Here is a list of all class members with links to the classes they belong to:
- s -
- S
: ExtendedIsotopeModel
, IsotopeModel
- s_bion
: CompNovoIonScoringBase::IonScore
- s_isotope_pattern_1
: CompNovoIonScoringBase::IonScore
- s_isotope_pattern_2
: CompNovoIonScoringBase::IonScore
- s_list
: MSDataAggregatingConsumer
- s_tmp
: MSDataAggregatingConsumer
- s_witness
: CompNovoIonScoringBase::IonScore
- s_yion
: CompNovoIonScoringBase::IonScore
- safeParse_()
: MzMLFile
- SALDI
: IonSource
- sameNrOfMSFilesPerFraction()
: ExperimentalDesign
- sample
: ExperimentalDesign::MSFileSectionEntry
, MzTabMetaData
- Sample()
: Sample
- sample_
: ExperimentalSettings
- sample_name
: AbsoluteQuantitationStandards::runConcentration
- sample_processing
: MzTabMetaData
- sample_ref
: MzTabAssayMetaData
- sample_refs
: MzTabStudyVariableMetaData
- sample_section_
: ExperimentalDesign
- sample_stddev()
: mean_and_stddev
- sample_to_rowindex_
: ExperimentalDesign::SampleSection
- 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_
: FIAMSScheduler
, MzMLHandler
- samples_labels_
: MultiplexDeltaMassesGenerator
- SampleSection()
: ExperimentalDesign::SampleSection
- 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
- satellites_
: MultiplexFilteredPeak
- satellites_profile_
: MultiplexFilteredPeak
- save_()
: XMLFile
- saveAll_()
: MetaDataBrowser
- saveallbutton_
: 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
- sc_charge_
: ProtonDistributionModel
- sc_charge_full_
: ProtonDistributionModel
- sc_charge_ion_c_term_
: ProtonDistributionModel
- sc_charge_ion_n_term_
: ProtonDistributionModel
- Scalar
: GumbelMaxLikelihoodFitter::Functor< _Scalar, NX, NY >
- scale_()
: AxisPainter
, ContinuousWaveletTransform
, EuclideanSimilarity
, LinearInterpolation< Key, Value >
, PeakPickerCWT
, ProductModel< 2 >
- scale_0_
: BilinearInterpolation< Key, Value >
- scale_1_
: BilinearInterpolation< Key, Value >
- scaleData()
: SVMWrapper
- scaleData_()
: SimpleSVM
- scaleDescriptorSet_()
: SvmTheoreticalSpectrumGenerator
- scaledIntensity_()
: Spectrum3DOpenGLCanvas
- scaledInversMZ_()
: Spectrum3DOpenGLCanvas
- scaledInversRT_()
: Spectrum3DOpenGLCanvas
- scaledMZ_()
: Spectrum3DOpenGLCanvas
- scaledRT_()
: Spectrum3DOpenGLCanvas
- ScaleMap
: SimpleSVM
- Scaler()
: Scaler
- scaleSingleFeature_()
: SvmTheoreticalSpectrumGenerator
- scaling_
: InterpolationModel
, SimpleSVM
- scaling_lower
: SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- scaling_upper
: SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- scan
: MS1Signal
, MS2Fragment
- SCAN
: MSPeak
- scan
: PSLPFormulation::IndexTriple
- scan_apex
: SHFeature
- scan_count_
: MzMLHandler
, MzXMLHandler
- scan_count_total_
: MzMLHandler
- scan_dir_
: MassAnalyzerVisualizer
- scan_direction_
: MassAnalyzer
- SCAN_END
: MS2Info
- scan_end
: SHFeature
- scan_event_number
: Ms2SpectrumStats::ScanEvent
- scan_index
: NucleicAcidSearchEngine::PrecursorInfo
, CsiFingerIdMzTabWriter::CsiAdapterIdentification
, SiriusMzTabWriter::SiriusAdapterIdentification
- scan_index_heavy
: OPXLDataStructs::CrossLinkSpectrumMatch
- scan_index_light
: OPXLDataStructs::CrossLinkSpectrumMatch
- scan_indices
: SiriusMSFile::CompoundInfo
- scan_law_
: MassAnalyzer
, MassAnalyzerVisualizer
- scan_map_
: PepXMLFile
- scan_mode_
: InstrumentSettings
- scan_number
: CsiFingerIdMzTabWriter::CsiAdapterIdentification
, SiriusMzTabWriter::SiriusAdapterIdentification
, SpectrumMetaDataLookup::SpectrumMetaData
- scan_rate_
: MassAnalyzer
, MassAnalyzerVisualizer
- scan_regexp_
: SpectrumLookup
- SCAN_START
: MS2Info
- scan_start
: SHFeature
- scan_time_
: MassAnalyzer
, MassAnalyzerVisualizer
- scan_windows_
: InstrumentSettings
- ScanDirection
: MassAnalyzer
- SCANDIRNULL
: MassAnalyzer
- scanEnd
: MS2Fragment
- ScanEvent()
: Ms2SpectrumStats::ScanEvent
- ScanLaw
: MassAnalyzer
- SCANLAWNULL
: MassAnalyzer
- ScanMode
: InstrumentSettings
- scans
: IsotopeCluster
- scans_
: SpectrumLookup
- scanStart
: MS2Fragment
- scanTRIndex_
: SuperHirnParameters
- ScanWindow()
: ScanWindow
- ScanWindowVisualizer()
: ScanWindowVisualizer
- scene_
: TOPPASWidget
- schema_location_
: XMLFile
- schema_version_
: MzIdentMLDOMHandler
, XMLFile
- scope_path_
: CVMappingRule
- score
: CompNovoIonScoringBase::IonScore
, CsiFingerIdMzTabWriter::CsiAdapterHit
, DeNovoIonScoring::IonScore
, DiaPrescore
, FeatureFinderAlgorithmIsotopeWavelet::BoxElement
, IDFilter::HasGoodScore< HitType >
, IDBoostGraph::ProteinGroup
, IsotopeWaveletTransform< PeakType >::BoxElement
, MorpheusScore::Result
- SCORE
: MSPeak
- score
: OPXLDataStructs::CrossLinkSpectrumMatch
- SCORE
: PercolatorOutfile
- score
: RNPxlReportRow
, SimpleSearchEngineAlgorithm::AnnotatedHit_
, SiriusMzTabWriter::SiriusAdapterHit
, TargetedSpectraExtractor::Match
- score_
: ChargePair
, CompNovoIdentificationBase::Permut
, DeconvPeak
, PeptideHit
, ProteinHit
- score_clas_pairs_
: ROCCurve
- score_cutoff_
: MapAlignmentAlgorithmIdentification
- SCORE_HOLDER
: SHFeature
- score_type
: PeptideHit::PepXMLAnalysisResult
- score_type_
: InspectOutfile
, PeptideIdentification
, PeptideIdentificationVisualizer
, ProteinIdentificationVisualizer
- score_type_names
: PercolatorOutfile
- score_type_ref
: IdentificationData::ModifyMultiIndexAddScore< ElementType >
- score_types_
: IdentificationData
- score_weights
: MRMFeatureSelector::SelectorParameters
- score_with_isotopes()
: DIAScoring
- scoreAllChromatograms_()
: OpenSwathWorkflow
- scoreAssay_()
: ConfidenceScoring
- scoreCalculation_()
: MapAlignmentAlgorithmSpectrumAlignment
- scoredistribution_
: 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
- scores
: ConsensusIDAlgorithm::HitInfo
, AppliedProcessingStep
, ParentMoleculeGroup
- scores_
: IsotopeWaveletTransform< PeakType >
- scoreSpectra()
: CompNovoIonScoring
, TargetedSpectraExtractor
- scoreSpectrum()
: CompNovoIonScoringCID
- scoreThis_()
: IsotopeWaveletTransform< PeakType >
- ScoreType
: IdentificationData
, ScoreType
, IDScoreSwitcherAlgorithm
, PercolatorOutfile
- ScoreTypeRef
: IdentificationData
- ScoreTypes
: IdentificationData
- scoreWitnessSet_()
: CompNovoIonScoring
, CompNovoIonScoringBase
, CompNovoIonScoringCID
- scoring_()
: MapAlignmentAlgorithmSpectrumAlignment
- scoring_method_
: ConsensusIDAlgorithmPEPMatrix
- scoring_model_
: MRMFeatureFinderScoring
- sd_map_
: MzIdentMLDOMHandler
- search()
: SimpleSearchEngineAlgorithm
- search_AC_pattern()
: MS2Info
- search_database_ref
: MzIdentMLDOMHandler::SpectrumIdentification
- search_engine
: MzTabNucleicAcidSectionRow
, MzTabOligonucleotideSectionRow
, MzTabOSMSectionRow
, MzTabPeptideSectionRow
, MzTabProteinSectionRow
, MzTabPSMSectionRow
, MzTabSmallMoleculeSectionRow
- search_engine_
: MzIdentMLDOMHandler
, PepXMLFile
, ProteinIdentification
- search_engine_score
: MzTabOSMSectionRow
, MzTabPSMSectionRow
- search_engine_score_ms_run
: MzTabNucleicAcidSectionRow
, MzTabOligonucleotideSectionRow
, MzTabPeptideSectionRow
, MzTabProteinSectionRow
, MzTabSmallMoleculeSectionRow
- search_engine_version_
: MzIdentMLDOMHandler
, ProteinIdentification
- search_id_
: PepXMLFile
- search_identifier_
: MascotRemoteQuery
- search_param_
: ConsensusXMLFile
, FeatureXMLFile
- search_parameters_
: MascotXMLHandler
, ProteinIdentification
- search_score_summary_
: PepXMLFile
- search_summary_
: PepXMLFile
- search_title_
: MascotInfile
- search_type_
: MascotInfile
- searchAndShow_()
: SpectraViewWidget
- searched_mass_
: AccurateMassSearchResult
- searchInScan_()
: TwoDOptimization
- searchMass_()
: AccurateMassSearchEngine
- searchModifications()
: ModificationsDB
- searchModificationsByDiffMonoMass()
: ModificationsDB
- searchModificationsFast()
: ModificationsDB
- searchNextCell_()
: HashGrid< Cluster >::ConstIterator
, HashGrid< Cluster >::Iterator
- SearchParameters()
: ProteinIdentification::SearchParameters
- SearchParamRef
: IdentificationData
- searchPrefix()
: StringListUtils
- searchSuffix()
: StringListUtils
- searchtype
: MzIdentMLDOMHandler::SpectrumIdentificationProtocol
- SECH_PEAK
: PeakShape
- second
: ProbablePhosphoSites
, TransformationModel::DataPoint
- second_nearest_gap_
: StablePairFinder
- secondary
: ProteinResolver::ProteinEntry
- secondary_id_
: SpectralMatch
- secondary_indistinguishable
: ProteinResolver::ProteinEntry
- secondary_types
: SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- SECTOR
: MassAnalyzer
- Seed
: FeatureFinderAlgorithmPicked
- seed_
: UniqueIdGenerator
- SeedList
: SeedListGenerator
- SeedListGenerator()
: SeedListGenerator
- seeds_
: FeatureFinderAlgorithmPicked
- seekGToSavedPosition()
: FuzzyStringComparator::InputLine
- seen_experiment_
: PepXMLFile
- segment_step_length
: MRMFeatureSelector::SelectorParameters
- segment_window_length
: MRMFeatureSelector::SelectorParameters
- SELDI
: IonSource
- select()
: MSSpectrum
- select_transition_group
: MRMFeatureSelector::SelectorParameters
- selectAll()
: Annotations1DContainer
- selectChromHelper_()
: MRMTransitionGroupPicker
- selectCompoundsForBatch_()
: OpenSwathWorkflow
- selected()
: ParamTree
- selected_
: Annotation1DItem
, MultiGradientSelector
- selected_activation_
: IsobaricChannelExtractor
- selected_color_
: MultiGradientSelector
- selected_ion_count_
: MzMLHandler
- SELECTED_ION_CURRENT_CHROMATOGRAM
: ChromatogramSettings
- SELECTED_ION_FLOW_TUBE
: Instrument
- SELECTED_ION_MONITORING_CHROMATOGRAM
: ChromatogramSettings
- selected_peak_
: Spectrum2DCanvas
, SpectrumCanvas
- selected_pen_
: Annotations1DContainer
- SELECTED_REACTION_MONITORING_CHROMATOGRAM
: ChromatogramSettings
- selectFragments()
: MRMFragmentSelection
- selectionChanged()
: ParamTree
- selectionCopied()
: TOPPASScene
- selectItemAt()
: Annotations1DContainer
- selectMRMFeature()
: MRMFeatureSelector
- selector_
: MRMFeatureSelector_test
- SelectorParameters()
: MRMFeatureSelector::SelectorParameters
- selectPivotIons_()
: CompNovoIdentificationBase
- selectSpectra()
: TargetedSpectraExtractor
- selectSwathTransitions()
: OpenSwathHelper
- SemanticValidator()
: SemanticValidator
- semi_cleavage_
: XTandemInfile
- SEND
: IonSource
- sendClipboardContent()
: TOPPASBase
- sendCursorStatus()
: SpectrumCanvas
, SpectrumWidget
, TOPPASWidget
- sendStatus()
: BaseVisualizerGUI
- sendStatusMessage()
: SpectrumCanvas
, SpectrumWidget
, TOPPASWidget
- Sense
: LPWrapper
- sep_
: MzTabStringList
, SVOutStream
, CSVWriter
- SEPTUM
: IonSource
- seq_
: NASequence
- seq_1
: ProbablePhosphoSites
- seq_2
: ProbablePhosphoSites
- SeqAndRTList
: MapAlignmentAlgorithmTreeGuided
- SeqAnScore
: ConsensusIDAlgorithmPEPMatrix
- SeqAnSequence
: ConsensusIDAlgorithmPEPMatrix
- SeqToList
: MapAlignmentAlgorithmIdentification
- SeqToValue
: MapAlignmentAlgorithmIdentification
- sequence
: NucleicAcidSearchEngine::AnnotatedHit
, FASTAFile::FASTAEntry
, IdentifiedSequence< SeqType >
, ParentMolecule
, MzIdentMLDOMHandler::DBSequence
, MSstatsFile::MSstatsLine_
, MSstatsFile::MSstatsTMTLine_
, MzTabOligonucleotideSectionRow
, MzTabOSMSectionRow
, MzTabPeptideSectionRow
, MzTabPSMSectionRow
, ProteinResolver::PeptideEntry
, SimpleSearchEngineAlgorithm::AnnotatedHit_
, Peptide
, Protein
, LightCompound
, LightProtein
, Peptide
, Protein
- sequence_
: IMSElement
, MSstatsFile::MSstatsLine_
, MSstatsFile::MSstatsTMTLine_
, PeptideHit
, ProteinHit
- sequence_header_filter_
: SequestInfile
- sequence_tag_min_length_
: OpenPepXLLFAlgorithm
- SequenceGrouping
: ConsensusIDAlgorithm
- SequenceIdentity_()
: DecoyGenerator
- SequenceMapT
: MRMAssay
- sequenceMatches()
: FASTAFile::FASTAEntry
- sequences
: SVMData
- sequences_
: PrecursorIonSelectionPreprocessing
- SequenceToChargeToPepHitP
: IDFilter
- SequestInfile()
: SequestInfile
- SequestOutfile()
: SequestOutfile
- seriesposition_regex_
: SpectrumAnnotator
- server_path_
: MascotRemoteQuery
- set()
: CentroidData
, Date
, DateTime
, EGHFitter1D::Data
, EmgFitter1D::Data
, 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_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()
: 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_to_zero_
: ParentPeakMower
- 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
- setQualityAts_
: QcMLFile
- setQualityQPs_
: QcMLFile
- setQualityQPs_members_
: QcMLFile
- 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
- setting
: MzTabSoftwareMetaData
- settings_
: FullSwathFileConsumer
, MSDataWritingConsumer
- 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
- sf
: RawMSSignalSimulation::ContaminantInfo
- sf_accession
: SiriusMSFile::AccessionInfo
- sf_path
: SiriusMSFile::AccessionInfo
- sf_type
: SiriusMSFile::AccessionInfo
- sfIsoDist10
: IsotopicDist
- sfIsoDist50
: IsotopicDist
- sfIsoDist90
: IsotopicDist
- sfIsoMass10
: IsotopicDist
- sfIsoMass50
: IsotopicDist
- sfIsoMass90
: IsotopicDist
- sfMassStep
: IsotopicDist
- sfMaxIsotopeIndex
: IsotopicDist
- sfMaxMass
: IsotopicDist
- sfMaxMassIndex
: IsotopicDist
- sfMinMass
: IsotopicDist
- sfNrIsotopes
: IsotopicDist
- sgfilter_
: FIAMSDataProcessor
- sgolay_
: PeakPickerMRM
- sgolay_frame_length_
: PeakPickerMRM
- sgolay_polynomial_order_
: PeakPickerMRM
- SHA1
: SourceFile
- SHADE_FLAT
: Spectrum3DCanvas
- SHADE_SMOOTH
: Spectrum3DCanvas
- ShadeModes
: Spectrum3DCanvas
- shape
: RawMSSignalSimulation::ContaminantInfo
, TOPPASEdge
, TOPPASVertex
- SHFeature()
: SHFeature
- shift
: RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_
- shiftDown_()
: PrecursorIonSelection
- shiftedIonsToString()
: RNPxlFragmentAnnotationHelper
- shiftedToPHFA()
: RNPxlFragmentAnnotationHelper
- shiftUp_()
: PrecursorIonSelection
- short_name
: MultiplexDeltaMassesGenerator::Label
- 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
, DeconvPeak
, LCElutionPeak
, LCMS
, MS2ConsensusSpectrum
, MS2Feature
, MS2Fragment
, MS2Info
, MSPeak
, SHFeature
- show_legend_
: AxisWidget
- show_splitters_
: HistogramWidget
- show_timing_
: SpectrumCanvas
- 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
- SI
: IonSource
- si_map_
: MzIdentMLDOMHandler
- si_pro_map_
: MzIdentMLDOMHandler
- SID
: Precursor
- SIDE
: Compomer
- SideChain
: ProtonDistributionModel
- sidx_
: SpectrumAccessSqMass
- sigma
: GaussFitter::GaussFitResult
- SIGMA
: SVMWrapper
- sigma_
: EGHTraceFitter
, GaussFilterAlgorithm
, GaussTraceFitter
, IsotopeWaveletTransform< PeakType >
, PrecursorIonSelectionPreprocessing
, SVMWrapper
- sigma_5_bound_
: EGHTraceFitter
- sigma_square_
: EGHFitter1D
, EGHModel
- sigma_square_2_
: EGHModel
- sigmas_
: SVMWrapper
- signal
: OptimizePeakDeconvolution::Data
, OptimizePick::Data
, TwoDOptimization::Data
- signal2D
: TwoDOptimization::Data
- signal_
: ContinuousWaveletTransform
- signal_length_
: ContinuousWaveletTransform
- signal_proportion
: PrecursorPurity::PurityScores
- signal_to_noise
: PeakShape
- signal_to_noise_
: FeatureFinderIdentificationAlgorithm
, PeakPickerCWT
, PeakPickerHiRes
, PeakPickerIterative
, PeakPickerMaxima
, PeakPickerMRM
- signal_weight
: PSLPFormulation::IndexTriple
- SignalToNoise
: MSPeak
, SHFeature
- signalToNoise_
: CentroidPeak
- SignalToNoiseEstimator()
: SignalToNoiseEstimator< Container >
- SignalToNoiseEstimatorMeanIterative()
: SignalToNoiseEstimatorMeanIterative< Container >
- SignalToNoiseEstimatorMedian()
: SignalToNoiseEstimatorMedian< Container >
- SignalToNoiseEstimatorMedianRapid()
: SignalToNoiseEstimatorMedianRapid
- SignalToNoiseOpenMS()
: SignalToNoiseOpenMS< ContainerT >
- significance_threshold_
: PeptideIdentification
- sil_2_sdat_
: MzIdentMLHandler
- sil_2_sdb_
: MzIdentMLHandler
- sil_2_sip_
: MzIdentMLHandler
- SILACLabeler()
: SILACLabeler
- SILI
: IonSource
- SIM
: InstrumentSettings
- similarities_
: ConsensusIDAlgorithmSimilarity
- similarity_()
: SimplePairFinder
- SimilarityCache
: ConsensusIDAlgorithmSimilarity
- 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
- simulators_
: SvmTheoreticalSpectrumGeneratorSet
- sine_table_
: IsotopeWavelet
- SingleLinkage()
: SingleLinkage
- singleMass_
: Adduct
- SingletonRegistry()
: SingletonRegistry
- singletonRegistryInstance_
: SingletonRegistry
- singletonsNeedNoFriends
: Factory< FactoryProduct >
, SingletonRegistry
- SiriusAdapterAlgorithm()
: SiriusAdapterAlgorithm
- SiriusTemporaryFileSystemObjects()
: SiriusAdapterAlgorithm::SiriusTemporaryFileSystemObjects
- site
: MzTabModificationMetaData
- sites_
: UnimodXMLHandler
- size()
: KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
, AASequence
, CalibrationData
, ConsensusFeature
, ConsensusMap::ColumnHeader
, ConstRefVector< ContainerT >
, DataFilters
- SIZE
: DataFilters
- size()
: DPosition< D, TCoordinateType >
, FASTAContainer< TFI_File >
, FASTAContainer< TFI_Vector >
, FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern
, HashGrid< Cluster >
, IMSAlphabet
, IMSIsotopeDistribution
- SIZE
: IMSIsotopeDistribution
- size()
: Weights
, IDBoostGraph::ProteinGroup
, MzMLHandlerHelper::BinaryData
, 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
- size_
: ClusterProxyKD
, StringView
- 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_DRIFTTIMEUNIT
: Precursor
- SIZE_OF_FLAGS
: LayerData
- SIZE_OF_FLOATINDICES
: PeakPickerMRM
- 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_MODELTYPE
: MZTrafoModel
- SIZE_OF_MT_QUANTMETHOD
: MassTrace
- SIZE_OF_NUMPRESSCOMPRESSION
: MSNumpressCoder
- 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_SCORETYPE
: PercolatorOutfile
- SIZE_OF_SPECIFICITY
: EnzymaticDigestion
- SIZE_OF_SPECIFICITYTYPE
: Modification
- SIZE_OF_SPECTRUMTYPE
: SpectrumSettings
- SIZE_OF_TYPE
: FileTypes
, IonDetector
- SIZE_OF_WEIGHTMODE
: WeightWrapper
- size_only_
: FeatureFileOptions
, FeatureXMLFile
- size_proportions_
: SaveImageDialog
- size_ratio_
: SaveImageDialog
- size_type
: KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
, ConstRefVector< ContainerT >
, HashGrid< Cluster >
, IMSAlphabet
, IMSElement
, IMSIsotopeDistribution
, IntegerMassDecomposer< ValueType, DecompositionValueType >
, Weights
, Matrix< Value >
- size_x_
: SaveImageDialog
- size_y_
: SaveImageDialog
- sizeHint()
: ColorSelector
- SizeOfNASFragmentType
: NASequence
- SizeOfResidueType
: Residue
- sizePair()
: Matrix< Value >
- sizeProfile()
: MultiplexFilteredPeak
- SizeType
: ConvexHull2D
, DistanceMatrix< Value >
, Matrix< Value >
, String
- SizeUnderflow()
: SizeUnderflow
- skip_chromatogram_
: MzMLHandler
- skip_data
: MzXMLHandler::SpectrumData
- skip_protein_acc_update_
: XTandemXMLFile
- skip_spectrum_
: MzDataHandler
, MzMLHandler
, MzXMLHandler
- skip_xml_checks_
: IndexedMzMLHandler
, MzMLSpectrumDecoder
, PeakFileOptions
- SLOF
: MSNumpressCoder
- slope_
: LinearRegression
, TransformationModelLinear
- slope_bound_
: FeatureFinderAlgorithmPicked
- slope_max_
: TransformationModelBSpline
- slope_min_
: TransformationModelBSpline
- slope_of_baseline
: PeakIntegrator::PeakShapeMetrics
- sm_
: XMLHandler
- small_molecule_data_
: MzTab
- small_molecule_quantification_unit
: MzTabMetaData
- smallest_score_
: PosteriorErrorProbabilityModel
- smallmolecule_abundance_assay
: MzTabSmallMoleculeSectionRow
- smallmolecule_abundance_std_error_study_variable
: MzTabSmallMoleculeSectionRow
- smallmolecule_abundance_stdev_study_variable
: MzTabSmallMoleculeSectionRow
- smallmolecule_abundance_study_variable
: MzTabSmallMoleculeSectionRow
- smallmolecule_search_engine_score
: MzTabMetaData
- smartFileNames_()
: TOPPASToolVertex
- smile
: IdentifiedCompound
- smiles
: CsiFingerIdMzTabWriter::CsiAdapterHit
, MzTabSmallMoleculeSectionRow
- SMILES
: TransitionTSVFile::TSVTransition
- smiles_string
: Compound
- smiles_string_
: SpectralMatch
- smooth()
: RawData
- smoothData()
: ElutionPeakDetection
, LowessSmoothing
- smoothed_intensities_
: MassTrace
- SMOOTHING
: DataProcessing
- smoothRTDistortion_()
: RTSimulation
- sn_
: SignalToNoiseOpenMS< ContainerT >
- sn_bin_count_
: MRMFeatureFinderScoring
, PeakPickerIterative
, PeakPickerMRM
- sn_ratio
: OpenSwath_Scores
- SN_statistics_
: SpectrumAnnotator
- sn_win_len_
: MRMFeatureFinderScoring
, PeakPickerIterative
, PeakPickerMRM
- sn_window_length_
: PeakPickerMaxima
- snap_factors_
: SpectrumCanvas
- snapShot_()
: StopWatch
- snapToGrid()
: TOPPASScene
- snd_database_
: SequestInfile
- snr_weight_
: TargetedSpectraExtractor
- snt_
: PeakPickerMRM
- software
: MzTabMetaData
, MzTabSoftwareMetaData
- Software()
: Software
- software_
: DataProcessing
, Instrument
, MzMLHandler
, TargetedExperiment
- software_name_
: SoftwareVisualizer
- software_ref
: DataProcessingStep
, Prediction
, RetentionTime
- software_version_
: SoftwareVisualizer
- SoftwareVisualizer()
: SoftwareVisualizer
- SOI
: IonSource
- SOLID
: Sample
- SOLUTION
: Sample
- solve()
: BSpline2d
, LPWrapper
, NonNegativeLeastSquaresSolver
- SOLVED
: NonNegativeLeastSquaresSolver
- solveILP()
: PSLPFormulation
- solveNNLS_()
: IsobaricIsotopeCorrector
- SOLVER
: LPWrapper
- solver_
: IsotopeWavelet
, LPWrapper
, OfflinePrecursorIonSelection
, PrecursorIonSelection
, PSLPFormulation
, PSProteinInference
- SOLVER_GLPK
: LPWrapper
- SolverParam()
: LPWrapper::SolverParam
- SolverStatus
: LPWrapper
- somethingHasChanged()
: TOPPASEdge
, TOPPASVertex
- sonar_
: OpenSwathOSWWriter
, OpenSwathTSVWriter
- sonar_diff
: OpenSwath_Scores
- sonar_lag
: OpenSwath_Scores
- sonar_rsq
: OpenSwath_Scores
- sonar_shape
: OpenSwath_Scores
- sonar_sn
: OpenSwath_Scores
- sonar_trend
: OpenSwath_Scores
- SONARScoring()
: SONARScoring
- sonarscoring_
: MRMFeatureFinderScoring
- SORI
: Precursor
- sort()
: ROCCurve
, PeptideIdentification
, ProteinIdentification
- sort_()
: ExperimentalDesign
, IsotopeDistribution
- sort_by_position_
: TheoreticalSpectrumGenerator
- sort_chromatograms_by_rt_
: PeakFileOptions
- sort_spectra_by_mz_
: PeakFileOptions
- 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
- Sorted
: IsotopeDistribution
- sorted_
: ROCCurve
- SortExtractionCoordinatesByMZ()
: ChromatogramExtractorAlgorithm::ExtractionCoordinates
- SortExtractionCoordinatesReverseByMZ()
: ChromatogramExtractorAlgorithm::ExtractionCoordinates
- sortPeptideIdentificationsByMapIndex()
: ConsensusMap
- sortPSM_()
: MzTabFile
- sortSpectra()
: MSExperiment
- sortTransitionsByProductMZ()
: TargetedExperiment
- source
: MzTabInstrumentMetaData
- SOURCE_DIR
: FTPeakDetectController
- source_feature_index_
: AccurateMassSearchResult
- source_file
: SiriusMSFile::CompoundInfo
- source_file_
: ChromatogramSettings
, SpectrumSettings
- source_files_
: ExperimentalSettings
, MzMLHandler
, TargetedExperiment
- source_format
: SiriusMSFile::CompoundInfo
- source_out_param_
: TOPPASEdge
- SourceClassification
: ResidueModification
- SourceFile()
: SourceFile
- SourceFileVisualizer()
: SourceFileVisualizer
- sourceHasChanged()
: TOPPASEdge
- sp_map_
: MzIdentMLDOMHandler
- spacer_
: Spectrum1DWidget
- spacing_
: ContinuousWaveletTransform
, GaussFilter
, GaussFilterAlgorithm
, LinearResampler
- spacing_difference_
: PeakPickerHiRes
, PeakPickerIterative
, PeakPickerMaxima
- spacing_difference_gap_
: PeakPickerHiRes
, PeakPickerMaxima
- spacing_for_spectra_resampling_
: MRMFeatureFinderScoring
, OpenSwathScoring
- sparse_window_percent_
: SignalToNoiseEstimatorMedian< Container >
- SparseVectorIndexType
: BinnedSpectrum
- SparseVectorIteratorType
: BinnedSpectrum
- SparseVectorType
: BinnedSpectrum
- spatiallyGreaterEqual()
: DPosition< D, TCoordinateType >
- spatiallyLessEqual()
: DPosition< D, TCoordinateType >
- Spawn()
: Spawn< TNeedle >
- SpawnCIt
: PatternAuxData< TNeedle >
- SpawnIt
: PatternAuxData< TNeedle >
- spawns
: PatternAuxData< TNeedle >
- Spawns
: PatternAuxData< TNeedle >
- spec_
: MzDataHandler
, MzMLHandler
, MSSpectrum::Chunks
- SPEC_FULL
: EnzymaticDigestion
- spec_id_
: MzMLSqliteHandler
, MzMLSqliteSwathHandler
- spec_name
: LCMS
- SPEC_NOCTERM
: EnzymaticDigestion
- SPEC_NONE
: EnzymaticDigestion
- SPEC_NONTERM
: EnzymaticDigestion
- spec_ref_
: MzTabSpectraRef
- SPEC_SEMI
: EnzymaticDigestion
- SPEC_UNKNOWN
: EnzymaticDigestion
- spec_write_counter_
: MzXMLHandler
- SpecArrayFile()
: SpecArrayFile
- species
: MzTabNucleicAcidSectionRow
, MzTabProteinSectionRow
, MzTabSampleMetaData
, MzTabSmallMoleculeSectionRow
- specificities
: MzIdentMLDOMHandler::ModificationParam
- Specificity
: EnzymaticDigestion
- specificity_
: EnzymaticDigestion
- specificity_type_
: Modification
- SpecificityType
: Modification
- specref_format
: SiriusMSFile::CompoundInfo
- specrefs
: SiriusMSFile::CompoundInfo
- spectra_
: InspectInfile
, MSDataSqlConsumer
, MSExperiment
, SpectrumAccessOpenMSInMemory
- spectra_addition_method_
: OpenSwathScoring
- spectra_all_peaks
: OPXLDataStructs::PreprocessedPairSpectra
- spectra_before_chroms_
: IndexedMzMLHandler
- spectra_combo_box_
: SpectraViewWidget
- spectra_data_ref
: MzIdentMLDOMHandler::SpectrumIdentification
, SpectrumMetaDataLookup
- spectra_expected_
: MSDataWritingConsumer
- spectra_identification_view_widget_
: TOPPViewBase
- spectra_index_
: CachedmzML
, CachedMzMLHandler
- spectra_linear_peaks
: OPXLDataStructs::PreprocessedPairSpectra
- spectra_meta_
: SpectrumAccessOpenMSInMemory
- spectra_native_ids_
: IndexedMzMLHandler
, OnDiscMSExperiment
- spectra_offsets_
: IndexedMzMLHandler
, MzMLHandler
- spectra_ref
: MzTabOSMSectionRow
, MzTabPeptideSectionRow
, MzTabPSMSectionRow
, MzTabSmallMoleculeSectionRow
- spectra_search_box_
: SpectraViewWidget
- spectra_treewidget_
: SpectraViewWidget
- spectra_view_widget_
: TOPPViewBase
- spectra_written_
: MSDataCachedConsumer
, MSDataWritingConsumer
- spectra_xlink_peaks
: OPXLDataStructs::PreprocessedPairSpectra
- SpectraDistance_()
: SpectraMerger::SpectraDistance_
- SpectraIdentificationViewWidget()
: SpectraIdentificationViewWidget
- SpectralMatch()
: SpectralMatch
- SpectraMap()
: QCBase::SpectraMap
- SpectraMerger()
: SpectraMerger
- spectrastAnnotationExtract()
: TransitionTSVFile
- spectrastRTExtract()
: TransitionTSVFile
- SpectraSTSimilarityScore()
: SpectraSTSimilarityScore
- spectraview_behavior_
: TOPPViewBase
- SpectraViewWidget()
: SpectraViewWidget
- spectrum
: FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern
, FeatureFinderAlgorithmPickedHelperStructs::Seed
- Spectrum()
: Spectrum
- spectrum
: MzMLHandler::SpectrumData
, MzXMLHandler::SpectrumData
, PeakIndex
, TargetedSpectraExtractor::Match
- Spectrum1DCanvas()
: Spectrum1DCanvas
- Spectrum1DGoToDialog()
: Spectrum1DGoToDialog
- Spectrum1DPrefDialog()
: Spectrum1DPrefDialog
- Spectrum1DWidget()
: Spectrum1DWidget
- Spectrum2DCanvas()
: Spectrum2DCanvas
- Spectrum2DGoToDialog()
: Spectrum2DGoToDialog
- Spectrum2DPrefDialog()
: Spectrum2DPrefDialog
- Spectrum2DWidget()
: Spectrum2DWidget
- Spectrum3DCanvas()
: Spectrum3DCanvas
, Spectrum3DOpenGLCanvas
- Spectrum3DOpenGLCanvas
: Spectrum3DCanvas
, Spectrum3DOpenGLCanvas
- Spectrum3DPrefDialog()
: Spectrum3DPrefDialog
- Spectrum3DWidget()
: Spectrum3DWidget
- spectrum_addition_method_
: MRMFeatureFinderScoring
- spectrum_data_
: MzMLHandler
, MzXMLHandler
- spectrum_id
: LCMS
- spectrum_ID
: SHFeature
- spectrum_identification_list_ref
: MzIdentMLDOMHandler::SpectrumIdentification
- spectrum_identification_protocol_ref
: MzIdentMLDOMHandler::SpectrumIdentification
- spectrum_identifications_
: Identification
- spectrum_ids_
: XTandemXMLFile
- spectrum_index_heavy_
: XQuestResultXMLHandler
- spectrum_index_light_
: XQuestResultXMLHandler
- spectrum_input_file_
: XQuestResultXMLHandler
- spectrum_widget_
: SpectrumCanvas
- 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
- SpectrumConstIteratorType
: SpectrumCanvas
- spectrumContextMenu_()
: SpectraViewWidget
- spectrumDeselected()
: SpectraIdentificationViewWidget
- spectrumDoubleClicked()
: SpectraIdentificationViewWidget
, SpectraViewWidget
- spectrumDoubleClicked_()
: SpectraViewWidget
- SpectrumIdentification()
: SpectrumIdentification
- SpectrumIteratorType
: AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
- SpectrumLookup()
: SpectrumLookup
- SpectrumMeta()
: SpectrumMeta
- SpectrumMetaData()
: SpectrumMetaDataLookup::SpectrumMetaData
- SpectrumMetaDataLookup()
: SpectrumMetaDataLookup
- SpectrumPrecursorComparator()
: SpectrumPrecursorComparator
- SpectrumPtrType
: DIAScoring
- spectrumSearchText_()
: SpectraViewWidget
- spectrumSelected()
: SpectraIdentificationViewWidget
, SpectraViewWidget
- spectrumSelectionChange_()
: SpectraIdentificationViewWidget
, SpectraViewWidget
- SpectrumSettings()
: SpectrumSettings
- SpectrumSettingsVisualizer()
: SpectrumSettingsVisualizer
- SpectrumType
: CachedSwathFileConsumer
, FeatureFinderAlgorithmMRM
, FeatureFinderAlgorithmPicked
, FeatureFinderAlgorithmSH
, FullSwathFileConsumer
, IMSDataConsumer
, CachedMzMLHandler
, MzDataHandler
, MzMLHandler
, MzXMLHandler
, MSDataCachedConsumer
, MSDataSqlConsumer
, MSDataWritingConsumer
, MSExperiment
, MzMLSwathFileConsumer
, RegularSwathFileConsumer
, SpectrumCanvas
, SpectrumSettings
, SpectrumWidget
, TOPPViewBase
, TOPPViewIdentificationViewBehavior
, TOPPViewSpectraViewBehavior
, MRMScoring
- SpectrumWidget()
: SpectrumWidget
- SPECXML
: FileTypes
- SPI
: IonSource
- SPLIB
: FileTypes
- spline_
: BSpline2d
, SplinePackage
, TransformationModelBSpline
- SplineInterpolatedPeaks()
: SplineInterpolatedPeaks
- SplinePackage()
: SplinePackage
- split()
: ConsensusMap
, String
, StringUtils
- split_quoted()
: String
, StringUtils
- splitByMiddle()
: XQuestResultXMLHandler
- splitByNth()
: XQuestResultXMLHandler
- SplitMeta
: ConsensusMap
- splitModificationBySpecifiedAA()
: MascotXMLHandler
- splitTransitionGroupsDetection_()
: MRMFeatureFinderScoring
- splitTransitionGroupsIdentification_()
: MRMFeatureFinderScoring
- SPS
: PrecursorIonSelection
- sptr
: SwathMap
- sptr_
: SpectrumAccessTransforming
- SQ
: MS2Info
- sql_batch_size_
: MzMLSqliteHandler
- SqliteConnector()
: SqliteConnector
- SQMASS
: FileTypes
- SqMassConfig()
: SqMassFile::SqMassConfig
- SqMassFile()
: SqMassFile
- sqrt2pi()
: BasicStatistics< RealT >
- SqrtMower()
: SqrtMower
- squared_difference_counted()
: squared_difference_counted< _Tp, _Dist >
- sr_map_
: MzIdentMLDOMHandler
- SRM
: InstrumentSettings
- ss_
: SVOutStream
- st_
: Annotation1DCaret
- 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_stddev()
: mean_and_stddev
- standard_variance()
: mean_and_stddev
- start()
: FakeProcess
, FeatureFinderIdentificationAlgorithm::RTRegion
, MzIdentMLDOMHandler::PeptideEvidence
, MSSpectrum::Chunk
, MzTabOligonucleotideSectionRow
, MzTabPSMSectionRow
, StopWatch
- start_
: PeptideEvidence
- start_point_
: Annotation1DDistanceItem
- start_pos
: MoleculeParentMatch
- start_position_at_10
: PeakIntegrator::PeakShapeMetrics
- start_position_at_5
: PeakIntegrator::PeakShapeMetrics
- start_position_at_50
: PeakIntegrator::PeakShapeMetrics
- start_time
: StopWatch::TimeDiff_
- start_time_usec
: StopWatch::TimeDiff_
- start_vertex()
: IDBoostGraph::dfs_ccsplit_visitor
- started_writing_
: MSDataWritingConsumer
- 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
- startScan
: MS2ConsensusSpectrum
- startScanParsing()
: FTPeakDetectController
- startTOPPView()
: GUIHelpers
- startTR
: MS2ConsensusSpectrum
- state_
: MzTabDouble
, MzTabInteger
, Sample
- states
: AnnotationStatistics
- states_
: HiddenMarkovModel
- STATIC_FIELD
: Instrument
- static_intensities
: SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- Statistics()
: PeptideAndProteinQuant::Statistics
- statistics1_
: BiGaussFitter1D
, BiGaussModel
- statistics2_
: BiGaussFitter1D
, BiGaussModel
- statistics_
: EGHModel
, EmgModel
, FeatureFinderIdentificationAlgorithm
, Fitter1D
, GaussModel
, PeptideProteinResolution
- stats_
: IsobaricQuantifier
, PeptideAndProteinQuant
- Status()
: QCBase::Status
- status_
: PepXMLFile
, TOPPASToolVertex
- status_list_
: MetaDataBrowser
- stddev()
: mean_and_stddev
- stdev_
: SignalToNoiseEstimatorMeanIterative< Container >
- SteinScottImproveScore()
: SteinScottImproveScore
- step_ref
: IdentificationData::ModifyMultiIndexAddProcessingStep< ElementType >
- steps_and_scores
: ScoredProcessingResult
- stickdata_
: Spectrum3DOpenGLCanvas
- stn_estimates_
: SignalToNoiseEstimator< Container >
- stop
: MzIdentMLDOMHandler::PeptideEvidence
, StopWatch
- stop_after_feature_
: MRMTransitionGroupPicker
- stop_after_intensity_ratio_
: MRMTransitionGroupPicker
- stop_condition_
: FineIsotopePatternGenerator
- stop_report_after_feature_
: MRMFeatureFinderScoring
- 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
- STORE
: XMLHandler
- store()
: 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
- store_
: DataMatrix
- store_compact_
: MascotGenericFile
- store_nucleic_acid_goterms_
: MzTabFile
- store_nucleic_acid_reliability_
: MzTabFile
- store_nucleic_acid_uri_
: MzTabFile
- store_oligonucleotide_reliability_
: MzTabFile
- store_oligonucleotide_uri_
: MzTabFile
- store_osm_reliability_
: MzTabFile
- store_osm_uri_
: MzTabFile
- store_peptide_reliability_
: MzTabFile
- store_peptide_uri_
: MzTabFile
- store_protein_goterms_
: MzTabFile
- store_protein_reliability_
: MzTabFile
- store_protein_uri_
: MzTabFile
- store_psm_reliability_
: MzTabFile
- store_psm_uri_
: MzTabFile
- store_smallmolecule_reliability_
: MzTabFile
- store_smallmolecule_uri_
: MzTabFile
- storeAllLowProbabilityMS2Scans()
: SuperHirnParameters
- 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
- strarray_
: TransitionTSVFile
- stream
: LogStreamBuf::StreamStruct
- stream_
: IDBoostGraph::PrintAddressVisitor< CharT >
, LogStreamNotifier
- stream_at_end_
: Bzip2Ifstream
, GzipIfstream
- stream_list_
: LogStreamBuf
- stream_type_map_
: LogConfigHandler
- StreamElement_()
: FuzzyStringComparator::StreamElement_
- streamEnd()
: Bzip2Ifstream
, GzipIfstream
- StreamHandler()
: StreamHandler
- StreamIterator
: LogStream
- StreamStruct()
: LogStreamBuf::StreamStruct
- StreamType
: StreamHandler
- strict_
: MRMFeatureFinderScoring
- STRING
: ListEditor
, ParameterInformation
, StreamHandler
- String()
: String
, MRMScoring
- string_data_arrays_
: MSChromatogram
, MSSpectrum
, ProteinIdentification::ProteinGroup
- STRING_LIST
: DataValue
- STRING_VALUE
: DataValue
- StringDataArray
: MSChromatogram
, MSSpectrum
, ProteinIdentification::ProteinGroup
- StringDataArrays
: MSChromatogram
, MSSpectrum
, ProteinIdentification::ProteinGroup
- STRINGLIST
: ParameterInformation
- stringListToIsotopCorrectionMatrix_()
: IsobaricQuantitationMethod
- StringListUtils()
: StringListUtils
- StringManager()
: StringManager
- StringView()
: StringView
- strip_namespaces_
: CVMappingFile
- stripExtension()
: FileHandler
- struct_size_in_datapoints_
: MorphologicalFilter
- study_variable
: MzTabMetaData
- stw_
: GUILock
- su_
: MRMFeatureFinderScoring
, OpenSwathScoring
- sub_scores
: PeptideHit::PepXMLAnalysisResult
- subordinate_feature_level_
: FeatureXMLFile
- subordinates_
: Feature
- subsamples_
: Sample
- subsections_
: DefaultParamHandler
, TOPPBase
- subsections_TOPP_
: TOPPBase
- subset()
: MRMTransitionGroup< ChromatogramType, TransitionType >
- subsetDependent()
: MRMTransitionGroup< ChromatogramType, TransitionType >
- subspec_to_sequences_
: CompNovoIdentificationBase
- substitute()
: String
, StringUtils
- substr()
: String
, StringUtils
, StringView
- SUBSTREESTATUS
: TOPPASVertex
- subtractIntensity()
: CentroidPeak
- subtractMatchingPeaks()
: IsotopicDist
- subvalue_type
: _Region< __K, _Val, _SubVal, _Acc, _Cmp >
, KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
- succ_states_
: HMMState
- success
: DecoyHelper::Result
- suffix()
: Param::ParamNode
, String
, StringUtils
- SUI
: IonSource
- suitability
: DBSuitability::SuitabilityData
- sum()
: BasicStatistics< RealT >
- sum_
: BasicStatistics< RealT >
- sum_formula
: LightCompound
- sum_formula_
: SpectralMatch
- sum_xx_
: LinearRegressionWithoutIntercept
- sum_xy_
: LinearRegressionWithoutIntercept
- SumFormula
: TransitionTSVFile::TSVTransition
- sumIntensity_()
: MSstatsFile
- Summary()
: Summary
- SummaryStatistics()
: SummaryStatistics< T >
- SuperHirnParameters()
: SuperHirnParameters
- superimposer_
: MapAlignmentAlgorithmPoseClustering
- support
: ConsensusIDAlgorithm::HitInfo
- 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_min_prob_
: FeatureFinderIdentificationAlgorithm
- svm_n_parts_
: FeatureFinderIdentificationAlgorithm
- svm_n_samples_
: FeatureFinderIdentificationAlgorithm
- SVM_parameter_type
: SVMWrapper
- svm_params_
: SimpleSVM
- svm_predictor_names_
: FeatureFinderIdentificationAlgorithm
- svm_probs_external_
: FeatureFinderIdentificationAlgorithm
- svm_probs_internal_
: FeatureFinderIdentificationAlgorithm
- svm_quality_cutoff
: FeatureFinderIdentificationAlgorithm
- SVM_TYPE
: SVMWrapper
- svm_xval_out_
: FeatureFinderIdentificationAlgorithm
- SVMData()
: SVMData
- svmFilter_()
: DetectabilitySimulation
- SVMPerformance
: SimpleSVM
- SvmTheoreticalSpectrumGenerator()
: SvmTheoreticalSpectrumGenerator
- SvmTheoreticalSpectrumGeneratorSet()
: SvmTheoreticalSpectrumGeneratorSet
- SvmTheoreticalSpectrumGeneratorTrainer
: SvmTheoreticalSpectrumGenerator
, SvmTheoreticalSpectrumGeneratorTrainer
- SVMWrapper()
: SVMWrapper
- SVOutStream()
: SVOutStream
- swap()
: ConsensusMap
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, ConstRefVector< ContainerT >
, DocumentIdentifier
, FeatureMap
, Weights
, MSExperiment
, UniqueIdIndexer< RandomAccessContainer >
, UniqueIdInterface
- swapExtension()
: FileHandler
- swapFeaturesOnly()
: FeatureMap
- swath_assay_
: PepXMLFile
- swath_consumers_
: CachedSwathFileConsumer
, MzMLSwathFileConsumer
- swath_map_boundaries_
: FullSwathFileConsumer
- swath_maps_
: FullSwathFileConsumer
- swath_param_
: SwathTabWidget
- swath_param_wizard_
: SwathTabWidget
- SwathLibraryStats()
: SwathLibraryStats
- SwathMap()
: SwathMap
- SwathMapMassCorrection()
: SwathMapMassCorrection
- SwathQC()
: SwathQC
- SwathTabWidget()
: SwathTabWidget
- SwathWizardBase()
: SwathWizardBase
- SWIFT
: MassAnalyzer
- switchScores()
: IDScoreSwitcherAlgorithm
- switchToGeneralScoreType()
: IDScoreSwitcherAlgorithm
- symbol_
: Element
- symbols_
: ElementDB
- symmetric_
: LevMarqFitter1D
, TransformationModelLinear
- symmetry_
: EmgFitter1D
, EmgModel
- sync()
: LogStreamBuf
- synchronizePeakAnnotations()
: LayerData
- syncLF_()
: LogStreamBuf
- syncParams_()
: MSSim
- synonym_trans_
: HiddenMarkovModel
- synonym_trans_names_
: HiddenMarkovModel
- synonyms
: ControlledVocabulary::CVTerm
- synonyms_
: DigestionEnzyme
, MSPGenericFile
, Residue
, ResidueModification
- synonyms_separator_
: MSPGenericFile