Here is a list of all class members with links to the classes they belong to:
- s -
- S
: ExtendedIsotopeModel
, IsotopeModel
, LmaIsotopeModel
, LmaIsotopeFitter1D
- s_
: SuffixArraySeqan
, SuffixArrayTrypticCompressed
- s_bion
: CompNovoIonScoringBase::IonScore
- s_byteorder_
: MzXMLHandler< MapType >
- s_centroided_
: MzXMLHandler< MapType >
- s_chargedeconvoluted_
: MzXMLHandler< MapType >
- s_completiontime_
: MzXMLHandler< MapType >
- s_compressionType_
: MzXMLHandler< MapType >
- s_count_
: MzXMLHandler< MapType >
- s_deisotoped_
: MzXMLHandler< MapType >
- s_email_
: MzXMLHandler< MapType >
- s_endmz_
: MzXMLHandler< MapType >
- s_filename_
: MzXMLHandler< MapType >
- s_filesha1_
: MzXMLHandler< MapType >
- s_filetype_
: MzXMLHandler< MapType >
- s_first_
: MzXMLHandler< MapType >
- s_intensitycutoff_
: MzXMLHandler< MapType >
- s_isotope_pattern_1
: CompNovoIonScoringBase::IonScore
- s_isotope_pattern_2
: CompNovoIonScoringBase::IonScore
- s_last_
: MzXMLHandler< MapType >
- s_mslevel_
: MzXMLHandler< MapType >
- s_name_
: MzXMLHandler< MapType >
- s_num_
: MzXMLHandler< MapType >
- s_pairorder_
: MzXMLHandler< MapType >
- s_peakscount_
: MzXMLHandler< MapType >
- s_phone_
: MzXMLHandler< MapType >
- s_polarity_
: MzXMLHandler< MapType >
- s_precision_
: MzXMLHandler< MapType >
- s_precursorcharge_
: MzXMLHandler< MapType >
- s_precursorintensity_
: MzXMLHandler< MapType >
- s_retentiontime_
: MzXMLHandler< MapType >
- s_scantype_
: MzXMLHandler< MapType >
- s_startmz_
: MzXMLHandler< MapType >
- s_type_
: MzXMLHandler< MapType >
- s_uri_
: MzXMLHandler< MapType >
- s_value_
: MzXMLHandler< MapType >
- s_version_
: MzXMLHandler< MapType >
- s_windowwideness_
: MzXMLHandler< MapType >
- s_witness
: CompNovoIonScoringBase::IonScore
- s_yion
: CompNovoIonScoringBase::IonScore
- sa_
: SuffixArrayPeptideFinder
- SALDI
: IonSource
- Sample()
: Sample
- sample_
: ExperimentalSettings
- sample_processing
: MzTabUnitIdMetaData
- sample_rate_
: ElutionPeakDetection
- sample_stddev()
: mean_and_stddev
- sample_variance()
: mean_and_stddev
- SampleAbundances
: PeptideAndProteinQuant
- samplecomment_
: SampleVisualizer
- sampleconcentration_
: SampleVisualizer
- samplemass_
: SampleVisualizer
- samplename_
: SampleVisualizer
- SAMPLENULL
: Sample
- samplenumber_
: SampleVisualizer
- sampleorganism_
: SampleVisualizer
- samplePeptideModel1D_()
: RawMSSignalSimulation
- samplePeptideModel2D_()
: RawMSSignalSimulation
- samples_
: MzMLHandler< MapType >
- SampleState
: Sample
- samplestate_
: SampleVisualizer
- SamplesType
: BaseModel< D >
, ProductModel< 2 >
- sampleTheCMarrWavelet_()
: IsotopeWaveletTransform< PeakType >
- SampleTreatment()
: SampleTreatment
- SampleVisualizer()
: SampleVisualizer
- samplevolume_
: SampleVisualizer
- sampling_points_per_FWHM_
: RawMSSignalSimulation
- sanityCheck_()
: TOPPASScene
- save()
: SuffixArray
, SuffixArraySeqan
, SuffixArrayTrypticCompressed
- save_()
: XMLFile
- saveAll_()
: MetaDataBrowser
- saveallbutton_
: MetaDataBrowser
- saveAsImage()
: Spectrum1DWidget
, SpectrumWidget
- saveCurrentLayer()
: Spectrum1DCanvas
, Spectrum2DCanvas
, Spectrum3DCanvas
, SpectrumCanvas
- saveCurrentPipelineAs()
: TOPPASBase
- saveFile()
: INIFileEditorWindow
- saveFileAs()
: INIFileEditorWindow
- saveIdXML_()
: SpectraIdentificationViewWidget
- saveIfChanged()
: TOPPASScene
- saveImageAs()
: IDEvaluationBase
- 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
- sc_charge_
: ProtonDistributionModel
- sc_charge_full_
: ProtonDistributionModel
- sc_charge_ion_c_term_
: ProtonDistributionModel
- sc_charge_ion_n_term_
: ProtonDistributionModel
- scale_
: EuclideanSimilarity
, LinearInterpolation< Key, Value >
, ProductModel< 2 >
, ContinuousWaveletTransform
, PeakPickerCWT
, AxisPainter
- scale_0_
: BilinearInterpolation< Key, Value >
- scale_1_
: BilinearInterpolation< Key, Value >
- scale_factor_
: LmaGaussFitter1D
, LmaGaussModel
- scaleData()
: SVMWrapper
- scaleDescriptorSet_()
: SvmTheoreticalSpectrumGenerator
- scaledIntensity()
: Spectrum3DOpenGLCanvas
- scaledInversMZ()
: Spectrum3DOpenGLCanvas
- scaledInversRT()
: Spectrum3DOpenGLCanvas
- scaledMZ()
: Spectrum3DOpenGLCanvas
- scaledRT()
: Spectrum3DOpenGLCanvas
- Scaler()
: Scaler
- scaleSingleFeature_()
: SvmTheoreticalSpectrumGenerator
- scaling_
: InterpolationModel
- scaling_lower
: SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- scaling_upper
: SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- SCAN
: MSPeak
- scan
: PSLPFormulation::IndexTriple
, MS1Signal
, MS2Fragment
- scan_apex
: SHFeature
- scan_dir_
: MassAnalyzerVisualizer
- scan_direction_
: MassAnalyzer
- SCAN_END
: MS2Info
- scan_end
: SHFeature
- scan_law_
: MassAnalyzer
, MassAnalyzerVisualizer
- scan_map_
: PepXMLFile
- scan_mode_
: InstrumentSettings
- scan_rate_
: MassAnalyzer
, MassAnalyzerVisualizer
- scan_regex_
: MascotXMLHandler
- SCAN_START
: MS2Info
- scan_start
: SHFeature
- scan_time_
: MassTrace
, MassAnalyzer
, MassAnalyzerVisualizer
- scan_windows_
: InstrumentSettings
- ScanDirection
: MassAnalyzer
- SCANDIRNULL
: MassAnalyzer
- scanEnd
: MS2Fragment
- ScanLaw
: MassAnalyzer
- SCANLAWNULL
: MassAnalyzer
- ScanMode
: InstrumentSettings
- scans
: IsotopeCluster
- scanStart
: MS2Fragment
- scanTRIndex_
: SuperHirnParameters
- ScanWindow()
: ScanWindow
- ScanWindowVisualizer()
: ScanWindowVisualizer
- scene_
: TOPPASWidget
- schema_location_
: XMLFile
- schema_version_
: XMLFile
- scope_path_
: CVMappingRule
- SCORE
: MSPeak
- score
: CompNovoIonScoringBase::IonScore
, DeNovoIonScoring::IonScore
, FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::BoxElement
, cudaHelp
, IsotopeWaveletTransform< PeakType >::BoxElement
, RNPxlReportRow
, DiaPrescore
- score_
: CompNovoIdentificationBase::Permut
, ChargePair
, PeptideHit
, ProteinHit
, DeconvPeak
- score_clas_pairs_
: ROCCurve
- SCORE_HOLDER
: SHFeature
- score_threshold_
: MapAlignmentAlgorithmIdentification
- score_type_
: InspectOutfile
, PeptideIdentification
, PeptideIdentificationVisualizer
, ProteinIdentificationVisualizer
- score_with_isotopes()
: DIAScoring
- scoreAssay_()
: ConfidenceScoring
- scoreCalculation_()
: MapAlignmentAlgorithmSpectrumAlignment
- scoredistribution_
: MapAlignmentAlgorithmSpectrumAlignment
- scoreETDFeatures_()
: CompNovoIonScoring
- scoreFeature_()
: ConfidenceScoring
- scoreHits()
: PILISCrossValidation
- scoreIsotopePattern_()
: DIAScoring
- scoreIsotopes()
: CompNovoIonScoringBase
- scoreIsotopes_()
: CompNovoIonScoringBase
- scoreMap()
: ConfidenceScoring
- scoreMZ2_()
: FeatureFindingMetabo
- scoreMZ_()
: FeatureFindingMetabo
- scorePeakgroups_()
: MRMFeatureFinderScoring
- scorer_
: PILISIdentification
- scoreRT_()
: FeatureFindingMetabo
- scores_
: IsotopeWaveletTransform< PeakType >
- scoreSpectra()
: CompNovoIonScoring
- scoreSpectra_()
: PILISCrossValidation
- scoreSpectrum()
: CompNovoIonScoringCID
- scoreThis_()
: IsotopeWaveletTransform< PeakType >
- scoreWitnessSet_()
: CompNovoIonScoring
, CompNovoIonScoringBase
, CompNovoIonScoringCID
- scoring_()
: MapAlignmentAlgorithmSpectrumAlignment
- sd_err_left_
: TransformationModelBSpline
- sd_err_right_
: TransformationModelBSpline
- search()
: StringList
- search_AC_pattern()
: MS2Info
- search_engine
: MzTabProteinSectionRow
, MzTabPeptideSectionRow
, MzTabSmallMoleculeSectionRow
- search_engine_
: PepXMLFile
, ProteinIdentification
- search_engine_score
: MzTabProteinSectionRow
, MzTabPeptideSectionRow
, MzTabSmallMoleculeSectionRow
- search_engine_version_
: ProteinIdentification
- search_id_
: PepXMLFile
- search_param_
: ConsensusXMLFile
, FeatureXMLFile
- search_parameters_
: MascotXMLHandler
, ProteinIdentification
- search_string_
: DBOpenDialog
- search_title_
: MascotInfile
- search_type_
: MascotInfile
- searchInScan_()
: TwoDOptimization
- searchMass_()
: AccurateMassSearchEngine
- searchModifications()
: ModificationsDB
- searchNextCell_()
: HashGrid< Cluster >::Iterator
, HashGrid< Cluster >::ConstIterator
- SearchParameters()
: ProteinIdentification::SearchParameters
- searchSuffix()
: StringList
- searchTerminalModifications()
: ModificationsDB
- searchTransformation_()
: CompareFouriertransform
- SECH_PEAK
: PeakShape
- second
: ProbablePhosphoSites
- second_nearest_gap_
: StablePairFinder
- secondary
: ProteinResolver::ProteinEntry
- secondary_indistinguishable
: ProteinResolver::ProteinEntry
- secondary_types
: SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- SECTOR
: MassAnalyzer
- Seed
: FeatureFinderAlgorithmPicked< PeakType, FeatureType >
- SeedList
: SeedListGenerator
- SeedListGenerator()
: SeedListGenerator
- seeds_
: FeatureFinderAlgorithmPicked< PeakType, FeatureType >
- seekGToSavedPosition()
: FuzzyStringComparator::InputLine
- seen_experiment_
: PepXMLFile
- SELDI
: IonSource
- selectAll()
: Annotations1DContainer
- selectColor()
: SILACAnalyzer
- selected()
: ParamTree
- selected_
: Annotation1DItem
, MultiGradientSelector
- selected_activation_
: IsobaricChannelExtractor
- selected_color_
: MultiGradientSelector
- selected_ion_count_
: MzMLHandler< MapType >
- SELECTED_ION_CURRENT_CHROMATOGRAM
: ChromatogramSettings
- SELECTED_ION_FLOW_TUBE
: Instrument
- SELECTED_ION_MONITORING_CHROMATOGRAM
: ChromatogramSettings
- selected_labels
: SILACAnalyzer
- selected_peak_
: Spectrum2DCanvas
, SpectrumCanvas
- selected_pen_
: Annotations1DContainer
- SELECTED_REACTION_MONITORING_CHROMATOGRAM
: ChromatogramSettings
- selectFragments()
: MRMFragmentSelection
- selectionChanged()
: ParamTree
- selectionCopied()
: TOPPASScene
- selectItemAt()
: Annotations1DContainer
- selectPivotIons_()
: CompNovoIdentificationBase
- selectSwathTransitions()
: OpenSwathHelper
- SemanticValidator()
: SemanticValidator
- semi_cleavage_
: XTandemInfile
- SEND
: IonSource
- sendClipboardContent()
: TOPPASBase
- sendCursorStatus()
: SpectrumCanvas
, SpectrumWidget
, TOPPASWidget
- sendStatus()
: BaseVisualizerGUI
- sendStatusMessage()
: SpectrumCanvas
, SpectrumWidget
, TOPPASWidget
- Sense
: LPWrapper
- sep_
: CSVWriter
, MzTabStringList
, SVOutStream
- sep_indices_
: BigString
- separator_
: BigString
- SEPTUM
: IonSource
- seq_1
: ProbablePhosphoSites
- seq_2
: ProbablePhosphoSites
- SeqToList
: MapAlignmentAlgorithmIdentification
- SeqToValue
: MapAlignmentAlgorithmIdentification
- sequence
: PILISCrossValidation::Peptide
, LightPeptide
, LightProtein
, Peptide
, Protein
, ProteinResolver::PeptideEntry
, Protein
, Peptide
, FASTAFile::FASTAEntry
, MzTabPeptideSectionRow
- sequence_
: IMSElement
, PeptideHit
, ProteinHit
- sequence_header_filter_
: SequestInfile
- sequence_string_
: AASequence
- sequences
: SVMData
- sequences_
: PrecursorIonSelectionPreprocessing
- SequestInfile()
: SequestInfile
- SequestOutfile()
: SequestOutfile
- server_path_
: MascotRemoteQuery
- set
: EGHFitter1D::Data
, EmgFitter1D::Data
, LmaGaussFitter1D::Data
, LmaIsotopeFitter1D::Data
, IsotopeDistribution
, GlobalExceptionHandler
, Date
, DateTime
, MzTabDouble
, MzTabDoubleList
, MzTabInteger
, MzTabBoolean
, MzTabString
, MzTabParameterList
, MzTabStringList
, MzTabModificationList
, CentroidData
, RawData
- set2DData()
: MSExperiment< PeakT, ChromatogramPeakT >
- 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()
: MSPeak
- set_CHRG()
: MS2Info
- set_chromatogram_flag()
: LayerData
- set_DELTA_CN()
: MS2Info
- set_dia_parameters()
: DIAScoring
- set_end_retention_time()
: LCElutionPeak
- set_feature_ID()
: SHFeature
- set_feature_match_status()
: SHFeature
- set_FEATURE_PI()
: SHFeature
- set_FULL_SQ()
: MS2Info
- 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_Name_ID_map_
: QcMLFile
- 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()
: SHFeature
- set_SCAN_END()
: MS2Info
- 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_to_zero_
: ParentPeakMower
- set_XCORR()
: MS2Info
- setAAAfter()
: PeptideHit
- setAABefore()
: PeptideHit
- setAcceptableAbsolute()
: FuzzyStringComparator
- setAcceptableRelative()
: FuzzyStringComparator
- setAccession()
: CVMappingTerm
, MzTabParameter
, CVTerm
, 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
- setAdductMass()
: AccurateMassSearchResult
- setAffectedAminoAcids()
: Modification
- setAllowChildren()
: CVMappingTerm
- setAllowedThreads()
: TOPPASScene
- setAllowShortNumbers()
: AxisWidget
- setAmount()
: Adduct
- setAnalysisSummaryQuantType()
: MSQuantifications
- setAngels()
: Spectrum3DOpenGLCanvas
- setAtomicNumber()
: Element
- setAverageMass()
: ResidueModification
- setAverageWeight()
: Element
, Residue
- setAxisBounds()
: AxisWidget
- setBackboneBasicityLeft()
: Residue
- setBackboneBasicityRight()
: Residue
- setBackgroundNoiseLevel()
: SHFeature
- setBinning()
: BinnedSpectrum
- setBinSize()
: BinnedSpectrum
- setBinSpread()
: BinnedSpectrum
- setBlind()
: InspectInfile
- setBoundary()
: MascotInfile
- setC13MassError()
: DeconvPeak
- setCalculatedMassToCharge()
: IdentificationHit
- setCanvas_()
: SpectrumWidget
- setCentroidSD()
: MassTrace
- setChanged()
: TOPPASScene
- setCharge()
: AccurateMassSearchResult
, EmpiricalFormula
, Adduct
, ChargePair
, FeatureHypothesis
, BaseFeature
, FeatureHandle
, IdentificationHit
, PeptideHit
, Precursor
, DeconvPeak
, OptimizePeakDeconvolution
- setCharges()
: MascotInfile
- setChargeState()
: Peptide
, TraMLProduct
- setChecksum()
: SourceFile
- setCheckTermValueTypes()
: SemanticValidator
- setCheckUnits()
: SemanticValidator
- setChromatograms()
: MSExperiment< PeakT, ChromatogramPeakT >
- setChromatogramType()
: ChromatogramSettings
- setCleavage()
: MascotInfile
- setClipboard()
: TOPPASScene
- setColor()
: Annotation1DPeakItem
, ColorSelector
, TOPPASEdge
- setColumn()
: HPLC
- setColumnBounds()
: LPWrapper
- setColumnName()
: LPWrapper
- setColumnType()
: LPWrapper
- setCombinationsLogic()
: CVMappingRule
- setComment()
: ChromatogramSettings
, ExperimentalSettings
, HPLC
, Sample
, SampleTreatment
, SpectrumSettings
- setCompletionTime()
: DataProcessing
- setCompomer()
: ChargePair
- setCompoundRef()
: ReactionMonitoringTransition
, IncludeExcludeTarget
- setCompounds()
: TargetedExperiment
- setCompression()
: PeakFileOptions
- setConcentration()
: Sample
- setConfigurations()
: IncludeExcludeTarget
- setConsensusMaps()
: MSQuantifications
- setContactInfo()
: ContactPerson
- setContacts()
: TargetedExperiment
, ExperimentalSettings
- setConvexHulls()
: Feature
- setCoverage()
: ProteinHit
- setCreationDate()
: Identification
- setCTerminalModification()
: AASequence
- setCurrentId()
: EnhancedTabBar
, TOPPASTabBar
- setCurrentLayerParameters()
: SpectrumCanvas
- setCurrentLayerPeakPenStyle()
: Spectrum1DCanvas
- setCurrentSpectrumIndex()
: LayerData
- setCustomizations()
: Instrument
- setCutOff()
: BaseModel< D >
- setCVIdentifierRef()
: CVMappingTerm
, CVTerm
- setCVLabel()
: MzTabParameter
- setCVReferences()
: CVMappings
- setCVs()
: TargetedExperiment
- setCVTerms()
: CVMappingRule
, CVTermList
- setData()
: BilinearInterpolation< Key, Value >
, LinearInterpolation< Key, Value >
, FeatureFinderAlgorithm< PeakType, FeatureType >
- setDatabase()
: SequestInfile
- setDataPoints()
: TransformationDescription
- setDataProcessing()
: ConsensusMap
, FeatureMap< FeatureT >
, ChromatogramSettings
, MetaInfoDescription
, SpectrumSettings
- setDataProcessingList()
: MSQuantifications
- setDate()
: DateTime
- setDateTime()
: ExperimentalSettings
, ProteinIdentification
- setDb()
: InspectInfile
- setDB()
: MascotInfile
- setDBSequenceRef()
: PeptideEvidence
- setDecoyTransitionType()
: ReactionMonitoringTransition
- setDefaultParametersFilename()
: XTandemInfile
- setDefaultParams_()
: IsobaricChannelExtractor
, IsobaricQuantifier
, ItraqChannelExtractor
, ItraqEightPlexQuantitationMethod
, ItraqFourPlexQuantitationMethod
, ItraqQuantifier
, TMTSixPlexQuantitationMethod
, DetectabilitySimulation
, DigestSimulation
, IonizationSimulation
, RawMSSignalSimulation
, RTSimulation
- setDefaults()
: Param
- setDelayInSeconds()
: FileWatcher
- setDescription()
: MetaInfoRegistry
, TOPPASScene
- setDFSColor()
: TOPPASVertex
- setDFSParent()
: TOPPASVertex
- setDiffAverageMass()
: ResidueModification
- setDiffFormula()
: ResidueModification
- setDiffMonoMass()
: ResidueModification
- setDigestionTime()
: Digestion
- setDrawMode()
: Spectrum1DCanvas
- setDrawMode1D()
: TOPPViewBase
- setEdgeScore()
: ChargePair
- setEditorData()
: ListEditorDelegate
, ParamEditorDelegate
- setElement()
: IMSAlphabet
, LPWrapper
- setElementIndex()
: ChargePair
- setElementPath()
: CVMappingRule
- setElutionPeakExtraInfo()
: LCElutionPeak
- setEmail()
: ContactPerson
- setEmpiricalFormula()
: AccurateMassSearchResult
- setEnd()
: PeptideEvidence
- setEndPoint()
: Annotation1DDistanceItem
- setEnzyme()
: EnzymaticDigestion
, InspectInfile
, SequestInfile
, Digestion
- setErrorPPM()
: AccurateMassSearchResult
- setExcludeTargets()
: TargetedExperiment
- setExperimentalMassToCharge()
: IdentificationHit
- setExperimentType()
: ConsensusMap
- setExtraPeakInfo()
: CentroidPeak
, MSPeak
- setFactor()
: SpectrumCheapDPCorr
- setFastaFile()
: EdwardsLippertIterator
, PepIterator
, TrypticIterator
, FastaIterator
, FastaIteratorIntern
- setFeature()
: FeatureEditDialog
- setFeatureExtraInformation()
: SHFeature
- setFeatureLCMSID()
: LCMS
- setFeatureProperties_()
: IonizationSimulation
- setFile()
: GlobalExceptionHandler
- setFileDescriptions()
: ConsensusMap
- setFileName()
: ListEditorDelegate
- setFilenames()
: TOPPASInputFileListVertex
- setFileSize()
: SourceFile
- setFileType()
: SourceFile
- setFilters()
: SpectrumCanvas
- setFinalMSExponent()
: MassAnalyzer
- setFirstColumn()
: FuzzyStringComparator
- setFirstName()
: ContactPerson
- setFittedIntensity()
: CentroidPeak
- setFitterParam()
: EmgScoring
- setFixedModification()
: ModificationDefinition
- setFixedModifications()
: PrecursorIonSelectionPreprocessing
- setFlags()
: Annotation1DTextItem
- setFlux()
: HPLC
- setFormula()
: Residue
, ResidueModification
, Adduct
- setFormVersion()
: MascotInfile
- setFoundAdduct()
: AccurateMassSearchResult
- setFoundMass()
: AccurateMassSearchResult
- setFractionIdentifier()
: ExperimentalSettings
- setFragmentMassErrorUnit()
: XTandemInfile
- setFragmentMassTolerance()
: XTandemInfile
- setFragmentMz()
: MS2Fragment
- setFragmentPeakArea()
: MS2Fragment
- setFrame()
: PeptideEvidence
- setFullId()
: ResidueModification
- setFullName()
: ResidueModification
- setFunction()
: GlobalExceptionHandler
- setGaussianParameters()
: PrecursorIonSelectionPreprocessing
- setGradient()
: HPLC
- setHidden()
: HMMState
- setHigherScoreBetter()
: PeptideIdentification
, ProteinIdentification
- setHits()
: MascotInfile
, PeptideIdentification
, ProteinIdentification
, SpectrumIdentification
- setHMM()
: PILISNeutralLossModel
- setHoverPos()
: TOPPASEdge
- setHPLC()
: ExperimentalSettings
- setHullPoints()
: ConvexHull2D
- setID()
: Compomer
, MS2Feature
- setId()
: ResidueModification
, IdentificationHit
, PeptideEvidence
- setIdentifier()
: CVMappingRule
, CVReference
, Acquisition
, DocumentIdentifier
, PeptideIdentification
, ProteinIdentification
- setIncludeTargets()
: TargetedExperiment
- setIndividualIntensities()
: AccurateMassSearchResult
- setInf()
: MzTabNullNaNAndInfAbleInterface
, MzTabNullNaNAndInfAbleBase
- setInitialParameters()
: GammaDistributionFitter
, GaussFitter
, GumbelDistributionFitter
- setInitialParameters_()
: EGHFitter1D
, EGHTraceFitter< PeakType >
, EmgFitter1D
, GaussTraceFitter< PeakType >
, LmaGaussFitter1D
, LmaIsotopeFitter1D
- setInitialTransitionProbability()
: HiddenMarkovModel
- setInitIsotopeDist()
: SuperHirnParameters
- setInletType()
: IonSource
- setInputFilename()
: XTandemInfile
- setInstitution()
: ContactPerson
- setInstrument()
: InspectInfile
, MascotInfile
, ExperimentalSettings
, HPLC
- setInstruments()
: TargetedExperiment
- setInstrumentSettings()
: ChromatogramSettings
, SpectrumSettings
- setIntensity()
: ChromatogramPeak
, Peak1D
, Peak2D
, CentroidPeak
- setIntensity32Bit()
: PeakFileOptions
- setIntensityArray()
: Chromatogram
, Spectrum
, Chromatogram
, Spectrum
- setIntensityMode()
: IDEvaluationBase
, TOPPViewBase
, SpectrumCanvas
, SpectrumWidget
- setIntensityRange()
: FeatureFileOptions
, PeakFileOptions
- setIntermediateProducts()
: ReactionMonitoringTransition
- setInterpolationMode()
: MultiGradient
, MultiGradientSelector
- setInterpolationStep()
: InterpolationModel
- setInterpretations()
: IncludeExcludeTarget
- setInvalid()
: QTCluster
- setInverseOrientation()
: AxisWidget
- setIonCutoffPercentage()
: SequestInfile
- setIonDetectors()
: Instrument
- setIonizationMethod()
: IonSource
- setIonOptics()
: Instrument
- setIonSeriesWeights()
: SequestInfile
- setIonSources()
: Instrument
- setIsDecoy()
: PeptideEvidence
- 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
- setLayerFlag()
: SpectrumCanvas
- setLayerName()
: SpectrumCanvas
- setLCelutionProfile()
: SHFeature
- setLeftEndpoint()
: PeakShape
- setLeftPaddingIndex()
: ContinuousWaveletTransform
- setLeftSplitter()
: HistogramDialog
, HistogramWidget
- setLegend()
: AxisWidget
, HistogramDialog
, HistogramWidget
- setLevel()
: LogStreamBuf
, LogStream
- setLibraryIntensity()
: ReactionMonitoringTransition
, LightTransition
- setLine()
: GlobalExceptionHandler
- setList()
: ListEditor
, ListTable
- setListRestrictions()
: ListEditor
- setLoadConvexHull()
: FeatureFileOptions
- setLoadedFilePath()
: DocumentIdentifier
- setLoadedFileType()
: DocumentIdentifier
- setLoadSubordinates()
: FeatureFileOptions
- setLogDestination()
: FuzzyStringComparator
- setLogMode()
: HistogramDialog
, HistogramWidget
- setLogModelEnabled()
: EnzymaticDigestion
- setLogProb()
: Adduct
- setLogScale()
: AxisWidget
- setLogThreshold()
: EnzymaticDigestion
- 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()
: Modification
, Sample
, CentroidPeak
- setMassAnalyzers()
: Instrument
- setMassDiff()
: ChargePair
- setMassShift()
: Tagging
- setMassType()
: MascotInfile
- setMassTypeFragment()
: SequestInfile
- setMassTypeParent()
: SequestInfile
- setMatchingHMDBids()
: AccurateMassSearchResult
- setMatchingIndex()
: AccurateMassSearchResult
- setMatchPeakAllowedError()
: SequestInfile
- setMatchPeakCount()
: SequestInfile
- setMatchPeakTolerance()
: SequestInfile
- setMatrix()
: Matrix< Value >
- setMax()
: DIntervalBase< D >
- setMaxAAPerModPerPeptide()
: SequestInfile
- setMaxAbsError()
: OptimizePick
, TwoDOptimization
- setMaxCharge()
: IsotopeWavelet
- setMaxFloat()
: Param
- setMaxFloat_()
: TOPPBase
- setMaxInt()
: Param
- setMaxInt_()
: TOPPBase
- setMaxInternalCleavageSites()
: SequestInfile
- setMaxIsotope()
: IsotopeDistribution
- setMaxIterations()
: TwoDOptimization
- setMaxModifications()
: ModificationDefinitionsSet
- setMaxModsPerPeptide()
: SequestInfile
- setMaxNumberOfThreads()
: TOPPBase
- setMaxOccurences()
: ModificationDefinition
- setMaxPeakDistance()
: TwoDOptimization
- setMaxPrecursorCharge()
: XTandemInfile
- setMaxPTMsize()
: InspectInfile
- setMaxRelError()
: OptimizePick
, TwoDOptimization
- 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
- setMethodOfCombination()
: AcquisitionInfo
- setMin()
: DIntervalBase< D >
- setMinFloat()
: Param
- setMinFloat_()
: TOPPBase
- setMinimumSize_()
: IMSIsotopeDistribution
- setMinInt()
: Param
- setMinInt_()
: TOPPBase
- setMinMax()
: DIntervalBase< D >
- setMinPeakGroupSize()
: Deisotoper
- setMinX()
: DIntervalBase< D >
- setMinY()
: DIntervalBase< D >
- setMirrorModeActive()
: Spectrum1DCanvas
- setMissedCleavages()
: EnzymaticDigestion
, MascotInfile
, PeptideEvidence
- setML1s()
: TOFCalibration
- setML2s()
: TOFCalibration
- setML3s()
: TOFCalibration
- setModel()
: PILISIdentification
, Instrument
, ProductModel< 2 >
- setModelData()
: ListEditorDelegate
, ParamEditorDelegate
- setModelDescription()
: Feature
- setModification()
: AASequence
, ModificationDefinition
, Residue
- setModificationDefinitionsSet()
: OMSSAXMLFile
, XTandemXMLFile
- setModificationOutputMethod()
: SuffixArrayPeptideFinder
- setModifications()
: ModificationDefinitionsSet
, MascotInfile
, PepNovoInfile
, XTandemInfile
- setModificationsPerPeptide()
: InspectInfile
- setModified()
: ParamEditor
- setModOrSubstIdentifier()
: MzTabModification
- setMonoIsotopicMass()
: ModelFitter< PeakType, FeatureType >
- setMonoMass()
: ResidueModification
- setMonoWeight()
: Element
, Residue
- setMSFile()
: MzTabSpectraRef
- setMSLevel()
: MSSpectrum< PeakT >
- setMSLevels()
: PeakFileOptions
- setMulticharge()
: InspectInfile
- setMZ()
: ChromatogramPeak
, Peak1D
, Peak2D
, Product
- setMz32Bit()
: PeakFileOptions
- setMZArray()
: Spectrum
- setMZRange()
: FeatureFileOptions
, PeakFileOptions
- setMZTolerance()
: TwoDOptimization
- setName()
: HMMState
, ReactionMonitoringTransition
, IncludeExcludeTarget
, Element
, IMSElement
, Residue
, ResidueModification
, GlobalExceptionHandler
, CVReference
, DefaultParamHandler
, MzTabParameter
, MSChromatogram< PeakT >
, MSSpectrum< PeakT >
, ContactPerson
, CVTerm
, IdentificationHit
, Instrument
, MetaInfoDescription
, PeptideEvidence
, Sample
, Software
, ModelDescription< D >
- setNameAttribute()
: SemanticValidator
- setNameOfFile()
: SourceFile
- setNaN()
: MzTabNullNaNAndInfAbleInterface
, MzTabNullNaNAndInfAbleBase
- setNativeID()
: ReactionMonitoringTransition
, ChromatogramSettings
, SpectrumSettings
- setNativeIDType()
: SourceFile
- setNeutralLossAverageMass()
: ResidueModification
- setNeutralLossDiffFormula()
: ResidueModification
- setNeutralLossesForIons()
: SequestInfile
- setNeutralLossMonoMass()
: ResidueModification
- setNoise()
: CentroidData
- setNominalMass()
: IMSIsotopeDistribution
- setNormalizedIntensityValues()
: ConsensusMapNormalizerAlgorithmQuantile
- setNormalizeXcorr()
: SequestInfile
- setNrIsotopes()
: DeconvPeak
- setNTerminalModification()
: AASequence
- setNTermLossFormulas()
: Residue
- setNTermLossNames()
: Residue
- setNucleotideReadingFrame()
: SequestInfile
- setNull()
: MzTabNullAbleInterface
, MzTabNullAbleBase
, MzTabNullNaNAndInfAbleBase
, MzTabDoubleList
, MzTabString
, MzTabParameter
, MzTabParameterList
, MzTabStringList
, MzTabModification
, MzTabModificationList
, MzTabSpectraRef
- setNumber()
: Sample
- setNumberIterations()
: OptimizePick
- setNumberOfMissedCleavages()
: XTandemInfile
- setNumberOfModifications()
: ModifierRep
, SuffixArray
, SuffixArrayPeptideFinder
, SuffixArraySeqan
, SuffixArrayTrypticCompressed
- setNumberOfThreads()
: XTandemInfile
- setObjective()
: LPWrapper
- setObjectiveSense()
: LPWrapper
- setObservedIntensity()
: AccurateMassSearchResult
- setObservedRT()
: AccurateMassSearchResult
- setOffset()
: LinearInterpolation< Key, Value >
, EGHModel
, BiGaussModel
, EmgModel
, ExtendedIsotopeModel
, GaussModel
, InterpolationModel
, IsotopeModel
, LmaGaussModel
, LmaIsotopeModel
- setOffset_0()
: BilinearInterpolation< Key, Value >
- setOffset_1()
: BilinearInterpolation< Key, Value >
- setOneLetterCode()
: Residue
- setOption()
: PILISCrossValidation
- setOptions()
: PILISCrossValidation
, FeatureXMLFile
, MzDataHandler< MapType >
, MzMLHandler< MapType >
, MzXMLHandler< MapType >
, MzDataFile
, MzMLFile
, MzXMLFile
- setOrder()
: IonDetector
, IonSource
, MassAnalyzer
- setOrganism()
: Sample
- setOrgIntensity()
: CentroidPeak
- setOrigin()
: ResidueModification
- setOutDir()
: TOPPASScene
- setOutputFilename()
: XTandemInfile
- setOutputLines()
: SequestInfile
- setOverallQuality()
: Feature
- setParam()
: ModelDescription< D >
, TOPPASToolVertex
- setParameter()
: SVMWrapper
- setParameters()
: DefaultParamHandler
- setParameters_()
: QTClusterFinder
- setPartialSequence()
: SequestInfile
- setPassThreshold()
: IdentificationHit
- setPathToFile()
: SourceFile
- setPeakMassTolerance()
: InspectInfile
, MascotInfile
, SequestInfile
- setPen()
: Annotations1DContainer
- setPenalties()
: OptimizePeakDeconvolution
, OptimizePick
, TwoDOptimization
- setPeptideGroupLabel()
: Peptide
- setPeptideIdentifications()
: BaseFeature
, SpectrumSettings
- setPeptideMassUnit()
: SequestInfile
- setPeptideProtonDistribution()
: ProtonDistributionModel
- setPeptideRef()
: ReactionMonitoringTransition
, IncludeExcludeTarget
- setPeptides()
: TargetedExperiment
- setPeptideSectionData()
: MzTab
- setPercentage()
: Gradient
- setPermut()
: CompNovoIdentificationBase::Permut
- setPersistenceId()
: PersistentObject
- setPh()
: Digestion
- setPipelineRunning()
: TOPPASScene
- setPka()
: Residue
- setPkb()
: Residue
- setPkc()
: Residue
- setPolarity()
: InstrumentSettings
, IonSource
- setPoolFile()
: DocumentIDTagger
- setPos()
: ChromatogramPeak
, Peak1D
- setPosition()
: ChromatogramPeak
, Peak1D
, Peak2D
, Annotation1DPeakItem
, Annotation1DTextItem
- setPositionsAndParameters()
: MzTabModification
- setPossibleChargeStates()
: Precursor
- setPost()
: PeptideEvidence
- setPre()
: PeptideEvidence
- setPrecision()
: Weights
- setPrecursor()
: ChromatogramSettings
- setPrecursorCHRG()
: MSPeak
- setPrecursorChrg()
: MS2ConsensusSpectrum
- setPrecursorCVTermList()
: ReactionMonitoringTransition
, IncludeExcludeTarget
- setPrecursorErrorType()
: XTandemInfile
- setPrecursorMassErrorUnit()
: XTandemInfile
- setPrecursorMassTolerance()
: InspectInfile
, MascotInfile
, SequestInfile
- setPrecursorMassToleranceMinus()
: XTandemInfile
- setPrecursorMassTolerancePlus()
: XTandemInfile
- setPrecursorMZ()
: ReactionMonitoringTransition
, IncludeExcludeTarget
, MS2Fragment
, MSPeak
- setPrecursors()
: SpectrumSettings
- setPrediction()
: ReactionMonitoringTransition
, IncludeExcludeTarget
- setPrefix()
: LogStream
- setPressure()
: HPLC
- setPrintDuplicateReferences()
: SequestInfile
- setProcessingActions()
: DataProcessing
- setProduct()
: ReactionMonitoringTransition
, ChromatogramSettings
- setProductCVTermList()
: IncludeExcludeTarget
- setProductMZ()
: ReactionMonitoringTransition
, IncludeExcludeTarget
- setProducts()
: SpectrumSettings
- setProgress()
: ProgressLogger
- setProteinAccessions()
: PeptideHit
- setProteinData()
: ProteinResolver
- setProteinIdentifications()
: ConsensusMap
, FeatureMap< FeatureT >
, ExperimentalSettings
- setProteinMassFilter()
: SequestInfile
- setProteins()
: TargetedExperiment
- setProteinSectionData()
: MzTab
- setPseudoCounts()
: HiddenMarkovModel
- setPSIMODAccession()
: ResidueModification
- setPublications()
: TargetedExperiment
- setQuality()
: BaseFeature
, Feature
- setQualityAts_
: QcMLFile
- setQualityQPs_
: QcMLFile
- setQualityQPs_members_
: QcMLFile
- setQueryMass()
: AccurateMassSearchResult
- setQuerySpectra()
: MascotRemoteQuery
- setRange()
: Spectrum1DGoToDialog
, Spectrum2DGoToDialog
- setRank()
: IdentificationHit
, PeptideHit
, ProteinHit
- setRatios()
: ConsensusFeature
- setReagentName()
: Modification
- setRecycling()
: TOPPASVertex
- setReference()
: FeatureGroupingAlgorithmUnlabeled
, MapAlignmentAlgorithm
, MapAlignmentAlgorithmIdentification
, MapAlignmentAlgorithmPoseClustering
- setRefine()
: XTandemInfile
- setReflectronState()
: MassAnalyzer
- setRemovePrecursorNearPeaks()
: SequestInfile
- setRequirementLevel()
: CVMappingRule
- setResidues()
: ResidueDB
- setResidueSets()
: Residue
- setResiduesInUpperCase()
: SequestInfile
- setResolution()
: IonDetector
, MassAnalyzer
- setResolutionMethod()
: MassAnalyzer
- setResolutionType()
: MassAnalyzer
- setRestrictions()
: ListEditorDelegate
- setRetentionTime()
: ReactionMonitoringTransition
, IncludeExcludeTarget
, CentroidPeak
, MS2Info
- setRightEndpoint()
: PeakShape
- setRightPaddingIndex()
: ContinuousWaveletTransform
- setRightSplitter()
: HistogramDialog
, HistogramWidget
- setRnd()
: BaseLabeler
- setRowBounds()
: LPWrapper
- setRowName()
: LPWrapper
- setRT()
: ChromatogramPeak
, MSSpectrum< PeakT >
, Peak2D
- setRTRange()
: FeatureFileOptions
, PeakFileOptions
- setSample()
: ExperimentalSettings
- setSamples()
: EGHModel
, BiGaussModel
, EmgModel
, ExtendedIsotopeModel
, GaussModel
, InterpolationModel
, IsotopeModel
, LmaGaussModel
, LmaIsotopeModel
- setSaveFileName()
: TOPPASScene
- setScale()
: EuclideanSimilarity
, LinearInterpolation< Key, Value >
, ProductModel< 2 >
, ContinuousWaveletTransform
- setScale_0()
: BilinearInterpolation< Key, Value >
- setScale_1()
: BilinearInterpolation< Key, Value >
- setScalingFactor()
: InterpolationModel
- setScanDirection()
: MassAnalyzer
- setScanLaw()
: MassAnalyzer
- setScanMode()
: InstrumentSettings
- setScanNumber()
: Deisotoper
- setScanRate()
: MassAnalyzer
- setScanTime()
: MassAnalyzer
- setScanWindows()
: InstrumentSettings
- setScopePath()
: CVMappingRule
- setScore()
: ProteinHit
, CompNovoIdentificationBase::Permut
, FeatureHypothesis
, PeptideHit
, DeconvPeak
- setScores()
: MRMFeature
- setScoreType()
: ProteinIdentification
, PeptideIdentification
- setSearchEngine()
: ProteinIdentification
- setSearchEngineVersion()
: ProteinIdentification
- setSearchParameters()
: ProteinIdentification
- setSearchType()
: MascotInfile
- setSectionDescription()
: Param
- setSeed()
: UniqueIdGenerator
- setSeeds()
: FeatureFinderAlgorithmPicked< PeakType, FeatureType >
, FeatureFinderAlgorithm< PeakType, FeatureType >
- setSelected()
: Annotation1DItem
- setSelectedPen()
: Annotations1DContainer
- setSemiCleavage()
: XTandemInfile
- setSeparator()
: BigString
, MzTabStringList
- setSequence()
: ProteinHit
, IMSElement
, PeptideHit
- 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
- setSmallMoleculeSectionData()
: MzTab
- setSmoothedIntensities()
: MassTrace
- setSNIntensityThreshold()
: LCElutionPeak
- setSoftware()
: TargetedExperiment
, DataProcessing
, Instrument
- setSolver()
: PSProteinInference
, LPWrapper
- 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< PeakT, ChromatogramPeakT >
- setSpectrum()
: TrypticIterator
, EdwardsLippertIterator
, PepIterator
, FastaIterator
, FastaIteratorIntern
- setSpectrumIdentifications()
: Identification
- setSpectrumWidget()
: SpectrumCanvas
- setStandardEnzymeInfo_()
: SequestInfile
- setStart()
: PeptideEvidence
- setStartPoint()
: Annotation1DDistanceItem
- setState()
: Sample
- setStatus()
: MetaDataBrowser
- setStrictFlag()
: MRMFeatureFinderScoring
- setStringSequence()
: AASequence
- setSubordinates()
: Feature
- setSubsamples()
: Sample
- setSum()
: BasicStatistics< RealT >
- setSwappedAxis()
: Spectrum1DCanvas
- setSymbol()
: Element
- setSynonyms()
: Residue
, ResidueModification
- setTableSteps()
: IsotopeWavelet
- setTabWidth()
: FuzzyStringComparator
- setTag()
: SemanticValidator
- setTagCount()
: InspectInfile
- setTags()
: SuffixArray
, SuffixArrayPeptideFinder
, SuffixArraySeqan
, SuffixArrayTrypticCompressed
- setTargetCVTerms()
: TargetedExperiment
- setTargetInParam()
: TOPPASEdge
- setTargetMetaValue()
: TargetedExperiment
- setTargetVertex()
: TOPPASEdge
- setTaxon()
: XTandemInfile
- setTaxonomy()
: MascotInfile
- setTaxonomyFilename()
: XTandemInfile
- setTemperature()
: Digestion
, HPLC
- setTermName()
: CVMappingTerm
- setTermSpecificity()
: ModificationDefinition
, ResidueModification
- setText()
: Annotation1DItem
- setTheta()
: Deisotoper
- setThreeLetterCode()
: Residue
- setThreshold()
: ClusterHierarchical
- setTickLevel()
: AxisWidget
- setTicks()
: Annotation1DDistanceItem
- setTime()
: DateTime
- setTimeArray()
: Chromatogram
- setTOFTotalPathLength()
: MassAnalyzer
- setTolerance()
: EdwardsLippertIterator
, TrypticIterator
, SuffixArray
, SuffixArrayPeptideFinder
, SuffixArraySeqan
, SuffixArrayTrypticCompressed
, FastaIterator
, FastaIteratorIntern
, PepIterator
- setTool_()
: ToolsDialog
- setToolDescriptions()
: ToolDescriptionHandler
- setTopoNr()
: TOPPASOutputFileListVertex
, TOPPASToolVertex
, TOPPASVertex
- setTopoSortMarked()
: TOPPASVertex
- setToString()
: FuzzyStringComparator::InputLine
- setTrainingEmissionProbability()
: HiddenMarkovModel
- setTrainingEmissionProbability_()
: HiddenMarkovModel
- setTrainingSample()
: SVMWrapper
- setTransIntensity()
: IsotopeWaveletTransform< PeakType >::TransSpectrum
- setTransitionGroupID()
: MRMTransitionGroup< SpectrumType, TransitionType >
- setTransitionProbability()
: HiddenMarkovModel
- setTransitionProbability_()
: HiddenMarkovModel
- setTransitions()
: TargetedExperiment
- setTranslationTableRef()
: PeptideEvidence
- setType()
: IonDetector
, MassAnalyzer
, SpectrumSettings
, ListEditorDelegate
- setTypeName()
: ListEditor
, ListEditorDelegate
- setUnassignedPeptideIdentifications()
: ConsensusMap
, FeatureMap< FeatureT >
- setUniModAccession()
: ResidueModification
- setUniqueId()
: UniqueIdInterface
- setUnit()
: DataValue
, CVTerm
, MetaInfoRegistry
- setUnitAccessionAttribute()
: SemanticValidator
- setUnitNameAttribute()
: SemanticValidator
- setUpHook()
: BaseLabeler
, ITRAQLabeler
, LabelFreeLabeler
, O18Labeler
, SILACLabeler
, ICPLLabeler
- setURL()
: ContactPerson
- setUseTags()
: SuffixArray
, SuffixArrayPeptideFinder
, SuffixArraySeqan
, SuffixArrayTrypticCompressed
- setUseTerm()
: CVMappingTerm
- setUseTermName()
: CVMappingTerm
- setValidFormats_()
: TOPPBase
- setValidStrings()
: Param
- setValidStrings_()
: TOPPBase
- setValue()
: DistanceMatrix< Value >
, Param
, MzTabParameter
, CVTerm
, MetaInfo
, Matrix< Value >
- setValueAttribute()
: SemanticValidator
- setValueQuick()
: DistanceMatrix< Value >
- setVariableModifications()
: HiddenMarkovModel
, MascotInfile
- setVariance()
: BasicStatistics< RealT >
- setVariant()
: Tagging
- setVendor()
: Instrument
- setVerboseLevel()
: FuzzyStringComparator
- setVersion()
: Software
- setVisibleArea()
: IDEvaluationBase
, SpectrumCanvas
, Spectrum1DCanvas
- setVisibleArea1D()
: TOPPViewIdentificationViewBehavior
- setVolume()
: Sample
- setWavelet()
: ContinuousWaveletTransform
- setWeightMode()
: WeightWrapper
- setWeights()
: SVMWrapper
- setWhitelist()
: FuzzyStringComparator
- setWidth()
: BaseFeature
, FeatureHandle
, CentroidData
- setWindowId()
: EnhancedTabBarWidgetInterface
, TOPPASWidget
, SpectrumWidget
- setWriteSupplementalData()
: PeakFileOptions
- setX()
: DPosition< D, TCoordinateType >
- setY()
: DPosition< D, TCoordinateType >
- setZoomScan()
: InstrumentSettings
- sf
: RawMSSignalSimulation::ContaminantInfo
- sfIsoDist10
: IsotopicDist
- sfIsoDist50
: IsotopicDist
- sfIsoDist90
: IsotopicDist
- sfIsoMass10
: IsotopicDist
- sfIsoMass50
: IsotopicDist
- sfIsoMass90
: IsotopicDist
- sfMassStep
: IsotopicDist
- sfMaxIsotopeIndex
: IsotopicDist
- sfMaxMass
: IsotopicDist
- sfMaxMassIndex
: IsotopicDist
- sfMinMass
: IsotopicDist
- sfNrIsotopes
: IsotopicDist
- sgolay_frame_length_
: MRMTransitionGroupPicker
- sgolay_polynomial_order_
: MRMTransitionGroupPicker
- SHA1
: SourceFile
- SHADE_FLAT
: Spectrum3DCanvas
- SHADE_SMOOTH
: Spectrum3DCanvas
- ShadeModes
: Spectrum3DCanvas
- shape
: RawMSSignalSimulation::ContaminantInfo
, TOPPASEdge
, TOPPASInputFileListVertex
, TOPPASMergerVertex
, TOPPASOutputFileListVertex
, TOPPASToolVertex
, TOPPASVertex
- SHFeature()
: SHFeature
- shiftDown_()
: PrecursorIonSelection
- shiftUp_()
: PrecursorIonSelection
- short_name_
: Residue
- shortDimensionName()
: Peak2D
- shortDimensionNameMZ()
: Peak2D
- shortDimensionNameRT()
: Peak2D
- shortDimensionUnit()
: Peak2D
- shortDimensionUnitMZ()
: Peak2D
- shortDimensionUnitRT()
: Peak2D
- SHOULD
: CVMappingRule
- show_alignment_
: Spectrum1DCanvas
- show_fragment_ions_
: SequestInfile
- show_grid_
: SpectrumCanvas
- show_info()
: CentroidPeak
, LCElutionPeak
, LCMS
, MS2ConsensusSpectrum
, MS2Fragment
, MS2Info
, MSPeak
, SHFeature
, MS2Feature
, DeconvPeak
- show_legend_
: AxisWidget
- show_splitters_
: HistogramWidget
- show_timing_
: SpectrumCanvas
- showAboutDialog()
: TOPPASBase
, TOPPViewBase
, IDEvaluationBase
- showAllHits_()
: MetaDataBrowser
- showAsWindow_()
: TOPPASBase
- showContextMenu()
: HistogramWidget
- showCurrentLayerPreferences()
: Spectrum1DCanvas
, Spectrum2DCanvas
, SpectrumCanvas
, Spectrum3DCanvas
- showCurrentPeaksAs2D()
: TOPPViewBase
, Spectrum1DCanvas
, Spectrum1DWidget
, Spectrum3DCanvas
, Spectrum3DWidget
- showCurrentPeaksAs3D()
: TOPPViewBase
, Spectrum1DWidget
, Spectrum2DCanvas
, Spectrum2DWidget
, Spectrum1DCanvas
- showCursorStatus()
: TOPPViewBase
, TOPPASBase
- showCursorStatusInvert()
: TOPPViewBase
- showDetails_()
: MetaDataBrowser
- showDistribution_()
: LayerStatisticsDialog
- showDocumentation()
: ParamEditor
- showFileDialog()
: TOPPASInputFileDialog
, TOPPASInputFilesDialog
, TOPPASOutputFilesDialog
- showFilesDialog()
: TOPPASInputFileListVertex
- showGoToDialog()
: TOPPViewBase
, Spectrum1DWidget
, Spectrum3DWidget
, SpectrumWidget
, Spectrum2DWidget
- showGridLines()
: SpectrumCanvas
- showIntensityDistribution()
: SpectrumWidget
- showIOMappingDialog()
: TOPPASEdge
- showLegend()
: AxisWidget
, Spectrum1DWidget
, Spectrum3DWidget
, SpectrumWidget
, Spectrum3DCanvas
- showLogMessage_()
: IDEvaluationBase
, TOPPASBase
, TOPPViewBase
- showMetaData()
: SpectrumCanvas
- showMetaDistribution()
: SpectrumWidget
- showMS2consensSpectraInfo()
: SHFeature
- showPipelineFinishedLogMessage()
: TOPPASBase
- showPreferences()
: TOPPViewBase
- showProjectionHorizontal()
: Spectrum2DCanvas
- showProjectionInfo()
: Spectrum2DCanvas
- showProjectionVertical()
: Spectrum2DCanvas
- showRange()
: Spectrum2DGoToDialog
- showSpectrumAlignmentDialog()
: TOPPViewBase
- showSpectrumAs1D()
: TOPPViewBase
, SpectraIdentificationViewWidget
, SpectraViewWidget
, Spectrum2DCanvas
, Spectrum2DWidget
, TOPPViewBehaviorInterface
, TOPPViewIdentificationViewBehavior
, TOPPViewSpectraViewBehavior
, Spectrum2DWidget
, TOPPViewBase
- showSpectrumBrowser()
: TOPPViewBase
- showSpectrumGenerationDialog()
: TOPPViewBase
- showSpectrumMetaData()
: TOPPViewBase
, SpectraViewWidget
, SpectraIdentificationViewWidget
- showSpectrumWidgetInWindow()
: TOPPViewBase
- showSplitters()
: HistogramWidget
- showStatistics()
: SpectrumWidget
- showStatusMessage()
: IDEvaluationBase
, TOPPASBase
, TOPPViewBase
- showTOPPDialog()
: TOPPViewBase
- showTOPPDialog_()
: TOPPViewBase
- showURL()
: IDEvaluationBase
, TOPPASBase
, TOPPViewBase
- shufflePeptide()
: MRMDecoy
- SI
: IonSource
- SID
: Precursor
- SIDE
: Compomer
- SideChain
: ProtonDistributionModel
- sigma
: GaussFitter::GaussFitResult
, LmaIsotopeFitter1D::Data
- SIGMA
: SVMWrapper
- sigma_
: SVMWrapper
, PrecursorIonSelectionPreprocessing
, GaussFilterAlgorithm
, IsotopeWaveletTransform< PeakType >
, GaussTraceFitter< PeakType >
- sigma_5_bound_
: EGHTraceFitter< PeakType >
- sigma_square_
: EGHFitter1D
, EGHTraceFitter< PeakType >
, EGHModel
- sigma_square_2_
: EGHModel
- sigmas_
: SVMWrapper
- signal
: OptimizePeakDeconvolution::Data
, OptimizePick::Data
, TwoDOptimization::Data
- signal2D
: TwoDOptimization::Data
- signal_
: ContinuousWaveletTransform
- signal_length_
: ContinuousWaveletTransform
- signal_to_noise
: PeakShape
- signal_to_noise_
: PeakPickerHiRes
, MRMTransitionGroupPicker
, PeakPickerCWT
- signal_weight
: PSLPFormulation::IndexTriple
- SignalToNoise
: MSPeak
, SHFeature
- signalToNoise_
: CentroidPeak
- SignalToNoiseEstimator()
: SignalToNoiseEstimator< Container >
- SignalToNoiseEstimatorMeanIterative()
: SignalToNoiseEstimatorMeanIterative< Container >
- SignalToNoiseEstimatorMedian()
: SignalToNoiseEstimatorMedian< Container >
- SignalToNoiseOpenMS()
: SignalToNoiseOpenMS< PeakT >
- significance_threshold_
: PeptideIdentification
- SILACAnalyzer()
: SILACAnalyzer
- SILACClustering()
: SILACClustering
- SILACFilter()
: SILACFilter
- SILACFiltering
: SILACFilter
, SILACFiltering
- SILACLabeler()
: SILACLabeler
- SILAClabels
: SILACAnalyzer
- SILACPoint()
: SILACPoint
- SILI
: IonSource
- SIM
: InstrumentSettings
- sim_specs_
: PILISIdentification
- similarity_()
: SimplePairFinder
- SimpleExtender()
: SimpleExtender< PeakType, FeatureType >
- SimplePairFinder()
: SimplePairFinder
- SimpleSeeder()
: SimpleSeeder< PeakType, FeatureType >
- simplify()
: String
- SimRandomNumberGenerator()
: SimRandomNumberGenerator
- simulate()
: MSSim
, SvmTheoreticalSpectrumGeneratorSet
, SvmTheoreticalSpectrumGenerator
- simulateILPBasedIPSRun_()
: PrecursorIonSelection
- simulateRun()
: PrecursorIonSelection
- simulateRun_()
: PrecursorIonSelection
- simulators_
: SvmTheoreticalSpectrumGeneratorSet
- sine_table_
: IsotopeWavelet
- SingleLinkage()
: SingleLinkage
- singleMass_
: Adduct
- SingletonRegistry()
: SingletonRegistry
- singletonRegistryInstance_
: SingletonRegistry
- singletonsNeedNoFriends
: SingletonRegistry
, Factory< FactoryProduct >
- sites_
: UnimodXMLHandler
- size()
: MSExperiment< PeakT, ChromatogramPeakT >
, IsotopeDistribution
, Param
, BigString
, IMSIsotopeDistribution
, MzMLHandler< MapType >::BinaryData
, FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern
- SIZE
: DataFilters
- size()
: ITransitionGroup
, MockTransitionGroup
, AASequence
, IMSAlphabet
, HierarchicalClustering< PointRef >::BoundingBox
, ConstRefVector< ContainerT >
, Param::ParamNode
, DataFilters
, ConsensusFeature
, MRMTransitionGroup< SpectrumType, TransitionType >
, Histogram< ValueType, BinSizeType >
, IsotopeWaveletTransform< PeakType >::TransSpectrum
- SIZE
: IMSIsotopeDistribution
- size
: ConsensusMap::FileDescription
, TransitionGroupOpenMS< SpectrumT, TransitionT >
, Weights
, HashGrid< Cluster >
, DPosition< D, TCoordinateType >
, QTCluster
, SparseVector< Value >
, MultiGradient
- size_
: TransformationModelBSpline
, TransformationModelInterpolated
, SparseVector< Value >
- SIZE_OF_ACQUISITIONMODE
: IonDetector
- SIZE_OF_ACTIVATIONMETHOD
: Precursor
- SIZE_OF_ANALYZERTYPE
: MassAnalyzer
- SIZE_OF_ANNOTATIONSTATE
: BaseFeature
- SIZE_OF_CHECKSUMTYPE
: SourceFile
- SIZE_OF_CHROMATOGRAM_TYPE
: ChromatogramSettings
- SIZE_OF_DIGESTIONENZYME
: ProteinIdentification
- SIZE_OF_ENZYMES
: EnzymaticDigestion
- SIZE_OF_FLAGS
: LayerData
- SIZE_OF_INLETTYPE
: IonSource
- SIZE_OF_IONIZATIONMETHOD
: IonSource
- SIZE_OF_IONOPTICSTYPE
: Instrument
- SIZE_OF_ISOTOPEVARIANT
: Tagging
- SIZE_OF_ITRAQ_TYPES
: ItraqConstants
- SIZE_OF_LABEL_TYPE
: LayerData
- SIZE_OF_PEAKMASSTYPE
: ProteinIdentification
- SIZE_OF_POLARITY
: IonSource
- SIZE_OF_PROCESSINGACTION
: DataProcessing
- SIZE_OF_QUANT_TYPES
: MSQuantifications
- SIZE_OF_REFLECTRONSTATE
: MassAnalyzer
- SIZE_OF_RESOLUTIONMETHOD
: MassAnalyzer
- SIZE_OF_RESOLUTIONTYPE
: MassAnalyzer
- SIZE_OF_SAMPLESTATE
: Sample
- SIZE_OF_SCANDIRECTION
: MassAnalyzer
- SIZE_OF_SCANLAW
: MassAnalyzer
- SIZE_OF_SCANMODE
: InstrumentSettings
- SIZE_OF_SPECIFICITY
: EnzymaticDigestion
- SIZE_OF_SPECIFICITYTYPE
: Modification
- SIZE_OF_SPECTRUMTYPE
: SpectrumSettings
- SIZE_OF_TYPE
: IonDetector
, FileTypes
- SIZE_OF_WEIGHTMODE
: WeightWrapper
- size_only_
: FeatureFileOptions
, FeatureXMLFile
- size_proportions_
: SaveImageDialog
- size_ratio_
: SaveImageDialog
- size_type
: Matrix< Value >
, SparseVector< Value >
, Weights
, ConstRefVector< ContainerT >
, IMSElement
, IMSIsotopeDistribution
, IntegerMassDecomposer< ValueType, DecompositionValueType >
, HashGrid< Cluster >
, IMSAlphabet
- size_x_
: SaveImageDialog
- size_y_
: SaveImageDialog
- sizeHint()
: ColorSelector
, IDEvaluationBase
- SizeOfResidueType
: Residue
- sizePair()
: Matrix< Value >
- SizeType
: ConvexHull2D
, DistanceMatrix< Value >
, Matrix< Value >
, String
- SizeUnderflow()
: SizeUnderflow
- skip_
: SuffixArrayTrypticCompressed
- skip_spectrum_
: MzXMLHandler< MapType >
, MzMLHandler< MapType >
, MzDataHandler< MapType >
- slope_
: TransformationModelLinear
, LinearRegression
- slope_bound_
: FeatureFinderAlgorithmPicked< PeakType, FeatureType >
- slope_max_
: TransformationModelBSpline
- slope_min_
: TransformationModelBSpline
- sm_
: XMLHandler
- small_molecule_quantification_unit
: MzTabUnitIdMetaData
- smallest_score_
: PosteriorErrorProbabilityModel
- smallmolecule_abundance_std_error_sub
: MzTabSmallMoleculeSectionRow
- smallmolecule_abundance_stdev_sub
: MzTabSmallMoleculeSectionRow
- smallmolecule_abundance_sub
: MzTabSmallMoleculeSectionRow
- smartFileNames_()
: TOPPASToolVertex
- smiles
: MzTabSmallMoleculeSectionRow
- smooth()
: RawData
- smoothData()
: LowessSmoothing
- smoothed_chroms_
: MRMTransitionGroupPicker
- smoothed_intensities_
: MassTrace
- SMOOTHING
: DataProcessing
- smoothRTDistortion_()
: RTSimulation
- sn_
: SignalToNoiseOpenMS< PeakT >
- sn_bin_count_
: MRMTransitionGroupPicker
- sn_win_len_
: MRMTransitionGroupPicker
- snap_factors_
: SpectrumCanvas
- snapToGrid()
: TOPPASScene
- snd_database_
: SequestInfile
- Software()
: Software
- software
: MzTabUnitIdMetaData
- Software()
: Software
- software_
: TargetedExperiment
, DataProcessing
, Instrument
, MzMLHandler< MapType >
- software_name_
: SoftwareVisualizer
- software_ref
: Prediction
, RetentionTime
- software_setting
: MzTabUnitIdMetaData
- software_version_
: SoftwareVisualizer
- SoftwareVisualizer()
: SoftwareVisualizer
- SOI
: IonSource
- SOLID
: Sample
- SOLUTION
: Sample
- solve()
: LPWrapper
, NonNegativeLeastSquaresSolver
- SOLVED
: NonNegativeLeastSquaresSolver
- solveGSL_()
: IsobaricIsotopeCorrector
- solveILP()
: PSLPFormulation
- solveNNLS_()
: IsobaricIsotopeCorrector
- SOLVER
: LPWrapper
- solver_
: PSLPFormulation
, LPWrapper
, OfflinePrecursorIonSelection
, PrecursorIonSelection
, PSProteinInference
- SOLVER_GLPK
: LPWrapper
- SolverParam()
: LPWrapper::SolverParam
- SolverStatus
: LPWrapper
- somethingHasChanged()
: TOPPASEdge
, TOPPASVertex
- SORI
: Precursor
- sort()
: ProteinIdentification
, PeptideIdentification
- sortByComparator()
: ConstRefVector< ContainerT >
- sortByIntensity()
: MSSpectrum< PeakT >
, FeatureMap< FeatureT >
, ConsensusMap
, ConstRefVector< ContainerT >
, MSChromatogram< PeakT >
- sortByMaps()
: ConsensusMap
- sortByMZ()
: ConsensusMap
, FeatureMap< FeatureT >
- sortByNames()
: IMSAlphabet
- sortByOverallQuality()
: FeatureMap< FeatureT >
- sortByPosition()
: MSSpectrum< PeakT >
, ConstRefVector< ContainerT >
, ConsensusMap
, FeatureMap< FeatureT >
, MSChromatogram< PeakT >
- sortByQuality()
: ConsensusMap
- sortByRT()
: ConsensusMap
, FeatureMap< FeatureT >
- sortBySize()
: ConsensusMap
- sortByTotalScore()
: PrecursorIonSelection
- sortByUnique_()
: ProteinInference
- sortByValues()
: IMSAlphabet
- sortChromatograms()
: MSExperiment< PeakT, ChromatogramPeakT >
- sortPSM_()
: MzTabFile
- sortSpectra()
: MSExperiment< PeakT, ChromatogramPeakT >
- sortTransitionsByProductMZ()
: TargetedExperiment
- Source_Classification
: ResidueModification
- SOURCE_DIR
: FTPeakDetectController
- source_feature_index_
: AccurateMassSearchResult
- source_file_
: ChromatogramSettings
, SpectrumSettings
- source_files_
: ExperimentalSettings
, TargetedExperiment
, MzMLHandler< MapType >
- source_out_param_
: TOPPASEdge
- SourceFile()
: SourceFile
- SourceFileVisualizer()
: SourceFileVisualizer
- sourceHasChanged()
: TOPPASEdge
- spacer_
: Spectrum1DWidget
- spacing_
: ContinuousWaveletTransform
, LinearResampler
, GaussFilter
, GaussFilterAlgorithm
- spacing_for_spectra_resampling_
: MRMFeatureFinderScoring
- sparse_element_
: SparseVector< Value >
- SparseVector()
: SparseVector< Value >
- SparseVector< Value >
: SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
- SparseVectorConstIterator()
: SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorConstIterator
- SparseVectorConstReverseIterator
: SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
- SparseVectorIterator
: SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorIterator
- SparseVectorReverseIterator()
: SparseVector< Value >::SparseVectorReverseIterator
- spatiallyGreaterEqual()
: DPosition< D, TCoordinateType >
- spatiallyLessEqual()
: DPosition< D, TCoordinateType >
- spec
: PILISCrossValidation::Peptide
- spec_
: MzDataHandler< MapType >
, MzMLHandler< MapType >
, EdwardsLippertIterator
- spec_1d_
: IDEvaluationBase
- SPEC_FULL
: EnzymaticDigestion
- spec_name
: LCMS
- SPEC_NONE
: EnzymaticDigestion
- spec_ref_
: MzTabSpectraRef
- SPEC_SEMI
: EnzymaticDigestion
- spec_write_counter_
: MzXMLHandler< MapType >
- SpecArrayFile()
: SpecArrayFile
- species
: MzTabSubIdMetaData
, MzTabSmallMoleculeSectionRow
, MzTabProteinSectionRow
- Specificity
: EnzymaticDigestion
- specificity_
: EnzymaticDigestion
- specificity_type_
: Modification
- SpecificityType
: Modification
- spectra_
: MSExperiment< PeakT, ChromatogramPeakT >
, InspectInfile
- spectra_aligner_
: PILISModel
- spectra_combo_box_
: SpectraViewWidget
- spectra_identification_view_widget_
: TOPPViewBase
- spectra_index_
: CachedmzML
- spectra_ref
: MzTabSmallMoleculeSectionRow
, MzTabPeptideSectionRow
- spectra_search_box_
: SpectraViewWidget
- spectra_treewidget_
: SpectraViewWidget
- spectra_view_widget_
: TOPPViewBase
- SpectraDistance_()
: SpectraMerger::SpectraDistance_
- SpectraIdentificationViewWidget()
: SpectraIdentificationViewWidget
- SpectraMerger()
: SpectraMerger
- SpectraSTSimilarityScore()
: SpectraSTSimilarityScore
- spectraview_behavior_
: TOPPViewBase
- SpectraViewWidget()
: SpectraViewWidget
- spectrum
: PeakIndex
- Spectrum()
: Spectrum
- spectrum
: FeatureFinderAlgorithmPickedHelperStructs::Seed
- Spectrum()
: Spectrum
- spectrum
: FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern
- Spectrum1DCanvas()
: Spectrum1DCanvas
- Spectrum1DGoToDialog()
: Spectrum1DGoToDialog
- Spectrum1DPrefDialog()
: Spectrum1DPrefDialog
- Spectrum1DWidget()
: Spectrum1DWidget
- Spectrum2DCanvas()
: Spectrum2DCanvas
- Spectrum2DGoToDialog()
: Spectrum2DGoToDialog
- Spectrum2DPrefDialog()
: Spectrum2DPrefDialog
- Spectrum2DWidget()
: Spectrum2DWidget
- Spectrum3DCanvas
: Spectrum3DOpenGLCanvas
, Spectrum3DCanvas
- Spectrum3DOpenGLCanvas()
: Spectrum3DOpenGLCanvas
, Spectrum3DCanvas
- Spectrum3DPrefDialog()
: Spectrum3DPrefDialog
- Spectrum3DWidget()
: Spectrum3DWidget
- spectrum_ID
: SHFeature
- spectrum_id
: TOPPViewBase
, LCMS
- spectrum_identifications_
: Identification
- spectrum_widget_
: SpectrumCanvas
- SpectrumAccessOpenMS()
: SpectrumAccessOpenMS
- SpectrumAccessOpenMSCached()
: SpectrumAccessOpenMSCached
- SpectrumAlignment()
: SpectrumAlignment
- SpectrumAlignmentDialog()
: SpectrumAlignmentDialog
- SpectrumAlignmentScore()
: SpectrumAlignmentScore
- spectrumBrowserHeaderContextMenu_()
: SpectraViewWidget
- SpectrumCanvas()
: SpectrumCanvas
- SpectrumCheapDPCorr()
: SpectrumCheapDPCorr
- SpectrumConstIteratorType
: SpectrumCanvas
- spectrumContextMenu_()
: SpectraViewWidget
- spectrumDeselected()
: SpectraIdentificationViewWidget
- spectrumDoubleClicked()
: SpectraIdentificationViewWidget
, SpectraViewWidget
- spectrumDoubleClicked_()
: SpectraViewWidget
- SpectrumIdentification()
: SpectrumIdentification
- SpectrumInterpolation()
: SILACFiltering::SpectrumInterpolation
- SpectrumIteratorType
: AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
- SpectrumMeta()
: SpectrumMeta
- SpectrumPrecursorComparator()
: SpectrumPrecursorComparator
- spectrumSelected()
: SpectraIdentificationViewWidget
, SpectraViewWidget
- spectrumSelected_()
: SpectraViewWidget
- spectrumSelectionChange_()
: SpectraViewWidget
, SpectraIdentificationViewWidget
- SpectrumSettings()
: SpectrumSettings
- SpectrumSettingsVisualizer()
: SpectrumSettingsVisualizer
- SpectrumType
: MzXMLHandler< MapType >
, MzMLHandler< MapType >
, FeatureFinderAlgorithmMRM< PeakType, FeatureType >
, MRMScoring
, TOPPViewBase
, TOPPViewSpectraViewBehavior
, TOPPViewIdentificationViewBehavior
, SpectrumWidget
, FeatureFinderAlgorithmPicked< PeakType, FeatureType >
, FeatureFinderAlgorithmSH< PeakType, FeatureType >
, FeaFiModule< PeakType, FeatureType >
, MSExperiment< PeakT, ChromatogramPeakT >
, DIAScoring
, MzDataHandler< MapType >
, SpectrumSettings
, SpectrumCanvas
, CachedmzML
- SpectrumWidget()
: SpectrumWidget
- SPI
: IonSource
- spline_
: TOFCalibration
, SILACFiltering::SpectrumInterpolation
- split()
: String
- split_quoted()
: String
- SPS
: PrecursorIonSelection
- SQ
: MS2Info
- sqrt2pi()
: BasicStatistics< RealT >
- SqrtMower()
: SqrtMower
- SRM
: InstrumentSettings
- ssize_
: DataValue
- ST_REFRESH_CHANGED
: TOPPASScene
- ST_REFRESH_CHANGEINVALID
: TOPPASScene
- ST_REFRESH_NOCHANGE
: TOPPASScene
- ST_REFRESH_REMAINSINVALID
: TOPPASScene
- StablePairFinder()
: StablePairFinder
- stack_
: Param::ParamIterator
- stairsInterpolation()
: MultiGradientSelector
- stand_dev_residuals_
: LinearRegression
- stand_error_slope_
: LinearRegression
- standard_deviation_
: LmaGaussFitter1D
, LmaGaussModel
- standard_stddev()
: mean_and_stddev
- standard_variance()
: mean_and_stddev
- start()
: FakeProcess
, StopWatch
- start_
: PeptideEvidence
- start_point_
: Annotation1DDistanceItem
- start_secs_
: StopWatch
- start_system_time_
: StopWatch
- start_usecs_
: StopWatch
- start_user_time_
: StopWatch
- startElement()
: ParamXMLHandler
, PTMXMLHandler
, TraMLHandler
, XMLHandler
, PepXMLFile
, ProtXMLFile
, TransformationXMLFile
, XTandemXMLFile
, SemanticValidator
, XTandemInfileXMLHandler
, IdXMLFile
, PepXMLFileMascot
, MzXMLHandler< MapType >
, ToolDescriptionHandler
, MzIdentMLHandler
, CVMappingFile
, MzMLValidator
, OMSSAXMLFile
, QcMLFile
, MascotXMLHandler
, UnimodXMLHandler
, MzQuantMLHandler
, FeatureXMLFile
, ConsensusXMLFile
, MzDataHandler< MapType >
, MzMLHandler< MapType >
- startFeatureMerging()
: MS1FeatureMerger
- startPos()
: TOPPASEdge
- startProgress()
: ProgressLogger
- startScan
: MS2ConsensusSpectrum
- startScanParsing()
: FTPeakDetectController
- startTR
: MS2ConsensusSpectrum
- state_
: MzTabNullNaNAndInfAbleBase
, Sample
- states
: AnnotationStatistics
- states_
: HiddenMarkovModel
- STATIC_FIELD
: Instrument
- static_intensities
: SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- Statistics()
: PeptideAndProteinQuant::Statistics
- statistics1_
: BiGaussModel
, BiGaussFitter1D
- statistics2_
: BiGaussModel
, BiGaussFitter1D
- statistics_
: LmaGaussModel
, EmgModel
, EGHModel
, GaussModel
, Fitter1D
- stats_
: PeptideAndProteinQuant
, IsobaricQuantifier
, ItraqQuantifier
- status_
: TOPPASToolVertex
- status_list_
: MetaDataBrowser
- stddev()
: mean_and_stddev
- stdev1_
: Fitter1D
- stdev2_
: Fitter1D
- stdev_
: SignalToNoiseEstimatorMeanIterative< Container >
- SteinScottImproveScore()
: SteinScottImproveScore
- stickdata_
: Spectrum3DOpenGLCanvas
- stn_estimates_
: SignalToNoiseEstimator< Container >
- stop()
: StopWatch
- stop_after_feature_
: MRMTransitionGroupPicker
- stop_after_intensity_ratio_
: MRMTransitionGroupPicker
- stop_report_after_feature_
: MRMFeatureFinderScoring
- stop_watch_
: ProgressLogger
- StopWatch()
: StopWatch
- store()
: ParamXMLFile
, QcMLFile
, InstrumentVisualizer
, AcquisitionVisualizer
, DataMatrix
, MzIdentMLFile
, MSPFile
, MzQuantMLFile
, MzIdentMLFile
, SpecArrayFile
, DTA2DFile
- STORE
: XMLHandler
- store()
: MzDataFile
, ToolDescriptionFile
, IonDetectorVisualizer
, TraMLFile
, TOPPASScene
, SequestInfile
, MzTabFile
, AcquisitionInfoVisualizer
, PTMXMLFile
, SVMData
, PrecursorVisualizer
, DataProcessingVisualizer
, ProtXMLFile
, EDTAFile
, BaseVisualizerGUI
, DTAFile
, ContactPersonVisualizer
, TaggingVisualizer
, DigestionVisualizer
, MzXMLFile
, FeatureXMLFile
, PepNovoInfile
, MascotInfile
, MascotGenericFile
, MzTabFile
, EDTAFile
, ExperimentalSettingsVisualizer
, MzMLFile
, HPLCVisualizer
, GradientVisualizer
, MetaInfoDescriptionVisualizer
, SourceFileVisualizer
, TextFile
, IonSourceVisualizer
, MascotInfile
, DocumentIdentifierVisualizer
, KroenikFile
, MetaInfoVisualizer
, PeptideIdentificationVisualizer
, ModificationVisualizer
, IdXMLFile
, MassAnalyzerVisualizer
, PeptideHitVisualizer
, ProductVisualizer
, InspectInfile
, ParamEditor
, SampleVisualizer
, ProteinIdentificationVisualizer
, SoftwareVisualizer
, CSVWriter
, ScanWindowVisualizer
, MsInspectFile
, FASTAFile
, PepXMLFile
, ProteinHitVisualizer
, TransformationXMLFile
, SpectrumSettingsVisualizer
, ConsensusXMLFile
, InstrumentSettingsVisualizer
, XMassFile
, MascotGenericFile
, TOPPASResources
, IDataFrameWriter
- store_
: DataMatrix
- storeAllLowProbabilityMS2Scans()
: SuperHirnParameters
- storeAllLowProbabilityMS2Scans_
: SuperHirnParameters
- storeExperiment()
: FileHandler
, DBAdapter
- storeFile_()
: DBAdapter
- storeINI_()
: TOPPASToolConfigDialog
, ToolsDialog
- storeLibSVMProblem()
: LibSVMEncoder
- storeMetaInfo_()
: DBAdapter
- storeRecursive_()
: ParamEditor
- storeRotationAndZoom()
: Spectrum3DOpenGLCanvas
- storeSample_()
: DBAdapter
- storeTIC()
: DTA2DFile
- str_
: DataValue
, OpenMSXMLFormatTarget
- str_list_
: DataValue
- strarray
: TransitionTSVReader
- stream
: LogStreamBuf::StreamStruct
- stream_
: LogStreamNotifier
- stream_at_end_
: GzipIfstream
, Bzip2Ifstream
- stream_list_
: LogStreamBuf
- stream_type_map_
: LogConfigHandler
- StreamElement_()
: FuzzyStringComparator::StreamElement_
- streamEnd()
: GzipIfstream
, Bzip2Ifstream
- StreamHandler()
: StreamHandler
- StreamIterator
: LogStream
- StreamStruct()
: LogStreamBuf::StreamStruct
- StreamType
: StreamHandler
- strict_
: MRMFeatureFinderScoring
- String()
: String
- STRING
: StreamHandler
- String()
: String
- STRING
: ParameterInformation
- String()
: String
, MRMScoring
- STRING
: ListEditor
- string_data_arrays_
: MSChromatogram< PeakT >
, MSSpectrum< PeakT >
- STRING_LIST
: DataValue
- STRING_VALUE
: DataValue
- StringDataArrays
: MSSpectrum< PeakT >
, MSChromatogram< PeakT >
- STRINGLIST
: PILISCrossValidation::Option
- StringList()
: StringList
- STRINGLIST
: ParameterInformation
- stringlist
: ParamXMLHandler
- StringList()
: StringList
- stringListToIsotopCorrectionMatrix_()
: IsobaricQuantitationMethod
- StringManager()
: StringManager
- strip_namespaces_
: CVMappingFile
- struct_size_in_datapoints_
: MorphologicalFilter
- sub_id_data
: MzTabUnitIdMetaData
- subordinate_feature_level_
: FeatureXMLFile
- subordinates_
: Feature
- subsamples_
: Sample
- subsections_
: DefaultParamHandler
, TOPPBase
- subsections_TOPP_
: TOPPBase
- subspec_to_sequences_
: CompNovoIdentificationBase
- substitute()
: String
- substr()
: String
- SUBSTREESTATUS
: TOPPASVertex
- subtractIntensity()
: CentroidPeak
- subtractMatchingPeaks()
: IsotopicDist
- succ_states_
: HMMState
- suffix()
: String
, Param::ParamNode
, String
- SuffixArray()
: SuffixArray
- SuffixArrayPeptideFinder()
: SuffixArrayPeptideFinder
- SuffixArraySeqan()
: SuffixArraySeqan
- SuffixArrayTrypticCompressed()
: SuffixArrayTrypticCompressed
- SuffixArrayTrypticSeqan()
: SuffixArrayTrypticSeqan
- SUI
: IonSource
- sum()
: BasicStatistics< RealT >
- sum_
: BasicStatistics< RealT >
- sum_neg_sigma()
: PosteriorErrorProbabilityModel
- sum_neg_x0()
: PosteriorErrorProbabilityModel
- sum_pos_sigma()
: PosteriorErrorProbabilityModel
- sum_pos_x0()
: PosteriorErrorProbabilityModel
- sum_post()
: PosteriorErrorProbabilityModel
- Summary()
: Summary
- sumPotentialIsotopePeaks_()
: IsobaricChannelExtractor
- SuperHirnParameters()
: SuperHirnParameters
- superimposer_
: MapAlignmentAlgorithmPoseClustering
- supported_schemes
: TOPPASResource
- 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 >
- SUSPENSION
: Sample
- svm_feat_centers_
: FeatureFindingMetabo
- svm_feat_scales_
: FeatureFindingMetabo
- SVM_kernel_type
: SVMWrapper
- SVM_parameter_type
: SVMWrapper
- SVM_TYPE
: SVMWrapper
- SVMData()
: SVMData
- svmFilter_()
: DetectabilitySimulation
- SvmTheoreticalSpectrumGenerator()
: SvmTheoreticalSpectrumGenerator
- SvmTheoreticalSpectrumGeneratorSet()
: SvmTheoreticalSpectrumGeneratorSet
- SvmTheoreticalSpectrumGeneratorTrainer
: SvmTheoreticalSpectrumGenerator
, SvmTheoreticalSpectrumGeneratorTrainer
- SVMWrapper()
: SVMWrapper
- SVOutStream()
: SVOutStream
- swap()
: MSExperiment< PeakT, ChromatogramPeakT >
, ConstRefVector< ContainerT >
, UniqueIdIndexer< RandomAccessContainer >
, ConstRefVector< ContainerT >
, ConsensusMap
, UniqueIdInterface
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, DocumentIdentifier
, FeatureMap< FeatureT >
, Weights
- swapFeaturesOnly()
: FeatureMap< FeatureT >
- SWIFT
: MassAnalyzer
- symbol_
: Element
- symbols_
: ElementDB
- symmetric_
: TransformationModelLinear
, LevMarqFitter1D
- symmetry_
: EmgFitter1D
, EmgModel
- sync()
: LogStreamBuf
- syncParams_()
: MSSim
- synonym_trans_
: HiddenMarkovModel
- synonym_trans_names_
: HiddenMarkovModel
- synonyms
: ControlledVocabulary::CVTerm
- synonyms_
: ResidueModification
, Residue