| OpenMS 2.5.0

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
- Scaler() : Scaler
- scaleSingleFeature_() : SvmTheoreticalSpectrumGenerator
- scaling_ : InterpolationModel
- 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 > , IsotopeWaveletTransform< PeakType >::BoxElement , MorpheusScore::Result
- SCORE : MSPeak
- score : OPXLDataStructs::CrossLinkSpectrumMatch
- SCORE : PercolatorOutfile
- score : RNPxlReportRow , SimpleSearchEngineAlgorithm::AnnotatedHit_ , SiriusMzTabWriter::SiriusAdapterHit , TargetedSpectraExtractor::Match , RateScorePair , SIPPeptide
- 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 : AppliedProcessingStep , ParentMoleculeGroup
- scores_ : IsotopeWaveletTransform< PeakType >
- scoreSpectra() : CompNovoIonScoring , TargetedSpectraExtractor
- scoreSpectrum() : CompNovoIonScoringCID
- scoreThis_() : IsotopeWaveletTransform< PeakType >
- ScoreType : IdentificationData , ScoreType , 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
- 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 , SIPPeptide
- sequence_ : IMSElement , MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , PeptideHit , ProteinHit
- sequence_header_filter_ : SequestInfile
- sequence_tag_min_length_ : OpenPepXLLFAlgorithm
- SequenceGrouping : ConsensusIDAlgorithm
- 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 , 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
- 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
- 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
- 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
- setFileName() : ListEditorDelegate
- setFilenames() : 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
- 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() : MzTabNullNaNAndInfAbleBase , MzTabNullNaNAndInfAbleInterface
- 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
- 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
- setModification_() : 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() : MzTabNullNaNAndInfAbleBase , MzTabNullNaNAndInfAbleInterface
- setNativeID() : ChromatogramSettings , ReactionMonitoringTransition , SpectrumSettings
- setNativeIDType() : SourceFile
- setNativeIDTypeAccession() : SourceFile
- setNeutralLossAverageMass() : ResidueModification
- setNeutralLossDiffFormula() : ResidueModification
- setNeutralLossesForIons() : SequestInfile
- setNeutralLossMonoMass() : 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() : MzTabDoubleList , MzTabIntegerList , MzTabModification , MzTabModificationList , MzTabNullAbleBase , MzTabNullAbleInterface , MzTabNullNaNAndInfAbleBase , 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() : 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() : 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
- 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() : 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
- setSolver() : LPWrapper , PSProteinInference
- 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
- 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 , TOPPASBase , TOPPViewBase
- 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() : TOPPASInputFileDialog , TOPPASInputFilesDialog , TOPPASOutputFilesDialog
- 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 , TOPPViewBase
- shufflePeptide() : MRMDecoy
- 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
- SIZE : IMSIsotopeDistribution
- size() : IMSIsotopeDistribution , Weights , 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
- 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
- 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
- SPEC_FULL : EnzymaticDigestion
- spec_id_ : MzMLSqliteHandler , MzMLSqliteSwathHandler
- spec_name : LCMS
- SPEC_NONE : EnzymaticDigestion
- spec_ref_ : MzTabSpectraRef
- SPEC_SEMI : 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_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() : String , StringUtils
- split_quoted() : String , StringUtils
- splitByMiddle() : XQuestResultXMLHandler
- splitByNth() : XQuestResultXMLHandler
- 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 , 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_secs_ : StopWatch
- start_system_time_ : StopWatch
- start_usecs_ : StopWatch
- start_user_time_ : StopWatch
- 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_ : MzTabNullNaNAndInfAbleBase , 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
- StopWatch() : StopWatch
- store() : AbsoluteQuantitationMethodFile , AcquisitionInfoVisualizer , AcquisitionVisualizer , BaseVisualizerGUI , CachedmzML , ConsensusXMLFile , ContactPersonVisualizer , CsvFile , DataProcessingVisualizer , DigestionVisualizer , DocumentIdentifierVisualizer , DTA2DFile , DTAFile , EDTAFile , ExperimentalSettingsVisualizer , FASTAFile , FeatureXMLFile , GradientVisualizer , HPLCVisualizer , IBSpectraFile , IdXMLFile , IndexedMzMLFileLoader , InspectInfile , InstrumentSettingsVisualizer , InstrumentVisualizer
- STORE : XMLHandler
- store() : IonDetectorVisualizer , IonSourceVisualizer , KroenikFile , MascotGenericFile , MascotInfile , MassAnalyzerVisualizer , MetaInfoDescriptionVisualizer , MetaInfoVisualizer , ModificationVisualizer , 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
- struct_size_in_datapoints_ : MorphologicalFilter
- study_variable : MzTabMetaData
- 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
- 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
- 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
- swapFeaturesOnly() : FeatureMap
- swath_assay_ : PepXMLFile
- swath_consumers_ : CachedSwathFileConsumer , MzMLSwathFileConsumer
- swath_map_boundaries_ : FullSwathFileConsumer
- swath_maps_ : FullSwathFileConsumer
- SwathMap() : SwathMap
- SwathMapMassCorrection() : SwathMapMassCorrection
- SwathQC() : SwathQC
- SWIFT : MassAnalyzer
- 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