , MzTabIntegerList , MzTabModificationList , MzTabParameterList , MzTabString , MzTabStringList , NASequence , RawData , TOPPASVertex::TOPPASFilenames
• set2DData() : MSExperiment
• set_AC() : MS2Info
• set_alignment_error_down() : SHFeature
• set_alignment_error_up() : SHFeature
• set_apex_peak_intensity() : SHFeature
• set_apex_retention_time() : LCElutionPeak
• set_charge_state() : SHFeature
• set_CHRG() : MS2Info
• set_Chrg() : MSPeak
• set_chromatogram_flag() : LayerData
• set_DELTA_CN() : MS2Info
• set_end_retention_time() : LCElutionPeak
• set_feature_ID() : SHFeature
• set_feature_match_status() : SHFeature
• set_FEATURE_PI() : SHFeature
• set_FULL_SQ() : MS2Info
• set_high_bound() : _Region< __K, _Val, _SubVal, _Acc, _Cmp >
• set_low_bound() : _Region< __K, _Val, _SubVal, _Acc, _Cmp >
• set_MASTER_ID() : LCMS , SHFeature
• set_MONO_MZ() : MS2Info
• set_MS2_TYPE_TAG() : MS2Info
• set_MZ() : SHFeature
• set_MZ_END() : SHFeature
• set_MZ_START() : SHFeature
• set_NEUTRAL_MR() : MS2Info
• set_peak_area() : SHFeature
• set_peak_score() : SHFeature
• set_PEP_PROB() : MS2Info
• set_PREV_AA() : MS2Info
• set_raw_MZ() : SHFeature
• set_raw_retention_time_apex() : SHFeature
• set_retention_time() : MSPeak , SHFeature
• set_retention_time_END() : SHFeature
• set_retention_time_START() : SHFeature
• set_SCAN_END() : MS2Info
• set_scan_end() : SHFeature
• set_scan_number() : SHFeature
• set_SCAN_START() : MS2Info
• set_scan_start() : SHFeature
• set_SCORE_HOLDER() : SHFeature
• set_spec_name() : LCMS
• set_spectrum_ID() : LCMS , SHFeature
• set_SQ() : MS2Info
• set_start_retention_time() : LCElutionPeak
• set_target_file() : FTPeakDetectController
• set_THEO_MASS_from_SQ() : MS2Info
• set_XCORR() : MS2Info
• setAAAfter() : PeptideEvidence
• setAABefore() : PeptideEvidence
• setAbsolute() : FineIsotopePatternGenerator
• setAcceptableAbsolute() : FuzzyStringComparator
• setAcceptableRelative() : FuzzyStringComparator
• setAccession() : CVMappingTerm , CVTerm , MzTabParameter , ProteinHit
• setAccessionAttribute() : SemanticValidator
• setAccuracy() : MassAnalyzer
• setAcquisitionInfo() : ChromatogramSettings , SpectrumSettings
• setAcquisitionMode() : IonDetector
• setActionMode() : TOPPASScene
• setActivationEnergy() : Precursor
• setActivationMethods() : Precursor
• setActive() : ChargePair , DataFilters
• setADCSamplingFrequency() : IonDetector
• setAdditionalContextMenu() : SpectrumCanvas
• setAddress() : ContactPerson
• setAdductBase() : MassExplainer
• setAffectedAminoAcids() : Modification
• setAllowChildren() : CVMappingTerm
• setAllowedThreads() : TOPPASScene
• setAllowIsotopeError() : XTandemInfile
• setAllowShortNumbers() : AxisWidget
• setAlwaysAppendData() : PeakFileOptions
• setAmount() : Adduct
• setAnalysisResults() : PeptideHit
• setAnalysisSummaryQuantType() : MSQuantifications
• setAtomicNumber() : Element
• setAverageMass() : ResidueModification
• setAverageWeight() : Element , Residue
• setAvgMass() : Ribonucleotide
• setAxisBounds() : AxisWidget
• setBackboneBasicityLeft() : Residue
• setBackboneBasicityRight() : Residue
• setBackgroundNoiseLevel() : SHFeature
• setBaselossFormula() : Ribonucleotide
• setBaseName() : PeptideIdentification
• setBiologicalRngSeed() : SimRandomNumberGenerator
• setBlind() : InspectInfile
• setBoundary() : MascotInfile
• setC13MassError() : DeconvPeak
• setCalculatedMassToCharge() : IdentificationHit
• setCalculatedMZ() : AccurateMassSearchResult
• setCallbacks() : ExternalProcess , ExternalProcessMBox
• setCanvas_() : SpectrumWidget
• setCastValue_() : AbsoluteQuantitationMethodFile , MRMFeaturePickerFile
• setCentroidSD() : MassTrace
• setChanged() : TOPPASScene
• setCharge() : AccurateMassSearchResult , Adduct , BaseFeature , ChargePair , DeconvPeak , EmpiricalFormula , FeatureHandle , FeatureHypothesis , IdentificationHit , OptimizePeakDeconvolution , PeptideHit , Precursor
• setCharges() : MascotInfile
• setChargeState() : PeptideCompound , TraMLProduct , LightCompound
• setChecksum() : SourceFile
• setCheckTermValueTypes() : SemanticValidator
• setCheckUnits() : SemanticValidator
• setChromatogramProcessingFunc() : MSDataTransformingConsumer
• setChromatograms() : MSExperiment
• setChromatogramType() : ChromatogramSettings
• setCleavage() : MascotInfile
• setCleavageSite() : XTandemInfile
• setClipboard() : TOPPASScene
• setCode() : Ribonucleotide
• setCoefficientLimits() : MZTrafoModel
• setCoefficients() : MZTrafoModel
• setColor() : Annotation1DCaret , Annotation1DPeakItem , ColorSelector , TOPPASEdge
• setColumn() : HPLC
• setColumnBounds() : LPWrapper
• setColumnHeaders() : ConsensusMap
• setColumnName() : LPWrapper
• setColumnType() : LPWrapper
• setCombinationsLogic() : CVMappingRule
• setCometID() : DigestionEnzymeProtein
• setComment() : ChromatogramSettings , ExperimentalSettings , HPLC , Sample , SampleTreatment , SpectrumSettings
• setCommentRows() : MzTab
• 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
• setConsensusMaps() : MSQuantifications
• setContactInfo() : ContactPerson
• setContacts() : ExperimentalSettings , TargetedExperiment
• setConvexHulls() : Feature
• setCorrelationCoefficient() : AbsoluteQuantitationMethod
• setCoverage() : ProteinHit
• setCreationDate() : Identification
• setCruxID() : DigestionEnzymeProtein
• setCTermGain() : DigestionEnzymeProtein
• setCTerminalModification() : AASequence
• setCurrentId() : EnhancedTabBar , TOPPASTabBar
• setCurrentLayerParameters() : SpectrumCanvas
• setCurrentLayerPeakPenStyle() : Spectrum1DCanvas
• setCurrentProcessingStep() : IdentificationData
• setCurrentSpectrumIndex() : LayerData
• setCustomizations() : Instrument
• setCutOff() : BaseModel< D >
• setCutsAfterRegEx() : DigestionEnzymeRNA
• setCutsBeforeRegEx() : DigestionEnzymeRNA
• setCVIdentifierRef() : CVMappingTerm , CVTerm
• setCVLabel() : MzTabParameter
• setCVReferences() : CVMappings
• setCVs() : TargetedExperiment
• setCVTerms() : CVMappingRule , CVTermList , CVTermListInterface
• setCWD() : InputFile , InputFileList
• setData() : FeatureFinderAlgorithm , BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value >
• setDatabase() : SequestInfile
• setDataPoints() : TransformationDescription
• setDataProcessing() : ChromatogramSettings , ConsensusMap , FeatureMap , MetaInfoDescription , SpectrumSettings
• setDataProcessingList() : MSQuantifications
• setDate() : DateTime
• setDateTime() : ExperimentalSettings , ProteinIdentification
• setDb() : InspectInfile
• setDB() : MascotInfile
• setDecoyTransitionType() : ReactionMonitoringTransition
• setDefaultParametersFilename() : XTandemInfile
• setDefaultParams_() : DetectabilitySimulation , DigestSimulation , IonizationSimulation , IsobaricChannelExtractor , IsobaricQuantifier , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , RawMSSignalSimulation , RTSimulation , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• setDefaults() : Param
• setDelayInSeconds() : FileWatcher
• setDescription() : MetaInfoRegistry , ProteinHit , TOPPASScene
• setDetectingTransition() : ReactionMonitoringTransition , LightTransition
• setDFSColor() : TOPPASVertex
• setDiffAverageMass() : ResidueModification
• setDiffFormula() : ResidueModification
• setDiffMonoMass() : ResidueModification
• setDigestionTime() : Digestion
• setDirectory() : OutputDirectory
• setDrawInterestingMZs() : Spectrum1DCanvas
• setDrawMode() : Spectrum1DCanvas
• setDrawMode1D() : TOPPViewBase
• setDriftTime() : MSSpectrum , Precursor , PeptideCompound , LightCompound
• setDriftTimeUnit() : MSSpectrum , Precursor
• setDriftTimeWindowLowerOffset() : Precursor
• setDriftTimeWindowUpperOffset() : Precursor
• setEdgeScore() : ChargePair
• setEditorData() : ListEditorDelegate , ParamEditorDelegate
• setElement() : IMSAlphabet , LPWrapper
• setElementIndex() : ChargePair
• setElementPath() : CVMappingRule
• setElutionPeakExtraInfo() : LCElutionPeak
• setEmail() : ContactPerson
• setEmpiricalFormula() : AccurateMassSearchResult
• setEmptyRows() : MzTab
• setEnd() : PeptideEvidence
• setEndPoint() : Annotation1DDistanceItem
• setEnzyme() : Digestion , EnzymaticDigestion , EnzymaticDigestionLogModel , 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
• setExtraPeakInfo() : CentroidPeak , MSPeak
• setFactor() : SpectrumCheapDPCorr
• setFeature() : FeatureEditDialog
• setFeatureExtraInformation() : SHFeature
• setFeatureLCMSID() : LCMS
• setFeatureName() : AbsoluteQuantitationMethod
• setFeatureProperties_() : IonizationSimulation
• setFeatures() : ConsensusFeature
• setFile() : GlobalExceptionHandler
• setFileFormatFilter() : InputFile , TOPPASInputFileDialog
• setFilename() : InputFile
• setFileName() : ListEditorDelegate
• setFilenames() : InputFileList , TOPPASInputFileListVertex
• setFileSize() : SourceFile
• setFileType() : SourceFile
• setFillData() : PeakFileOptions
• setFilters() : SpectrumCanvas
• setFinalMSExponent() : MassAnalyzer
• setFirstColumn() : FuzzyStringComparator
• setFirstName() : ContactPerson
• setFittedIntensity() : CentroidPeak
• setFitterParam() : EmgScoring
• setFivePrimeGain() : DigestionEnzymeRNA
• setFivePrimeMod() : NASequence
• setFixedModification() : ModificationDefinition
• setFixedModifications() : PrecursorIonSelectionPreprocessing
• setFlags() : Annotation1DTextItem
• setFloatDataArrays() : MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
• setFlux() : HPLC
• setForceMQCompatability() : PeakFileOptions
• setForceTPPCompatability() : PeakFileOptions
• setFormula() : Adduct , Residue , ResidueModification , Ribonucleotide
• setFormVersion() : MascotInfile
• setFoundAdduct() : AccurateMassSearchResult
• setFoundMass() : AccurateMassSearchResult
• setFoundPrecursorCharge() : SpectralMatch
• setFoundPrecursorMass() : SpectralMatch
• setFractionIdentifier() : ExperimentalSettings
• setFragmentMassErrorUnit() : XTandemInfile
• setFragmentMassTolerance() : XTandemInfile
• setFragmentMz() : MS2Fragment
• setFragmentPeakArea() : MS2Fragment
• setFreeText() : PythonModuleRequirement
• setFullId() : ResidueModification
• setFullName() : ResidueModification
• setFunction() : GlobalExceptionHandler
• setGaussianParameters() : PrecursorIonSelectionPreprocessing
• setGradient() : HPLC
• setHidden() : HMMState
• setHigherScoreBetter() : PeptideIdentification , ProteinIdentification
• setHits() : MascotInfile , PeptideIdentification , ProteinIdentification , SpectrumIdentification
• setHoverPos() : TOPPASEdge
• setHPLC() : ExperimentalSettings
• setHTMLCode() : Ribonucleotide
• setHullPoints() : ConvexHull2D
• setID() : Compomer
• setId() : IdentificationHit
• setID() : MS2Feature
• setId() : ResidueModification
• setIdentifier() : Acquisition , CVMappingRule , CVReference , DocumentIdentifier , PeptideIdentification , ProteinIdentification
• setIdentifyingTransition() : ReactionMonitoringTransition , LightTransition
• setInchiString() : SpectralMatch
• setIncludeTargets() : TargetedExperiment
• setIndividualIntensities() : AccurateMassSearchResult
• setInf() : MzTabDouble , MzTabInteger
• setInferenceEngine() : ProteinIdentification
• setInferenceEngineVersion() : ProteinIdentification
• setInitialParameters() : GammaDistributionFitter , GaussFitter , GumbelDistributionFitter , GumbelMaxLikelihoodFitter
• setInitialParameters_() : EGHFitter1D , EGHTraceFitter , EmgFitter1D , GaussTraceFitter
• setInitialTransitionProbability() : HiddenMarkovModel
• setInitIsotopeDist() : SuperHirnParameters
• setInletType() : IonSource
• setInputFilename() : XTandemInfile
• setInstitution() : ContactPerson
• setInstrument() : ExperimentalSettings , HPLC , InspectInfile , MascotInfile
• setInstruments() : TargetedExperiment
• setInstrumentSettings() : ChromatogramSettings , SpectrumSettings
• setIntegerDataArrays() : MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
• setIntensity() : CentroidPeak , ChromatogramPeak , Peak1D , Peak2D
• setIntensity32Bit() : PeakFileOptions
• setIntensityArray() : Chromatogram , Spectrum , OSChromatogram , OSSpectrum
• setIntensityMode() : SpectrumCanvas , SpectrumWidget , TOPPViewBase
• setIntensityRange() : FeatureFileOptions , PeakFileOptions
• setIntermediateProducts() : ReactionMonitoringTransition
• setInterpolationMode() : MultiGradient , MultiGradientSelector
• setInterpolationStep() : InterpolationModel
• setInterpretations() : IncludeExcludeTarget
• setInterProtein_() : XFDRAlgorithm
• setIntraProtein_() : XFDRAlgorithm
• setInvalid() : QTCluster
• setInverseOrientation() : AxisWidget
• setIonCutoffPercentage() : SequestInfile
• setIonDetectors() : Instrument
• setIonizationMethod() : IonSource
• setIonLadderVisible() : Spectrum1DCanvas
• setIonOptics() : Instrument
• setIonSeriesWeights() : SequestInfile
• setIonSources() : Instrument
• setISName() : AbsoluteQuantitationMethod
• setIsolationWidth() : MassAnalyzer
• setIsolationWindowLowerOffset() : Precursor , Product
• setIsolationWindowUpperOffset() : Precursor , Product
• setIsotopeDistribution() : Element , IMSElement
• setIsotopesSimScore() : AccurateMassSearchResult
• setIsotopicPeaks() : DeconvPeak
• setIsotopIdx() : CentroidPeak
• setIsRepeatable() : CVMappingTerm
• setKey() : TOPPASInputFileListVertex
• setLabel() : MassTrace , SpectrumCanvas
• setLastName() : ContactPerson
• setLayer() : SpectraIdentificationViewWidget
• setLayerFlag() : SpectrumCanvas
• setLayerName() : SpectrumCanvas
• setLCelutionProfile() : SHFeature
• setLeftEndpoint() : PeakShape
• setLeftPaddingIndex() : ContinuousWaveletTransform
• 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
• setLogMode() : HistogramDialog , HistogramWidget
• setLogProb() : Adduct
• setLogScale() : AxisWidget
• setLogThreshold() : EnzymaticDigestionLogModel
• setLogType() : ProgressLogger
• setLossFormulas() : Residue
• setLossNames() : Residue
• setLowMassIons() : Residue
• setLPSolver() : OfflinePrecursorIonSelection , PrecursorIonSelection , PSLPFormulation
• setMagneticFieldStrength() : MassAnalyzer
• setMapIndex() : FeatureHandle
• setMapping() : LinearInterpolation< Key, Value >
• setMapping_0() : BilinearInterpolation< Key, Value >
• setMapping_1() : BilinearInterpolation< Key, Value >
• setMappingRules() : CVMappings
• setMargin() : AxisWidget
• setMass() : CentroidPeak , Modification , Sample
• setMassAnalyzers() : Instrument
• setMassDiff() : ChargePair
• setMassShift() : Tagging
• setMasstraceIntensities() : AccurateMassSearchResult
• setMassType() : MascotInfile
• setMassTypeFragment() : SequestInfile
• setMassTypeParent() : SequestInfile
• setMatchedWhitelist() : FuzzyStringComparator
• setMatchingHMDBids() : AccurateMassSearchResult
• setMatchingIndex() : AccurateMassSearchResult
• setMatchingScore() : SpectralMatch
• setMatchingSpectrumIndex() : SpectralMatch
• setMatchPeakAllowedError() : SequestInfile
• setMatchPeakCount() : SequestInfile
• setMatchPeakTolerance() : SequestInfile
• setMatrix() : Matrix< Value >
• setMax() : DIntervalBase< D >
• setMaxAAPerModPerPeptide() : SequestInfile
• setMaxCharge() : IsotopeWavelet , Tagger
• setMaxDataPoolSize() : PeakFileOptions
• setMaxFloat() : Param
• setMaxFloat_() : TOPPBase
• setMaxInt() : Param
• setMaxInt_() : TOPPBase
• setMaxInternalCleavageSites() : SequestInfile
• setMaxIsotope() : CoarseIsotopePatternGenerator
• setMaxIterations() : TwoDOptimization
• setMaxLength() : TOPPASLogWindow
• setMaxModifications() : ModificationDefinitionsSet
• setMaxModsPerPeptide() : SequestInfile
• setMaxNumberOfThreads() : TOPPBase
• setMaxOccurrences() : ModificationDefinition
• setMaxPeakDistance() : TwoDOptimization
• setMaxPrecursorCharge() : XTandemInfile
• setMaxPTMsize() : InspectInfile
• setMaxScanDistance() : ProcessData
• setMaxScore() : PrecursorIonSelection
• setMaxValidEValue() : XTandemInfile
• setMaxX() : DIntervalBase< D >
• setMaxY() : DIntervalBase< D >
• setMean() : BasicStatistics< RealT >
• setMergeLayers() : TOPPViewOpenDialog
• setMessage() : BaseException , GlobalExceptionHandler
• setMetaData() : MzTab
• setMetadataOnly() : FeatureFileOptions , PeakFileOptions
• setMetaValue() : MetaInfoInterface , MRMFeatureFilter
• setMethodOfCombination() : AcquisitionInfo
• setMin() : DIntervalBase< D >
• setMinFloat() : Param
• setMinFloat_() : TOPPBase
• setMinimumSize_() : IMSIsotopeDistribution
• setMinInt() : Param
• setMinInt_() : TOPPBase
• setMinMax() : DIntervalBase< D >
• setMinMaxOfRange() : Spectrum1DGoToDialog , Spectrum2DGoToDialog
• setMinPeakGroupSize() : Deisotoper
• setMinX() : DIntervalBase< D >
• setMinY() : DIntervalBase< D >
• setMirrorModeActive() : Spectrum1DCanvas
• setMissedCleavages() : EnzymaticDigestion , MascotInfile
• setML1s() : TOFCalibration
• setML2s() : TOFCalibration
• setML3s() : TOFCalibration
• setModel() : Instrument , ProductModel< 2 >
• setModelData() : ListEditorDelegate , ParamEditorDelegate
• setModification() : AASequence , ModificationDefinition , Residue
• setModificationDefinitionsSet() : OMSSAXMLFile
• setModificationIdentifier() : MzTabModification
• setModifications() : MascotInfile , ModificationDefinitionsSet , PepNovoInfile , ProteinHit , XTandemInfile
• setModificationsPerPeptide() : InspectInfile
• setModified() : ParamEditor
• setMonoMass() : ResidueModification , Ribonucleotide
• setMonoWeight() : Element , Residue
• setMS1Map() : MRMFeatureFinderScoring
• setMSDataConsumer() : MzMLHandler , MzXMLHandler
• setMSFile() : MzTabSpectraRef
• setMSFileSection() : ExperimentalDesign
• setMSGFID() : DigestionEnzymeProtein
• setMSLevel() : MSSpectrum
• setMSLevels() : PeakFileOptions
• setMulticharge() : InspectInfile
• setMZ() : ChromatogramPeak , Peak1D , Peak2D , PeptideIdentification , Product , TraMLProduct
• setMz32Bit() : PeakFileOptions
• setMZArray() : Spectrum , OSSpectrum
• setMZErrorPPM() : AccurateMassSearchResult
• setMZRange() : FeatureFileOptions , PeakFileOptions
• setMZTolerance() : TwoDOptimization
• setName() : ContactPerson , CVReference , CVTerm , DefaultParamHandler , DigestionEnzyme , Element , GlobalExceptionHandler , HMMState , IdentificationHit , IMSElement , IncludeExcludeTarget , Instrument , MetaInfoDescription , ModelDescription< D > , MSChromatogram , MSSpectrum , MzTabParameter , ReactionMonitoringTransition , Residue , ResidueModification , Ribonucleotide , Sample , Software
• setNameAttribute() : SemanticValidator
• setNameOfFile() : SourceFile
• setNaN() : MzTabDouble , MzTabInteger
• setNativeID() : ChromatogramSettings , ReactionMonitoringTransition , SpectrumSettings
• setNativeIDType() : SourceFile
• setNativeIDTypeAccession() : SourceFile
• setNeutralLossAverageMasses() : ResidueModification
• setNeutralLossDiffFormulas() : ResidueModification
• setNeutralLossesForIons() : SequestInfile
• setNeutralLossMonoMasses() : ResidueModification
• setNewCode() : Ribonucleotide
• setNoise() : CentroidData
• setNoiseSuppression() : XTandemInfile
• setNominalMass() : IMSIsotopeDistribution
• setNormalizedIntensityValues() : ConsensusMapNormalizerAlgorithmQuantile
• setNormalizeXcorr() : SequestInfile
• setNPoints() : AbsoluteQuantitationMethod
• setNrIsotopes() : DeconvPeak
• setNrMS1Spectra() : SwathQC
• setNTermGain() : DigestionEnzymeProtein
• setNTerminalModification() : AASequence
• setNTermLossFormulas() : Residue
• setNTermLossNames() : Residue
• setNucleicAcidSectionRows() : MzTab
• setNucleotideReadingFrame() : SequestInfile
• setNull() : MzTabBoolean , MzTabDouble , MzTabDoubleList , MzTabInteger , MzTabIntegerList , MzTabModification , MzTabModificationList , MzTabParameter , MzTabParameterList , MzTabSpectraRef , MzTabString , MzTabStringList
• setNumber() : Sample
• setNumberIterations() : OptimizePick
• setNumberOfMissedCleavages() : XTandemInfile
• setNumberOfPeaks_() : OptimizePeakDeconvolution
• setNumberOfThreads() : XTandemInfile
• setNumpressConfigurationFloatDataArray() : PeakFileOptions
• setNumpressConfigurationIntensity() : PeakFileOptions
• setNumpressConfigurationMassTime() : PeakFileOptions
• setObjective() : LPWrapper
• setObjectiveSense() : LPWrapper
• setObservedIntensity() : AccurateMassSearchResult
• setObservedMZ() : AccurateMassSearchResult
• setObservedPrecursorMass() : SpectralMatch
• setObservedPrecursorRT() : SpectralMatch
• setObservedRT() : AccurateMassSearchResult
• setObservedSpectrumIndex() : SpectralMatch
• setOffset() : BiGaussModel , EGHModel , EmgModel , ExtendedIsotopeModel , GaussModel , InterpolationModel , IsotopeModel , LinearInterpolation< Key, Value >
• setOffset_0() : BilinearInterpolation< Key, Value >
• setOffset_1() : BilinearInterpolation< Key, Value >
• setOligonucleotideSectionRows() : MzTab
• setOMSSAID() : DigestionEnzymeProtein
• setOnDiscPeakData() : LayerData
• setOneLetterCode() : Residue
• setOptions() : FeatureXMLFile , FileHandler , IndexedMzMLFileLoader , MzDataHandler , MzMLHandler , MzXMLHandler , MzDataFile , MzMLFile , MzXMLFile
• setOrder() : IonDetector , IonSource , MassAnalyzer
• setOrganism() : Sample
• setOrgIntensity() : CentroidPeak
• setOrigin() : ResidueModification , Ribonucleotide
• setOSMSectionRows() : MzTab
• setOutDir() : TOPPASScene
• setOutputFilename() : XTandemInfile
• setOutputFolderName() : TOPPASOutputFileListVertex
• setOutputLines() : SequestInfile
• setOutputResults() : XTandemInfile
• setOverallQuality() : Feature
• setPairValue_() : MRMFeatureQCFile
• setParam() : TOPPViewPrefDialog , ModelDescription< D > , TOPPASToolVertex
• setParameter() : SVMWrapper
• setParameters() : DefaultParamHandler
• setParameters_() : QTClusterFinder
• setPartialSequence() : SequestInfile
• setPassThreshold() : IdentificationHit
• setPathToFile() : SourceFile
• setPeakAnnotations() : PeptideHit
• setPeakData() : LayerData
• setPeakMassTolerance() : InspectInfile , MascotInfile , SequestInfile
• setPen() : Annotations1DContainer
• setPenalties() : OptimizePeakDeconvolution , OptimizePick , TwoDOptimization
• setPeptideEvidence_() : XQuestResultXMLHandler
• setPeptideEvidences() : PeptideHit
• setPeptideGroupLabel() : Peptide
• setPeptideIdentifications() : BaseFeature , SpectrumSettings
• setPeptideMassUnit() : SequestInfile
• setPeptideProtonDistribution() : ProtonDistributionModel
• setPeptideRef() : IncludeExcludeTarget , ReactionMonitoringTransition
• setPeptides() : TargetedExperiment
• setPeptideScoresForMap_() : IDScoreGetterSetter
• setPeptideSectionRows() : MzTab
• setPercentage() : Gradient
• setPermut() : CompNovoIdentificationBase::Permut
• setPh() : Digestion
• setPipelineRunning() : TOPPASScene
• setPka() : Residue
• setPkb() : Residue
• setPkc() : Residue
• setPolarity() : InstrumentSettings , IonSource
• setPoolFile() : DocumentIDTagger
• setPos() : ChromatogramPeak , Peak1D
• setPosition() : Annotation1DCaret , Annotation1DPeakItem , Annotation1DTextItem , ChromatogramPeak , FASTAFile , Peak1D , Peak2D
• setPositionsAndParameters() : MzTabModification
• setPossibleChargeStates() : Precursor
• setPrecision() : Weights
• setPrecursor() : ChromatogramSettings
• setPrecursorAdduct() : SpectralMatch
• setPrecursorChrg() : MS2ConsensusSpectrum
• setPrecursorCHRG() : MSPeak
• setPrecursorCVTermList() : IncludeExcludeTarget , ReactionMonitoringTransition
• setPrecursorErrorType() : XTandemInfile
• setPrecursorMassErrorUnit() : XTandemInfile
• setPrecursorMassTolerance() : InspectInfile , MascotInfile , SequestInfile
• setPrecursorMassToleranceMinus() : XTandemInfile
• setPrecursorMassTolerancePlus() : XTandemInfile
• setPrecursorMZ() : IncludeExcludeTarget , MS2Fragment , MSPeak , ReactionMonitoringTransition
• setPrecursorMZSelectedIon() : PeakFileOptions
• setPrecursors() : SpectrumSettings
• setPrediction() : IncludeExcludeTarget , ReactionMonitoringTransition
• setPrefix() : LogStream
• setPresenceAndScanEventNumber_() : Ms2SpectrumStats
• setPressure() : HPLC
• 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() : AhoCorasickAmbiguous
• setProteinAccession() : PeptideEvidence
• setProteinData() : ProteinResolver
• setProteinIdentifications() : ConsensusMap , ExperimentalSettings , FeatureMap
• setProteinMassFilter() : SequestInfile
• setProteins() : TargetedExperiment
• setProteinSectionRows() : MzTab
• setPseudoCounts() : HiddenMarkovModel
• setPSIID() : DigestionEnzymeProtein
• setPSIMODAccession() : ResidueModification
• setPSMSectionRows() : MzTab
• setPublications() : TargetedExperiment
• setQuality() : BaseFeature , Feature
• setQuantifyingTransition() : ReactionMonitoringTransition , LightTransition
• setQuantMethod() : MassTrace
• setQuantMethods() : AbsoluteQuantitation
• setQueryMass() : AccurateMassSearchResult
• setQuerySpectra() : MascotRemoteQuery
• setRange() : MRMFeatureFilter , Spectrum1DGoToDialog , Spectrum2DGoToDialog
• setRank() : IdentificationHit , PeptideHit , ProteinHit
• setRANSACParams() : MZTrafoModel
• setRatios() : ConsensusFeature
• setReagentName() : Modification
• setRecycling() : TOPPASVertex
• setReference() : FeatureGroupingAlgorithmUnlabeled , MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering
• setReflectronState() : MassAnalyzer
• setRegEx() : DigestionEnzyme
• setRegExDescription() : DigestionEnzyme
• setRemovePrecursorNearPeaks() : SequestInfile
• setRequiredModules() : PythonModuleRequirement
• setRequirementLevel() : CVMappingRule
• setResidues_() : ResidueDB
• setResidueSets() : Residue
• setResiduesInUpperCase() : SequestInfile
• setResolution() : IonDetector , MassAnalyzer
• setResolutionMethod() : MassAnalyzer
• setResolutionType() : MassAnalyzer
• setRestrictions() : ListEditorDelegate
• setRetentionTime() : CentroidPeak , IncludeExcludeTarget , MS2Info , ReactionMonitoringTransition
• setRichText() : Annotation1DCaret
• setRightEndpoint() : PeakShape
• setRightPaddingIndex() : ContinuousWaveletTransform
• setRightSplitter() : HistogramDialog , HistogramWidget
• setRnd() : BaseLabeler
• setRoundMasses() : CoarseIsotopePatternGenerator
• setRowBounds() : LPWrapper
• setRowName() : LPWrapper
• setRT() : ChromatogramPeak , MSSpectrum , Peak2D , PeptideIdentification , RetentionTime
• setRTRange() : FeatureFileOptions , PeakFileOptions
• setSample() : ExperimentalSettings
• setSamples() : BiGaussModel , EGHModel , EmgModel , ExtendedIsotopeModel , GaussModel , InterpolationModel , IsotopeModel
• setSampleSection() : ExperimentalDesign
• setSaveFileName() : TOPPASScene
• setScale() : ContinuousWaveletTransform , EuclideanSimilarity , LinearInterpolation< Key, Value > , ProductModel< 2 >
• setScale_0() : BilinearInterpolation< Key, Value >
• setScale_1() : BilinearInterpolation< Key, Value >
• setScalingFactor() : InterpolationModel
• setScanDirection() : MassAnalyzer
• setScanEventNumber_() : Ms2SpectrumStats
• setScanLaw() : MassAnalyzer
• setScanMode() : InstrumentSettings
• setScanNumber() : Deisotoper
• setScanRate() : MassAnalyzer
• setScanRegExp_() : SpectrumLookup
• setScanTime() : MassAnalyzer
• setScanWindows() : InstrumentSettings
• setScopePath() : CVMappingRule
• setScore() : CompNovoIdentificationBase::Permut , DeconvPeak , FeatureHypothesis , PeptideHit , ProteinHit
• setScore_() : IDScoreGetterSetter
• setScoreAndMoveIfTarget_() : IDScoreGetterSetter
• setScores() : MRMFeature
• setScores_() : IDScoreGetterSetter
• setScoresAndRemoveDecoys_() : IDScoreGetterSetter
• setScoreType() : PeptideIdentification , ProteinIdentification
• setScoreType_() : IDScoreGetterSetter
• setScoreTypeAndSettings_() : BayesianProteinInferenceAlgorithm
• setSearchEngine() : ProteinIdentification
• setSearchEngineVersion() : ProteinIdentification
• setSearchParameters() : ProteinIdentification
• setSearchType() : MascotInfile
• setSecondaryIdentifier() : SpectralMatch
• setSectionDescription() : Param
• setSeed() : DecoyGenerator , UniqueIdGenerator
• setSeeds() : FeatureFinderAlgorithm , FeatureFinderAlgorithmPicked
• setSelected() : Annotation1DItem
• setSelectedPen() : Annotations1DContainer
• setSemiCleavage() : XTandemInfile
• setSeparator() : MzTabStringList
• setSequence() : IMSElement , NASequence , PeptideHit , ProteinHit
• setSequenceHeaderFilter() : SequestInfile
• setShortName() : Residue
• setShortReportFlag() : Deisotoper
• setShowFragmentIons() : SequestInfile
• setSideChainBasicity() : Residue
• setSigma() : IsotopeWaveletTransform< PeakType >
• setSignal() : ContinuousWaveletTransform
• setSignalLength() : ContinuousWaveletTransform
• setSignalToNoise() : CentroidPeak , MSPeak , SHFeature
• setSignificanceThreshold() : PeptideIdentification , ProteinIdentification
• setSingleMass() : Adduct
• setSize() : SaveImageDialog
• setSizeOnly() : FeatureFileOptions
• setSizeRatio_() : SaveImageDialog
• setSkipXMLChecks() : IndexedMzMLHandler , MzMLSpectrumDecoder , OnDiscMSExperiment , PeakFileOptions
• setSmallMoleculeSectionRows() : MzTab
• setSMILESString() : SpectralMatch
• setSmoothedIntensities() : MassTrace
• setSNIntensityThreshold() : LCElutionPeak
• setSoftware() : DataProcessing , Instrument , TargetedExperiment
• setSortChromatogramsByRT() : PeakFileOptions
• setSortSpectraByMZ() : PeakFileOptions
• setSourceClassification() : ResidueModification
• setSourceFeatureIndex() : AccurateMassSearchResult
• setSourceFile() : ChromatogramSettings , SpectrumSettings
• setSourceFiles() : ExperimentalSettings , TargetedExperiment
• setSourceOutParam() : TOPPASEdge
• setSourceVertex() : TOPPASEdge
• setSpacing() : ContinuousWaveletTransform
• setSpecificity() : EnzymaticDigestion
• setSpecificityType() : Modification
• setSpecRef() : MzTabSpectraRef
• setSpecRefFile() : MzTabSpectraRef
• setSpectra() : InspectInfile , MSExperiment
• setSpectraDataRef() : SpectrumMetaDataLookup
• setSpectraProcessingFunc() : MSDataTransformingConsumer
• setSpectrumIdentifications() : Identification
• setSpectrumWidget() : SpectrumCanvas
• setStandardEnzymeInfo_() : SequestInfile
• setStart() : PeptideEvidence
• setStartPoint() : Annotation1DDistanceItem
• setState() : Sample
• setStatus() : MetaDataBrowser
• setStrictFlag() : MRMFeatureFinderScoring
• setStringDataArrays() : MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
• setSubordinates() : Feature
• setSubsamples() : Sample
• setSum() : BasicStatistics< RealT >
• setSumFormula() : SpectralMatch
• setSwappedAxis() : Spectrum1DCanvas
• setSymbol() : Element
• setSynonyms() : DigestionEnzyme , Residue , ResidueModification
• setTableSteps() : IsotopeWavelet
• setTabWidth() : FuzzyStringComparator
• setTag() : SemanticValidator
• setTagCount() : InspectInfile
• setTargetCVTerms() : TargetedExperiment
• setTargetInParam() : TOPPASEdge
• setTargetMetaValue() : TargetedExperiment
• setTargetVertex() : TOPPASEdge
• setTaxon() : XTandemInfile
• setTaxonomy() : MascotInfile
• setTaxonomyFilename() : XTandemInfile
• setTechnicalRngSeed() : SimRandomNumberGenerator
• setTemperature() : Digestion , HPLC
• setTermName() : CVMappingTerm
• setTermSpecificity() : ResidueModification , Ribonucleotide
• setText() : Annotation1DItem
• setTextBox() : Spectrum1DCanvas
• setTheta() : Deisotoper
• 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() : TOPPASOutputFileListVertex , TOPPASToolVertex , TOPPASVertex
• setTopoSortMarked() : TOPPASVertex
• setToString() : FuzzyStringComparator::InputLine
• setTotalProbability() : FineIsotopePatternGenerator
• setTrainingEmissionProbability() : HiddenMarkovModel
• setTrainingEmissionProbability_() : HiddenMarkovModel
• setTrainingSample() : SVMWrapper
• setTransformationModel() : AbsoluteQuantitationMethod
• setTransformationModelParams() : AbsoluteQuantitationMethod
• setTransIntensity() : IsotopeWaveletTransform< PeakType >::TransSpectrum
• setTransitionGroupID() : MRMTransitionGroup< ChromatogramType, TransitionType >
• setTransitionProbability() : HiddenMarkovModel
• setTransitionProbability_() : HiddenMarkovModel
• 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
• setUpHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
• 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 >
• setVariableModifications() : HiddenMarkovModel , MascotInfile
• setVariance() : BasicStatistics< RealT >
• setVariant() : Tagging
• setVendor() : Instrument
• setVerboseLevel() : FuzzyStringComparator
• setVersion() : Software
• setVisibleArea() : Spectrum1DCanvas , SpectrumCanvas
• setVisibleArea1D() : TOPPViewIdentificationViewBehavior
• setVolume() : Sample
• setWavelet() : ContinuousWaveletTransform
• setWeightMode() : WeightWrapper
• setWeights() : SVMWrapper
• setWhitelist() : FuzzyStringComparator
• setWidth() : BaseFeature , CentroidData , FeatureHandle
• setWindowId() : EnhancedTabBarWidgetInterface , SpectrumWidget , TOPPASWidget
• setWriteIndex() : PeakFileOptions
• setWriteSupplementalData() : PeakFileOptions
• setX() : DPosition< D, TCoordinateType >
• setXLabel() : Spectrum3DOpenGLCanvas
• setXTandemID() : DigestionEnzymeProtein
• setY() : DPosition< D, TCoordinateType >
• setYLabel() : Spectrum3DOpenGLCanvas
• setZLabel() : Spectrum3DOpenGLCanvas
• setZoomScan() : InstrumentSettings
• shape() : TOPPASEdge , TOPPASVertex
• SHFeature() : SHFeature
• shiftDown_() : PrecursorIonSelection
• shiftedIonsToString() : RNPxlFragmentAnnotationHelper
• shiftedToPHFA() : RNPxlFragmentAnnotationHelper
• shiftUp_() : PrecursorIonSelection
• shortDimensionName() : Peak2D
• shortDimensionNameMZ() : Peak2D
• shortDimensionNameRT() : Peak2D
• shortDimensionUnit() : Peak2D
• shortDimensionUnitMZ() : Peak2D
• shortDimensionUnitRT() : Peak2D
• show_info() : CentroidPeak , DeconvPeak , LCElutionPeak , LCMS , MS2ConsensusSpectrum , MS2Feature , MS2Fragment , MS2Info , MSPeak , SHFeature
• showAboutDialog() : QApplicationTOPP , SwathWizardBase , TOPPASBase
• showAllHits_() : MetaDataBrowser
• showAsWindow_() : TOPPASBase
• showContextMenu() : HistogramWidget
• showCurrentLayerPreferences() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas
• showCurrentPeaksAs2D() : Spectrum1DCanvas , Spectrum1DWidget , Spectrum3DCanvas , Spectrum3DWidget , TOPPViewBase
• showCurrentPeaksAs3D() : Spectrum1DCanvas , Spectrum1DWidget , Spectrum2DCanvas , Spectrum2DWidget , TOPPViewBase
• showCurrentPeaksAsDIA() : Spectrum1DCanvas , Spectrum1DWidget , TOPPViewBase
• showCurrentPeaksAsIonMobility() : Spectrum1DCanvas , Spectrum1DWidget , TOPPViewBase
• showCursorStatus() : TOPPASBase , TOPPViewBase
• showCursorStatusInvert() : TOPPViewBase
• showDetails_() : MetaDataBrowser
• showDistribution_() : LayerStatisticsDialog
• showDocumentation() : ParamEditor
• showFileDialog() : InputFile , InputFileList , OutputDirectory , TOPPASOutputFilesDialog
• showFileDialog_() : PythonSelector
• showFilesDialog() : TOPPASInputFileListVertex
• showGoToDialog() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget , TOPPViewBase
• showGridLines() : SpectrumCanvas
• showIntensityDistribution() : SpectrumWidget
• showIOMappingDialog() : TOPPASEdge
• showLegend() : AxisWidget , Spectrum1DWidget , Spectrum3DCanvas , Spectrum3DWidget , SpectrumWidget
• showLogMessage_() : TOPPASBase , TOPPViewBase
• showMetaData() : SpectrumCanvas
• showMetaDistribution() : SpectrumWidget
• showMS2consensSpectraInfo() : SHFeature
• showPipelineFinishedLogMessage() : TOPPASBase
• showPreferences() : TOPPViewBase
• showProjectionHorizontal() : Spectrum2DCanvas
• showProjectionInfo() : Spectrum2DCanvas
• showProjectionVertical() : Spectrum2DCanvas
• showRange() : Spectrum2DGoToDialog
• showSpectrumAlignmentDialog() : TOPPViewBase
• showSpectrumAs1D() : SpectraIdentificationViewWidget , SpectraViewWidget , Spectrum2DCanvas , Spectrum2DWidget , TOPPViewBase , TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• showSpectrumBrowser() : TOPPViewBase
• showSpectrumGenerationDialog() : TOPPViewBase
• showSpectrumMetaData() : SpectraIdentificationViewWidget , SpectraViewWidget , TOPPViewBase
• showSpectrumWidgetInWindow() : TOPPViewBase
• showSplitters() : HistogramWidget
• showStatistics() : SpectrumWidget
• showStatusMessage() : TOPPASBase , TOPPViewBase
• showTOPPDialog() : TOPPViewBase
• showTOPPDialog_() : TOPPViewBase
• showURL() : TOPPASBase
• shuffle_() : DecoyGenerator
• shufflePeptide() : MRMDecoy
• shufflePeptides() : DecoyGenerator
• SignalToNoiseEstimator() : SignalToNoiseEstimator< Container >
• SignalToNoiseEstimatorMeanIterative() : SignalToNoiseEstimatorMeanIterative< Container >
• SignalToNoiseEstimatorMedian() : SignalToNoiseEstimatorMedian< Container >
• SignalToNoiseEstimatorMedianRapid() : SignalToNoiseEstimatorMedianRapid
• SignalToNoiseOpenMS() : SignalToNoiseOpenMS< ContainerT >
• SILACLabeler() : SILACLabeler
• similarity_() : SimplePairFinder
• simpleExtractChromatograms_() : OpenSwathCalibrationWorkflow
• simpleFindBestFeature() : OpenSwathHelper
• SimplePairFinder() : SimplePairFinder
• SimplePeak() : SimpleTSGXLMS::SimplePeak
• SimpleSearchEngineAlgorithm() : SimpleSearchEngineAlgorithm
• SimpleSVM() : SimpleSVM
• SimpleTSGXLMS() : SimpleTSGXLMS
• simplify() : String , StringUtils
• SimProtein() : SimProtein
• simpson_() : PeakIntegrator
• simulate() : MSSim , SvmTheoreticalSpectrumGenerator , SvmTheoreticalSpectrumGeneratorSet
• simulateILPBasedIPSRun_() : PrecursorIonSelection
• simulateRun() : PrecursorIonSelection
• simulateRun_() : PrecursorIonSelection
• SingleLinkage() : SingleLinkage
• SingletonRegistry() : SingletonRegistry
• SiriusAdapterAlgorithm() : SiriusAdapterAlgorithm
• SiriusTemporaryFileSystemObjects() : SiriusAdapterAlgorithm::SiriusTemporaryFileSystemObjects
• size() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , AASequence , CalibrationData , ConsensusFeature , ConstRefVector< ContainerT > , DataFilters , DPosition< D, TCoordinateType > , FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector > , FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern , HashGrid< Cluster > , IMSAlphabet , IMSIsotopeDistribution , Weights , IsotopeDistribution , IsotopeWaveletTransform< PeakType >::TransSpectrum , KDTreeFeatureMaps , Histogram< ValueType, BinSizeType > , MRMFeatureOpenMS , MRMTransitionGroup< ChromatogramType, TransitionType > , MSExperiment , MultiGradient , MultiplexFilteredMSExperiment , MultiplexFilteredPeak , NASequence , OnDiscMSExperiment , Param::ParamNode , Param , QCBase::SpectraMap , QTCluster , SplineInterpolatedPeaks , StringView , TOPPASVertex::TOPPASFilenames , TransitionGroupOpenMS< SpectrumT, TransitionT > , IMRMFeature , ITransitionGroup , MockMRMFeature , MockTransitionGroup
• sizeHint() : ColorSelector
• sizePair() : Matrix< Value >
• sizeProfile() : MultiplexFilteredPeak
• SizeUnderflow() : SizeUnderflow
• smartFileNames_() : TOPPASToolVertex
• smooth() : RawData
• smoothData() : ElutionPeakDetection , LowessSmoothing
• smoothRTDistortion_() : RTSimulation
• snapShot_() : StopWatch
• snapToGrid() : TOPPASScene
• Software() : Software
• SoftwareVisualizer() : SoftwareVisualizer
• solve() : BSpline2d , LPWrapper , NonNegativeLeastSquaresSolver
• solveILP() : PSLPFormulation
• solveNNLS_() : IsobaricIsotopeCorrector
• SolverParam() : LPWrapper::SolverParam
• somethingHasChanged() : TOPPASEdge , TOPPASVertex
• SONARScoring() : SONARScoring
• sort() : ROCCurve , PeptideIdentification , ProteinIdentification
• sort_() : ExperimentalDesign , IsotopeDistribution
• sortByComparator() : ConstRefVector< ContainerT >
• sortByIntensity() : ConsensusMap , ConstRefVector< ContainerT > , FeatureMap , IsotopeDistribution , MSChromatogram , MSSpectrum
• sortByMaps() : ConsensusMap
• sortByMass() : IsotopeDistribution
• sortByMZ() : ConsensusMap , FeatureMap
• sortByNames() : IMSAlphabet
• sortByOverallQuality() : FeatureMap
• sortByPosition() : ConsensusMap , ConstRefVector< ContainerT > , FeatureMap , MSChromatogram , MSSpectrum
• sortByPositionPresorted() : MSSpectrum
• sortByQuality() : ConsensusMap
• sortByRank() : PeptideIdentification
• sortByRT() : CalibrationData , ConsensusMap , FeatureMap
• sortBySize() : ConsensusMap
• sortByTotalScore() : PrecursorIonSelection
• sortByUnique_() : ProteinInference
• sortByValues() : IMSAlphabet
• sortChromatograms() : MSExperiment
• sortCurrentSpectrumByPosition() : LayerData
• SortExtractionCoordinatesByMZ() : ChromatogramExtractorAlgorithm::ExtractionCoordinates
• SortExtractionCoordinatesReverseByMZ() : ChromatogramExtractorAlgorithm::ExtractionCoordinates
• sortPeptideIdentificationsByMapIndex() : ConsensusMap
• sortPSM_() : MzTabFile
• sortSpectra() : MSExperiment
• sortTransitionsByProductMZ() : TargetedExperiment
• SourceFile() : SourceFile
• SourceFileVisualizer() : SourceFileVisualizer
• sourceHasChanged() : TOPPASEdge
• spatiallyGreaterEqual() : DPosition< D, TCoordinateType >
• spatiallyLessEqual() : DPosition< D, TCoordinateType >
• Spawn() : Spawn< TNeedle >
• SpecArrayFile() : SpecArrayFile
• SpectraDistance_() : SpectraMerger::SpectraDistance_
• SpectraIdentificationViewWidget() : SpectraIdentificationViewWidget
• SpectralMatch() : SpectralMatch
• SpectraMap() : QCBase::SpectraMap
• SpectraMerger() : SpectraMerger
• spectrastAnnotationExtract() : TransitionTSVFile
• spectrastRTExtract() : TransitionTSVFile
• SpectraSTSimilarityScore() : SpectraSTSimilarityScore
• SpectraViewWidget() : SpectraViewWidget
• Spectrum() : Spectrum
• Spectrum1DCanvas() : Spectrum1DCanvas
• Spectrum1DGoToDialog() : Spectrum1DGoToDialog
• Spectrum1DPrefDialog() : Spectrum1DPrefDialog
• Spectrum1DWidget() : Spectrum1DWidget
• Spectrum2DCanvas() : Spectrum2DCanvas
• Spectrum2DGoToDialog() : Spectrum2DGoToDialog
• Spectrum2DPrefDialog() : Spectrum2DPrefDialog
• Spectrum2DWidget() : Spectrum2DWidget
• Spectrum3DCanvas() : Spectrum3DCanvas
• Spectrum3DOpenGLCanvas() : Spectrum3DOpenGLCanvas
• Spectrum3DPrefDialog() : Spectrum3DPrefDialog
• Spectrum3DWidget() : Spectrum3DWidget
• SpectrumAccessOpenMS() : SpectrumAccessOpenMS
• SpectrumAccessOpenMSCached() : SpectrumAccessOpenMSCached
• SpectrumAccessOpenMSInMemory() : SpectrumAccessOpenMSInMemory
• SpectrumAccessQuadMZTransforming() : SpectrumAccessQuadMZTransforming
• SpectrumAccessSqMass() : SpectrumAccessSqMass
• SpectrumAccessTransforming() : SpectrumAccessTransforming
• SpectrumAlignment() : SpectrumAlignment
• SpectrumAlignmentDialog() : SpectrumAlignmentDialog
• SpectrumAlignmentScore() : SpectrumAlignmentScore
• SpectrumAnnotator() : SpectrumAnnotator
• spectrumBrowserHeaderContextMenu_() : SpectraViewWidget
• SpectrumCanvas() : SpectrumCanvas
• SpectrumCheapDPCorr() : SpectrumCheapDPCorr
• spectrumContextMenu_() : SpectraViewWidget
• spectrumDeselected() : SpectraIdentificationViewWidget
• spectrumDoubleClicked() : SpectraIdentificationViewWidget , SpectraViewWidget
• spectrumDoubleClicked_() : SpectraViewWidget
• SpectrumIdentification() : SpectrumIdentification
• SpectrumLookup() : SpectrumLookup
• SpectrumMeta() : SpectrumMeta
• SpectrumMetaData() : SpectrumMetaDataLookup::SpectrumMetaData
• SpectrumMetaDataLookup() : SpectrumMetaDataLookup
• SpectrumPrecursorComparator() : SpectrumPrecursorComparator
• spectrumSearchText_() : SpectraViewWidget
• spectrumSelected() : SpectraIdentificationViewWidget , SpectraViewWidget
• spectrumSelectionChange_() : SpectraIdentificationViewWidget , SpectraViewWidget
• SpectrumSettings() : SpectrumSettings
• SpectrumSettingsVisualizer() : SpectrumSettingsVisualizer
• SpectrumWidget() : SpectrumWidget
• SplineInterpolatedPeaks() : SplineInterpolatedPeaks
• SplinePackage() : SplinePackage
• split() : ConsensusMap , String , StringUtils
• split_quoted() : String , StringUtils
• splitByMiddle() : XQuestResultXMLHandler
• splitByNth() : XQuestResultXMLHandler
• splitModificationBySpecifiedAA() : MascotXMLHandler
• splitTransitionGroupsDetection_() : MRMFeatureFinderScoring
• splitTransitionGroupsIdentification_() : MRMFeatureFinderScoring
• SqliteConnector() : SqliteConnector
• SqMassConfig() : SqMassFile::SqMassConfig
• SqMassFile() : SqMassFile
• sqrt2pi() : BasicStatistics< RealT >
• SqrtMower() : SqrtMower
• 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() : ConsensusXMLFile , CVMappingFile , FeatureXMLFile , IdXMLFile , MascotXMLHandler , MzDataHandler , MzIdentMLHandler , MzMLHandler , MzMLValidator , MzQuantMLHandler , MzXMLHandler , ParamXMLHandler , PTMXMLHandler , SemanticValidator , ToolDescriptionHandler , TraMLHandler , UnimodXMLHandler , XMLHandler , XQuestResultXMLHandler , OMSSAXMLFile , PepXMLFile , PepXMLFileMascot , ProtXMLFile , QcMLFile , TransformationXMLFile , XTandemXMLFile
• startFeatureMerging() : MS1FeatureMerger
• startPos() : TOPPASEdge
• startProgress() : GUIProgressLoggerImpl , ProgressLogger::ProgressLoggerImpl , ProgressLogger
• startScanParsing() : FTPeakDetectController
• startTOPPView() : GUIHelpers
• Statistics() : PeptideAndProteinQuant::Statistics
• statistics_() : FeatureFinderIdentificationAlgorithm
• Status() : QCBase::Status
• stddev() : mean_and_stddev
• SteinScottImproveScore() : SteinScottImproveScore
• stop() : StopWatch
• store() : AbsoluteQuantitationMethodFile , AcquisitionInfoVisualizer , AcquisitionVisualizer , BaseVisualizerGUI , CachedmzML , ConsensusXMLFile , ContactPersonVisualizer , CsvFile , DataProcessingVisualizer , DigestionVisualizer , DocumentIdentifierVisualizer , DTA2DFile , DTAFile , EDTAFile , ExperimentalSettingsVisualizer , FASTAFile , FeatureXMLFile , GradientVisualizer , HPLCVisualizer , IBSpectraFile , IdXMLFile , IndexedMzMLFileLoader , InspectInfile , InstrumentSettingsVisualizer , InstrumentVisualizer , IonDetectorVisualizer , IonSourceVisualizer , KroenikFile , MascotGenericFile , MascotInfile , MassAnalyzerVisualizer , MetaInfoDescriptionVisualizer , MetaInfoVisualizer , ModificationVisualizer , MRMFeatureQCFile , MsInspectFile , MSPFile , MzDataFile , MzIdentMLFile , MzMLFile , MzQuantMLFile , MzTabFile , MzXMLFile , ParamEditor , ParamXMLFile , PepNovoInfile , PeptideHitVisualizer , PeptideIdentificationVisualizer , PepXMLFile , PrecursorVisualizer , ProductVisualizer , ProteinHitVisualizer , ProteinIdentificationVisualizer , ProtXMLFile , PTMXMLFile , QcMLFile , SampleVisualizer , ScanWindowVisualizer , SequestInfile , SiriusMSFile , SoftwareVisualizer , SourceFileVisualizer , SpecArrayFile , SpectrumSettingsVisualizer , SqMassFile , SVMData , TaggingVisualizer , TextFile , ToolDescriptionFile , TOPPASResources , TOPPASScene , TraMLFile , TransformationXMLFile , XMassFile , XQuestResultXMLFile , CSVWriter , DataMatrix , IDataFrameWriter
• storeAllLowProbabilityMS2Scans() : SuperHirnParameters
• storeBuffer() : MzMLFile
• storeElement_() : ElementDB
• storeExperiment() : FileHandler
• storeINI_() : ToolsDialog , TOPPASToolConfigDialog
• storeISO() : MSstatsFile
• storeJSON() : SwathQC
• storeLFQ() : MSstatsFile
• storeLibSVMProblem() : LibSVMEncoder
• storeOriginalRT_() : MapAlignmentTransformer
• storePeptideReliabilityColumn() : MzTabFile
• storePeptideUriColumn() : MzTabFile
• storeProteinGoTerms() : MzTabFile
• storeProteinReliabilityColumn() : MzTabFile
• storeProteinUriColumn() : MzTabFile
• storePSMReliabilityColumn() : MzTabFile
• storePSMUriColumn() : MzTabFile
• storeRecursive_() : ParamEditor
• storeRotationAndZoom() : Spectrum3DOpenGLCanvas
• storeSmallMoleculeReliabilityColumn() : MzTabFile
• storeSmallMoleculeUriColumn() : MzTabFile
• storeSpectrum_() : FIAMSDataProcessor
• storeTIC() : DTA2DFile
• StreamElement_() : FuzzyStringComparator::StreamElement_
• streamEnd() : Bzip2Ifstream , GzipIfstream
• StreamHandler() : StreamHandler
• StreamStruct() : LogStreamBuf::StreamStruct
• String() : String
• stringListToIsotopCorrectionMatrix_() : IsobaricQuantitationMethod
• StringListUtils() : StringListUtils
• StringManager() : StringManager
• StringView() : StringView
• stripExtension() : FileHandler
• subset() : MRMTransitionGroup< ChromatogramType, TransitionType >
• subsetDependent() : MRMTransitionGroup< ChromatogramType, TransitionType >
• substitute() : String , StringUtils
• substr() : String , StringUtils , StringView
• subtractIntensity() : CentroidPeak
• subtractMatchingPeaks() : IsotopicDist
• suffix() : Param::ParamNode , String , StringUtils
• sum() : BasicStatistics< RealT >
• sumIntensity_() : MSstatsFile
• Summary() : Summary
• SummaryStatistics() : SummaryStatistics< T >
• SuperHirnParameters() : SuperHirnParameters
• 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 >
• SVMData() : SVMData
• svmFilter_() : DetectabilitySimulation
• SvmTheoreticalSpectrumGenerator() : SvmTheoreticalSpectrumGenerator
• SvmTheoreticalSpectrumGeneratorSet() : SvmTheoreticalSpectrumGeneratorSet
• SvmTheoreticalSpectrumGeneratorTrainer() : SvmTheoreticalSpectrumGeneratorTrainer
• SVMWrapper() : SVMWrapper
• SVOutStream() : SVOutStream
• swap() : ConsensusMap , ConstRefVector< ContainerT > , DocumentIdentifier , FeatureMap , Weights , MSExperiment , UniqueIdIndexer< RandomAccessContainer > , UniqueIdInterface
• swapExtension() : FileHandler
• swapFeaturesOnly() : FeatureMap
• SwathLibraryStats() : SwathLibraryStats
• SwathMap() : SwathMap
• SwathMapMassCorrection() : SwathMapMassCorrection
• SwathQC() : SwathQC
• SwathTabWidget() : SwathTabWidget
• SwathWizardBase() : SwathWizardBase
• switchScores() : IDScoreSwitcherAlgorithm
• switchToGeneralScoreType() : IDScoreSwitcherAlgorithm
• sync() : LogStreamBuf
• synchronizePeakAnnotations() : LayerData
• syncLF_() : LogStreamBuf
• syncParams_() : MSSim