Here is a list of all class members with links to the classes they belong to:

- s -

S : ExtendedIsotopeModel, IsotopeModel
s_list : MSDataAggregatingConsumer
s_tmp : MSDataAggregatingConsumer
safeParse_() : MzMLFile
sameNrOfMSFilesPerFraction() : ExperimentalDesign
sample : ExperimentalDesign::MSFileSectionEntry, MzTabMetaData, MzTabMMetaData
Sample() : Sample
sample_ : ExperimentalSettings
sample_name : AbsoluteQuantitationStandards::runConcentration, ExperimentalDesign::MSFileSectionEntry
sample_processing : MzTabMetaData, MzTabMMetaData
SAMPLE_RATE : MassTraceDetection
sample_ref : MzTabAssayMetaData, MzTabMAssayMetaData
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
sampleExperiment() : OpenSwathHelper
samplemass_ : SampleVisualizer
samplename_ : SampleVisualizer
SAMPLENULL : Sample
samplenumber_ : SampleVisualizer
sampleorganism_ : SampleVisualizer
samples_ : FIAMSScheduler, MzMLHandler
samples_labels_ : MultiplexDeltaMassesGenerator
SampleSection() : ExperimentalDesign::SampleSection
SampleState : Sample
samplestate_ : SampleVisualizer
sampleStateToString() : Sample
SamplesType : BaseModel
SampleVisualizer() : SampleVisualizer
samplevolume_ : SampleVisualizer
sanityCheck_() : TOPPASScene
satellites_ : MultiplexFilteredPeak
satellites_profile_ : MultiplexFilteredPeak
save_() : XMLFile
saveAll_() : MetaDataBrowser
saveallbutton_ : MetaDataBrowser
saveAsImage() : Plot1DWidget, PlotWidget
saveCurrentLayer() : PlotCanvas
saveCurrentPipelineAs() : TOPPASBase
saveFeatureCompoundInfoAsTSV() : SiriusMSFile
saveFile() : INIFileEditorWindow
saveFileAs() : INIFileEditorWindow
saveIDs_() : SpectraIDViewTab
saveIfChanged() : TOPPASScene
SaveImageDialog() : SaveImageDialog
saveLayerAll() : TOPPViewBase
saveLayerVisible() : TOPPViewBase
saveMe() : TOPPASScene
savePipeline() : TOPPASBase
savePipelineAs() : TOPPASBase
savePipelineResourceFile() : TOPPASBase
savePreferences() : TOPPASBase, TOPPViewBase
saveToClipboard() : TOPPASBase
saveToFile() : LayerStoreData, LayerStoreDataConsensusMapAll, LayerStoreDataConsensusMapVisible, LayerStoreDataFeatureMapAll, LayerStoreDataFeatureMapVisible, LayerStoreDataIdentAll, LayerStoreDataIdentVisible, LayerStoreDataPeakMapAll, LayerStoreDataPeakMapVisible
SavitzkyGolayFilter() : SavitzkyGolayFilter
scale_() : AxisPainter, EuclideanSimilarity, LinearInterpolation< Key, Value >
scale_0_ : BilinearInterpolation< Key, Value >
scale_1_ : BilinearInterpolation< Key, Value >
scaleBy() : RangeBase, RangeManager< RangeBases >
scaledIntensity_() : Plot3DOpenGLCanvas
scaledInversMZ_() : Plot3DOpenGLCanvas
scaledInversRT_() : Plot3DOpenGLCanvas
scaledMZ_() : Plot3DOpenGLCanvas
scaledRT_() : Plot3DOpenGLCanvas
ScaleMap : SimpleSVM
scaling_ : InterpolationModel
scan : FLASHHelperClasses::IsobaricQuantities
scan_count_ : MzMLHandler, MzXMLHandler
scan_count_total_ : MzMLHandler
scan_counter : MassTraceDetection::TraceExtensionState
scan_dir_ : MassAnalyzerVisualizer
scan_direction_ : MassAnalyzer
scan_event_number : Ms2SpectrumStats::ScanEvent
scan_idx : MassTraceDetection::Apex
scan_index : NucleicAcidSearchEngine::PrecursorInfo
scan_index_heavy : OPXLDataStructs::CrossLinkSpectrumMatch
scan_index_light : OPXLDataStructs::CrossLinkSpectrumMatch
scan_indices : Biosaur2Algorithm::Hill, SiriusMSFile::CompoundInfo
scan_law_ : MassAnalyzer, MassAnalyzerVisualizer
scan_map_ : PepXMLFile
scan_mode_ : InstrumentSettings, TOPPViewBase
scan_number : FLASHHelperClasses::MassFeature, SpectrumMetaDataLookup::SpectrumMetaData
scan_number_ : DeconvolvedSpectrum, PeakGroup
scan_polarity : MzTabMMSRunMetaData
scan_rate_ : MassAnalyzer, MassAnalyzerVisualizer
scan_regexp_ : SpectrumLookup
scan_time_ : MassAnalyzer, MassAnalyzerVisualizer
scan_windows_ : InstrumentSettings
ScanDirection : MassAnalyzer
scanDirectionToString() : MassAnalyzer
SCANDIRNULL : MassAnalyzer
ScanEvent() : Ms2SpectrumStats::ScanEvent
ScanLaw : MassAnalyzer
SCANLAWNULL : MassAnalyzer
scanLawToString() : MassAnalyzer
ScanMode : InstrumentSettings
scanModeToString() : InstrumentSettings
scannr_ : PepXMLFile
scans : IsotopeCluster
scans_ : SpectrumLookup
ScanWindow() : ScanWindow
ScanWindowVisualizer() : ScanWindowVisualizer
scene_ : TOPPASWidget
schema_location_ : XMLFile, ParamCTDFile
schema_version_ : MzIdentMLDOMHandler, XMLFile, ParamCTDFile
scope_path_ : CVMappingRule
score() : DiaPrescore, IDFilter::HasGoodScore< HitType >, IDBoostGraph::ProteinGroup, MorpheusScore::Result, NuXLAnnotatedHit, NuXLReportRow, OPXLDataStructs::CrossLinkSpectrumMatch, OSWFile::PercolatorFeature, PeptideSearchEngineFIAlgorithm::AnnotatedHit_
SCORE : PercolatorOutfile
score : SimpleSearchEngineAlgorithm::AnnotatedHit_, TargetedSpectraExtractor::Match
score_ : ChargePair, PeptideHit, ProteinHit
score_clas_pairs_ : ROCCurve
score_cutoff_ : MapAlignmentAlgorithmIdentification
score_name : IDScoreSwitcherAlgorithm::ScoreSearchResult
score_switched : IDScoreSwitcherAlgorithm::IDSwitchResult
score_type : PeptideHit::PepXMLAnalysisResult
score_type_ : InspectOutfile, MapAlignmentAlgorithmIdentification, PeptideIdentification, PeptideIdentificationVisualizer, ProteinIdentificationVisualizer
score_type_keys_ : OMSFileStore
score_type_names : PercolatorOutfile
score_type_refs : IdentificationData::RefTranslator
score_type_refs_ : OMSFileLoad
score_types_ : IdentificationData
score_weights : MRMFeatureSelector::SelectorParameters
score_with_isotopes() : DIAScoring
scoreAllChromatograms_() : OpenSwathWorkflow
scoreAndFilterPeakGroups_() : SpectralDeconvolution
scoreAssay_() : ConfidenceScoring
ScoredProcessingResult : IdentificationData, ScoredProcessingResult
scoreFeature_() : ConfidenceScoring
scoreHullpoints() : MasstraceCorrelator
scoreIdentification_() : MRMFeatureFinderScoring
scoreIsotopePattern_() : DIAScoring
scoreMap() : ConfidenceScoring
scoreMZ_() : FeatureFindingMetabo
scoreMZByExpectedMean_() : FeatureFindingMetabo
scoreMZByExpectedRange_() : FeatureFindingMetabo
scorePeakgroups() : MRMFeatureFinderScoring
scoreRT_() : FeatureFindingMetabo
scores : ConsensusIDAlgorithm::HitInfo, AppliedProcessingStep, ParentGroup
scoreSpectra() : TargetedSpectraExtractor
ScoreType : IdentificationData, ScoreType, IDScoreSwitcherAlgorithm, PercolatorOutfile
ScoreTypeRef : IdentificationData
ScoreTypes : IdentificationData
scoring_model_ : MRMFeatureFinderScoring
ScoringMatrix : NeedlemanWunsch
scouts : ACTrieState
sd_ : FLASHDeconvAlgorithm
sd_map_ : MzIdentMLDOMHandler
sd_noise_decoy_ : FLASHDeconvAlgorithm
sd_signal_decoy_ : FLASHDeconvAlgorithm
search() : PeptideSearchEngineFIAlgorithm, SimpleSearchEngineAlgorithm
search_database_ref : MzIdentMLDOMHandler::SpectrumIdentification
search_engine : MzTabNucleicAcidSectionRow, MzTabOligonucleotideSectionRow, MzTabOSMSectionRow, MzTabPeptideSectionRow, MzTabProteinSectionRow, MzTabPSMSectionRow, MzTabSmallMoleculeSectionRow
search_engine_ : MzIdentMLDOMHandler, PepXMLFile, ProteinIdentification
search_engine_identifier : AccurateMassSearchEngine
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_ : ConsensusXMLHandler, FeatureXMLHandler
search_param_keys_ : OMSFileStore
search_param_refs : IdentificationData::RefTranslator
search_param_refs_ : OMSFileLoad
search_parameters_ : MascotXMLHandler, ProteinIdentification
search_score_ : TriqlerFile::TriqlerLine_
search_score_summary_ : PepXMLFile
search_summary_ : PepXMLFile
searchAndShow_() : DIATreeTab, SpectraTreeTab
searchDifferentPrecursorRanges() : FragmentIndex
searched_mass_ : AccurateMassSearchResult
SearchEngineBase() : SearchEngineBase
searchMass_() : AccurateMassSearchEngine
searchModification() : ModificationsDB
searchModifications() : ModificationsDB
searchModificationsByDiffMonoMass() : ModificationsDB
searchModificationsByDiffMonoMassSorted() : ModificationsDB
searchModificationsFast() : ModificationsDB
searchNextCell_() : HashGrid< Cluster >::ConstIterator, HashGrid< Cluster >::Iterator
SearchParameters() : ProteinIdentification::SearchParameters
SearchParamRef : IdentificationData
searchPrefix() : StringListUtils
searchSpectrum() : TargetedSpectraExtractor
searchSuffix() : StringListUtils
searchtype : MzIdentMLDOMHandler::SpectrumIdentificationProtocol
second : ProbablePhosphoSites, TransformationModel::DataPoint
second_nearest_gap_ : StablePairFinder
second_row_ : NeedlemanWunsch
secondary_id_ : SpectralMatch
SECTOR : MassAnalyzer
Seed : FeatureFinderAlgorithmPicked
seed() : RandomShuffler
seed_ : UniqueIdGenerator
seed_rt_window_ : FeatureFinderIdentificationAlgorithm
SeedList : SeedListGenerator
SeedListGenerator() : SeedListGenerator
seeds_ : FeatureFinderAlgorithmPicked
seekGToSavedPosition() : FuzzyStringComparator::InputLine
seen_experiment_ : PepXMLFile
segment_step_length : MRMFeatureSelector::SelectorParameters
segment_window_length : MRMFeatureSelector::SelectorParameters
select() : MSSpectrum
select_sql : TransitionPQPFile::PQPSqlQueryInfo
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_ : Plot2DCanvas, PlotCanvas
selected_pen_ : Annotations1DContainer
SELECTED_REACTION_MONITORING_CHROMATOGRAM : ChromatogramSettings
selectFeaturesFromCandidates_() : FeatureFinderAlgorithmMetaboIdent
selection_view_ : TOPPViewBase
selectionChanged() : ParamTree
selectionCopied() : TOPPASScene
selectItemAt() : Annotations1DContainer
selectMRMFeature() : MRMFeatureSelector
selectNonOverlappingPatterns_() : Biosaur2Algorithm
selector_ : MRMFeatureSelector_test
SelectorParameters() : MRMFeatureSelector::SelectorParameters
selectPeptidesForQuantification_() : PeptideAndProteinQuant
selectSpectra() : TargetedSpectraExtractor
selectSwathTransitions() : OpenSwathHelper
selectSwathTransitionsPasef() : OpenSwathHelper
SemanticValidator() : SemanticValidator
semi_cleavage_ : XTandemInfile
semiSpecificDigestion_() : EnzymaticDigestion
sendClipboardContent() : TOPPASBase
sendCursorStatus() : PlotCanvas, PlotWidget, TOPPASWidget
sendStatus() : BaseVisualizerGUI
sendStatusMessage() : PlotCanvas, PlotWidget, TOPPASWidget
Sense : LPWrapper
sep_ : MzTabStringList, SVOutStream, CSVWriter
seq_ : FASTAFile, NASequence, OSWPeptidePrecursor
seq_1 : ProbablePhosphoSites
seq_2 : ProbablePhosphoSites
seq_type_ : TheoreticalSpectrumGenerationDialog
SeqAndRTList : MapAlignmentAlgorithmTreeGuided
SeqToList : MapAlignmentAlgorithmIdentification
SeqToValue : MapAlignmentAlgorithmIdentification
seqTypeSwitch_() : TheoreticalSpectrumGenerationDialog
sequence : NucleicAcidSearchEngine::AnnotatedHit, FASTAFile::FASTAEntry, IdentifiedSequence< SeqType >, ParentSequence, MzIdentMLDOMHandler::DBSequence, MSstatsFile::MSstatsLine_, MSstatsFile::MSstatsTMTLine_, MzTabOligonucleotideSectionRow, MzTabOSMSectionRow, MzTabPeptideSectionRow, MzTabPSMSectionRow, NuXLAnnotatedHit, PeptideSearchEngineFIAlgorithm::AnnotatedHit_, SimpleSearchEngineAlgorithm::AnnotatedHit_, Peptide, Protein, LightCompound, LightProtein, Peptide, Protein
sequence_ : FragmentIndex::Peptide, IMSElement, MSstatsFile::MSstatsLine_, MSstatsFile::MSstatsTMTLine_, PeptideHit, ProteinHit, TriqlerFile::TriqlerLine_
sequence_header_filter_ : SequestInfile
sequence_score : NuXLAnnotatedHit
SequenceGrouping : ConsensusIDAlgorithm
SequenceIdentity_() : DecoyGenerator
SequenceMapT : MRMAssay
sequenceMatches() : FASTAFile::FASTAEntry
SequenceToChargeToPepHitP : IDFilter
SequenceToChargeToPSM : BasicProteinInferenceAlgorithm
SequenceType : TheoreticalSpectrumGenerationDialog
SequestInfile() : SequestInfile
SequestOutfile() : SequestOutfile
seriesposition_regex_ : SpectrumAnnotator
server_path_ : MascotRemoteQuery
set() : Bitset, Date, DateTime, EmgFitter1D::Data, GlobalExceptionHandler, FilterList, IsotopeDistribution, MzTabBoolean, MzTabDouble, MzTabDoubleList, MzTabInteger, MzTabIntegerList, MzTabModificationList, MzTabParameterList, MzTabString, MzTabStringList, NASequence, RecentFilesMenu, TOPPASVertex::TOPPASFilenames
set2DData() : MSExperiment
set_chromatogram_flag() : LayerDataPeak
set_high_bound() : _Region< __K, _Val, _SubVal, _Acc, _Cmp >
set_low_bound() : _Region< __K, _Val, _SubVal, _Acc, _Cmp >
set_Name_ID_map_ : QcMLFile
setAAAfter() : PeptideEvidence
setAABefore() : PeptideEvidence
setAbsChargeRange() : PeakGroup
setAbsolute() : FineIsotopePatternGenerator
setAcceptableAbsolute() : FuzzyStringComparator
setAcceptableRelative() : FuzzyStringComparator
setAccession() : CVMappingTerm, CVTerm, MzTabParameter, ProteinHit
setAccessionAttribute() : SemanticValidator
setAccuracy() : MassAnalyzer
setAcquisitionInfo() : ChromatogramSettings, SpectrumSettings
setAcquisitionMode() : IonDetector
setActionMode() : TOPPASScene
setActivationEnergy() : Precursor
setActivationMethod() : DeconvolvedSpectrum
setActivationMethods() : Precursor
setActive() : ChargePair, DataFilters
setADCSamplingFrequency() : IonDetector
setAdditionalContextMenu() : PlotCanvas
setAddress() : ContactPerson
setAdductBase() : MassExplainer
setAllowChildren() : CVMappingTerm
setAllowedThreads() : TOPPASScene
setAllowIsotopeError() : XTandemInfile
setAllowShortNumbers() : AxisWidget
setAlwaysAppendData() : PeakFileOptions
setAmount() : Adduct
setAnalysisResults() : PeptideHit
setArea() : Area< N_DIM >
setAtBottomRow() : TableView
setAtomicNumber() : Element
setAverageMass() : ResidueModification
setAverageWeight() : Element, Residue
setAveragine() : SpectralDeconvolution
setAvgMass() : Ribonucleotide
setAvgPPMError() : PeakGroup
setAxisBounds() : AxisWidget
setBackboneBasicityLeft() : Residue
setBackboneBasicityRight() : Residue
setBaselossFormula() : Ribonucleotide
setBaseName() : PeptideIdentification
setBlacklistItems() : FilterableList
setBlind() : InspectInfile
setCalculatedMassToCharge() : IdentificationHit
setCalculatedMZ() : AccurateMassSearchResult
setCallbacks() : ExternalProcess, ExternalProcessMBox
setCanvas_() : PlotWidget
setCastValue_() : AbsoluteQuantitationMethodFile, MRMFeaturePickerFile
setCentroidIM() : MassTrace
setCentroidSD() : MassTrace
setChanged() : TOPPASScene
setCharge() : AccurateMassSearchResult, Adduct, BaseFeature, ChargePair, EmpiricalFormula, FeatureHandle, FeatureHypothesis, IdentificationHit, PeptideHit, Precursor
setChargeIsotopeCosine() : PeakGroup
setChargeScore() : PeakGroup
setChargeSNR() : PeakGroup
setChargeState() : PeptideCompound, TraMLProduct, LightCompound
setChecksum() : SourceFile
setCheckTermValueTypes() : SemanticValidator
setCheckUnits() : SemanticValidator
setChromatogramAnnotation() : LayerDataChrom
setChromatogramProcessingFunc() : MSDataTransformingConsumer
setChromatograms() : MSExperiment
setChromatogramType() : ChromatogramSettings
setChromData() : LayerDataChrom
setCleavageSite() : XTandemInfile
setClipboard() : TOPPASScene
setCode() : Ribonucleotide
setCoefficientLimits() : MZTrafoModel
setCoefficients() : MZTrafoModel
setColor() : Annotation1DCaret< DataPoint >, Annotation1DPeakItem< DataPoint >, ColorSelector, TOPPASEdge
setColumn() : HPLC
setColumnBounds() : LPWrapper
setColumnHeaders() : ConsensusMap
setColumnName() : LPWrapper
setColumnType() : LPWrapper
setCombinationsLogic() : CVMappingRule
setCometID() : DigestionEnzymeProtein
setComment() : ChromatogramSettings, ExperimentalSettings, HPLC, Sample, SpectrumSettings
setCommentRows() : MzTab, MzTabM
setCommonName() : SpectralMatch
setCompletionTime() : DataProcessing
setCompomer() : ChargePair
setComponentName() : AbsoluteQuantitationMethod
setCompoundRef() : IncludeExcludeTarget, ReactionMonitoringTransition
setCompounds() : TargetedExperiment
setCompression() : MSNumpressCoder::NumpressConfig, PeakFileOptions
setConcentration() : Sample
setConcentrationUnits() : AbsoluteQuantitationMethod
setConfig() : MzMLSqliteHandler, SqMassFile
setConfigurations() : IncludeExcludeTarget
setContactInfo() : ContactPerson
setContacts() : ExperimentalSettings, TargetedExperiment
setConvexHulls() : Feature
setCorrectionFactor() : DBSuitability::SuitabilityData
setCorrelationCoefficient() : AbsoluteQuantitationMethod
setCoverage() : ProteinHit
setCreationDate() : Identification
setCTermGain() : DigestionEnzymeProtein
setCTerminalModification() : AASequence
setCTerminalModificationByDiffMonoMass() : AASequence
setCurrentIndex() : LayerData1DBase
setCurrentLayer() : LayerStack
setCurrentLayerParameters() : PlotCanvas
setCurrentLayerPeakPenStyle() : Plot1DCanvas
setCurrentProcessingStep() : IdentificationData
setCustomizations() : Instrument
setCutOff() : BaseModel
setCutsAfterRegEx() : DigestionEnzymeRNA
setCutsBeforeRegEx() : DigestionEnzymeRNA
setCVIdentifierRef() : CVMappingTerm, CVTerm
setCVLabel() : MzTabParameter
setCVReferences() : CVMappings
setCVs() : TargetedExperiment
setCVTerms() : CVMappingRule, CVTermList, CVTermListInterface
setCWD() : InputFile, InputFileList
setData() : FeatureFinderAlgorithm, FeatureFinderAlgorithmPicked, BilinearInterpolation< Key, Value >, LinearInterpolation< Key, Value >
setDataArrays() : OSChromatogram, OSSpectrum
setDatabase() : SequestInfile
setDataPoints() : TransformationDescription
setDataProcessing() : ChromatogramSettings, ConsensusMap, FeatureMap, MetaInfoDescription, SpectrumSettings
setDate() : DateTime
setDateTime() : ExperimentalSettings, ProteinIdentification
setDb() : InspectInfile
setDecoy() : LightTransition
setDecoyTransitionType() : ReactionMonitoringTransition
setDefaultParametersFilename() : XTandemInfile
setDefaultParams_() : IsobaricChannelExtractor, IsobaricQuantifier, ItraqEightPlexQuantitationMethod, ItraqFourPlexQuantitationMethod, TMTEighteenPlexQuantitationMethod, TMTElevenPlexQuantitationMethod, TMTSixPlexQuantitationMethod, TMTSixteenPlexQuantitationMethod, TMTTenPlexQuantitationMethod, TopDownIsobaricQuantification
setDefaults() : Param
setDelayInSeconds() : FileWatcher
setDescription() : MetaInfoRegistry, ProteinHit, TOPPASScene
setDetectingTransition() : ReactionMonitoringTransition, LightTransition
setDFSColor() : TOPPASVertex
setDiffAverageMass() : ResidueModification
setDiffFormula() : ResidueModification
setDiffMonoMass() : ResidueModification
setDimMinMax() : DIntervalBase< D >
setDirectory() : OutputDirectory
setDrawInterestingMZs() : Plot1DCanvas
setDrawMode() : Plot1DCanvas
setDrawMode1D() : TOPPViewBase
setDriftTime() : MSSpectrum, Precursor, PeptideCompound, LightCompound
setDriftTimeArray() : OSSpectrum
setDriftTimeUnit() : Mobilogram, MSSpectrum, Precursor
setDriftTimeWindowLowerOffset() : Precursor
setDriftTimeWindowUpperOffset() : Precursor
setEdgeScore() : ChargePair
setEditorData() : ListEditorDelegate, ParamEditorDelegate
setElement() : IMSAlphabet, LPWrapper
setElementIndex() : ChargePair
setElementPath() : CVMappingRule
setEmail() : ContactPerson
setEmpiricalFormula() : AccurateMassSearchResult
setEmptyRows() : MzTab, MzTabM
setEnd() : PeptideEvidence
setEnzyme() : EnzymaticDigestion, InspectInfile, ProteaseDigestion, RNaseDigestion, SequestInfile
setEstimatedImWindow() : OpenSwathCalibrationWorkflow
setEstimatedMs1ImWindow() : OpenSwathCalibrationWorkflow
setEstimatedMs1MzWindow() : OpenSwathCalibrationWorkflow
setEstimatedMzWindow() : OpenSwathCalibrationWorkflow
setExcludeTargets() : TargetedExperiment
setExpectedSize() : FullSwathFileConsumer, IMSDataConsumer, MSDataAggregatingConsumer, MSDataCachedConsumer, MSDataChainingConsumer, MSDataSqlConsumer, MSDataStoringConsumer, MSDataTransformingConsumer, MSDataWritingConsumer, NoopMSDataConsumer
setExperimentalMassToCharge() : IdentificationHit
setExperimentalSettings() : FullSwathFileConsumer, IMSDataConsumer, MSDataAggregatingConsumer, MSDataCachedConsumer, MSDataChainingConsumer, MSDataSqlConsumer, MSDataStoringConsumer, MSDataTransformingConsumer, MSDataWritingConsumer, NoopMSDataConsumer, NoopMSDataWritingConsumer
setExperimentalSettingsFunc() : MSDataTransformingConsumer
setExperimentLabel() : PeptideIdentification
setExperimentType() : ConsensusMap
setExportDecoys() : MascotRemoteQuery
setFactor() : SpectrumCheapDPCorr
setFeatOptions() : FileHandler
setFeature() : FeatureEditDialog
setFeatureIndex() : PeakGroup
setFeatureName() : AbsoluteQuantitationMethod
setFeatures() : ConsensusFeature
setFile() : GlobalExceptionHandler
setFileFormatFilter() : InputFile, TOPPASInputFileDialog
setFilename() : InputFile
setFileName() : ListEditorDelegate
setFilenames() : InputFileList, TOPPASInputFileListVertex
setFileSize() : SourceFile
setFileType() : SourceFile
setFillData() : PeakFileOptions
setFilters() : PlotCanvas
setFilters_() : SpectralDeconvolution
setFinalMSExponent() : MassAnalyzer
setFirstColumn() : FuzzyStringComparator
setFirstName() : ContactPerson
setFitterParam() : EmgScoring
setFivePrimeGain() : DigestionEnzymeRNA
setFivePrimeMod() : NASequence
setFixedModification() : ModificationDefinition
setFlags() : Annotation1DTextItem
setFloatDataArrays() : Mobilogram, MSChromatogram, MSSpectrum, ProteinIdentification::ProteinGroup
setFlux() : HPLC
setForceMQCompatability() : PeakFileOptions
setForceTPPCompatability() : PeakFileOptions
setFormula() : Adduct, Residue, ResidueModification, Ribonucleotide
setFoundAdduct() : AccurateMassSearchResult
setFoundMass() : AccurateMassSearchResult
setFoundPrecursorCharge() : SpectralMatch
setFoundPrecursorMass() : SpectralMatch
setFractionIdentifier() : ExperimentalSettings
setFragmentImWindow() : SwathMapMassCorrection
setFragmentMassErrorUnit() : XTandemInfile
setFragmentMassTolerance() : XTandemInfile
setFragmentMzWindow() : SwathMapMassCorrection
setFragmentType() : LightTransition
setFreeText() : PythonModuleRequirement
setFromParam() : RecentFilesMenu
setFullId() : ResidueModification
setFullName() : ResidueModification
setFunction() : GlobalExceptionHandler
setGradient() : HPLC
setGravityAxis() : Gravitator
setHeaderExportName() : TableView
setHeaders() : TableView, TreeView
setHigherScoreBetter() : PeptideIdentification, ProteinIdentification
setHits() : SpectrumIdentification, PeptideIdentification, ProteinIdentification
setHoverPos() : TOPPASEdge
setHPLC() : ExperimentalSettings
setHTMLCode() : Ribonucleotide
setHullPoints() : ConvexHull2D
setID() : Compomer
setId() : IdentificationHit, ResidueModification
setIdentifier() : Acquisition, CVMappingRule, CVReference, DocumentIdentifier, PeptideIdentification, ProteinIdentification
setIdentifyingTransition() : ReactionMonitoringTransition, LightTransition
setIMFormat() : SpectrumSettings
setIMUnit() : IMDataConverter
setInchiString() : SpectralMatch
setIncludeTargets() : TargetedExperiment
setIndex() : PeakGroup
setIndividualIntensities() : AccurateMassSearchResult
setInf() : MzTabDouble, MzTabInteger
setInferenceEngine() : ProteinIdentification
setInferenceEngineVersion() : ProteinIdentification
setInitialParameters() : GammaDistributionFitter, GaussFitter, GumbelDistributionFitter, GumbelMaxLikelihoodFitter
setInitialParameters_() : EGHTraceFitter, EmgFitter1D, GaussTraceFitter
setInitialParametersMOM_() : EmgFitter1D
setInletType() : IonSource
setInputFilename() : XTandemInfile
setInputOutputCombo_() : ToolsDialog
setInstitution() : ContactPerson
setInstrument() : ExperimentalSettings, HPLC, InspectInfile
setInstruments() : TargetedExperiment
setInstrumentSettings() : ChromatogramSettings, SpectrumSettings
setIntegerDataArrays() : Mobilogram, MSChromatogram, MSSpectrum, ProteinIdentification::ProteinGroup
setIntensity() : ChromatogramPeak, MobilityPeak1D, MobilityPeak2D, Peak1D, Peak2D
setIntensity32Bit() : PeakFileOptions
setIntensityArray() : Chromatogram, Spectrum, OSChromatogram, OSSpectrum
setIntensityAsGravity() : Gravitator
setIntensityMode() : PlotCanvas, PlotWidget, TOPPViewBase
setIntensityRange() : FeatureFileOptions, PeakFileOptions
setIntermediateProducts() : ReactionMonitoringTransition
setInternalChars_() : Colorizer
setInterpolationMode() : MultiGradient, MultiGradientSelector
setInterpolationStep() : InterpolationModel
setInterpretations() : IncludeExcludeTarget
setInterProtein_() : XFDRAlgorithm
setIntraProtein_() : XFDRAlgorithm
setInvalid() : QTCluster
setInverseOrientation() : AxisWidget
setIonCutoffPercentage() : SequestInfile
setIonDetectors() : Instrument
setIonizationMethod() : IonSource
setIonLadderVisible() : Plot1DCanvas
setIonOptics() : Instrument
setIonSeriesWeights() : SequestInfile
setIonSources() : Instrument
setISName() : AbsoluteQuantitationMethod
setIsolationWidth() : MassAnalyzer
setIsolationWindowLowerOffset() : Precursor, Product
setIsolationWindowUpperOffset() : Precursor, Product
setIsotopeCosine() : PeakGroup
setIsotopeDaDistance() : PeakGroup
setIsotopeDistribution() : Element, IMSElement
setIsotopesSimScore() : AccurateMassSearchResult
setIsRepeatable() : CVMappingTerm
setItems() : FilterableList, ListFilterDialog
setKey() : TOPPASInputFileListVertex
setLabel() : MassTrace, PlotCanvas
setLastName() : ContactPerson
setLayerFlag() : PlotCanvas
setLayerName() : PlotCanvas
setLeftSplitter() : HistogramDialog, HistogramWidget
setLegend() : AxisWidget, HistogramDialog, HistogramWidget
setLevel() : LogStream, LogStreamBuf
setLibraryIntensity() : ReactionMonitoringTransition, LightTransition
setLine() : GlobalExceptionHandler
setList() : ListTable, ListEditor
setListRestrictions() : ListEditor
setLLOD() : AbsoluteQuantitationMethod
setLLOQ() : AbsoluteQuantitationMethod
setLoadConvexHull() : FeatureFileOptions
setLoadDetail() : MzMLHandler, MzXMLHandler, XMLHandler
setLoadedFilePath() : DocumentIdentifier
setLoadedFileType() : DocumentIdentifier
setLoadSubordinates() : FeatureFileOptions
setLogDestination() : FuzzyStringComparator
setLogger() : ProgressLogger
setLogLevel() : LogConfigHandler
setLogMode() : HistogramDialog, HistogramWidget
setLogProb() : Adduct
setLogScale() : AxisWidget
setLogType() : ProgressLogger
setLossFormulas() : Residue
setLossNames() : Residue
setLowMassIons() : Residue
setMagneticFieldStrength() : MassAnalyzer
setMandatoryExportColumns() : TableView
setMapIndex() : FeatureHandle::FeatureHandleMutable_, FeatureHandle
setMapper() : Plot1DWidget, Plot2DWidget, Plot3DWidget, PlotCanvas, PlotWidget
setMapping() : LinearInterpolation< Key, Value >
setMapping_0() : BilinearInterpolation< Key, Value >
setMapping_1() : BilinearInterpolation< Key, Value >
setMappingRules() : CVMappings
setMargin() : AxisWidget
setMass() : Sample
setMassAnalyzers() : Instrument
setMassDiff() : ChargePair
setMasstraceIntensities() : AccurateMassSearchResult
setMassTypeFragment() : SequestInfile
setMassTypeParent() : SequestInfile
setMatchedWhitelist() : FuzzyStringComparator
setMatchingHMDBids() : AccurateMassSearchResult
setMatchingIndex() : AccurateMassSearchResult
setMatchingScore() : SpectralMatch
setMatchingSpectrumIndex() : SpectralMatch
setMatchPeakAllowedError() : SequestInfile
setMatchPeakCount() : SequestInfile
setMatchPeakTolerance() : SequestInfile
setMatrix() : Matrix< Value >, NeedlemanWunsch
setMax() : DIntervalBase< D >, RangeBase
setMaxAAACount() : ACTrie
setMaxAAPerModPerPeptide() : SequestInfile
setMaxCharge() : Tagger
setMaxDataPoolSize() : PeakFileOptions
setMaxFloat() : Param
setMaxFloat_() : TOPPBase
setMaxInt() : Param
setMaxInt_() : TOPPBase
setMaxIntensity() : RangeIntensity
setMaxInternalCleavageSites() : SequestInfile
setMaxIsotope() : CoarseIsotopePatternGenerator
setMaxIsotopeIndex() : FLASHHelperClasses::PrecalculatedAveragine
setMaxLength() : LogWindow
setMaxMMCount() : ACTrie
setMaxMobility() : RangeMobility
setMaxModifications() : ModificationDefinitionsSet
setMaxModsPerPeptide() : SequestInfile
setMaxMZ() : RangeMZ
setMaxNumberOfThreads() : TOPPBase
setMaxOccurrences() : ModificationDefinition
setMaxPrecursorCharge() : XTandemInfile
setMaxPTMsize() : InspectInfile
setMaxRT() : RangeRT
setMaxValidEValue() : XTandemInfile
setMaxX() : DIntervalBase< D >
setMaxY() : DIntervalBase< D >
setMean() : BasicStatistics< RealT >
setMergeLayers() : TOPPViewOpenDialog
setMessage() : GlobalExceptionHandler
setMetaData() : MzTab, MzTabM
setMetadataOnly() : FeatureFileOptions, PeakFileOptions
setMetaValue() : IdentificationData, MetaInfoInterface, MRMFeatureFilter
setMethodOfCombination() : AcquisitionInfo
setMin() : DIntervalBase< D >, RangeBase
setMinFloat() : Param
setMinFloat_() : TOPPBase
setMinimumSize_() : IMSIsotopeDistribution
setMinInt() : Param
setMinInt_() : TOPPBase
setMinIntensity() : RangeIntensity
setMinMax() : DIntervalBase< D >
setMinMaxOfRange() : Plot1DGoToDialog, Plot2DGoToDialog
setMinMobility() : RangeMobility
setMinMZ() : RangeMZ
setMinRT() : RangeRT
setMinX() : DIntervalBase< D >
setMinY() : DIntervalBase< D >
setMirrorModeActive() : Plot1DCanvas
setMissedCleavages() : EnzymaticDigestion
setMobility() : MobilityPeak1D, MobilityPeak2D
setMobilityData() : LayerDataIonMobility
setModel() : Instrument
setModelData() : ListEditorDelegate, ParamEditorDelegate
setModification() : AASequence, ModificationDefinition, Residue
setModificationByDiffMonoMass() : AASequence, Residue
setModificationDefinitionsSet() : OMSSAXMLFile
setModificationIdentifier() : MzTabModification
setModifications() : ModificationDefinitionsSet, PepNovoInfile, ProteinHit, XTandemInfile
setModificationsPerPeptide() : InspectInfile
setModified() : ParamEditor
setMonoisotopicMass() : PeakGroup
setMonoMass() : ResidueModification, Ribonucleotide
setMonoWeight() : Element, Residue
setMS1Map() : MRMFeatureFinderScoring
setMSData() : Biosaur2Algorithm, FeatureFinderAlgorithmMetaboIdent, FeatureFinderIdentificationAlgorithm
setMSDataConsumer() : MzMLHandler, MzXMLHandler
setMSExperiment() : AnnotatedMSRun
setMSFile() : MzTabSpectraRef
setMSFileSection() : ExperimentalDesign
setMSGFID() : DigestionEnzymeProtein
setMSLevel() : MSSpectrum
setMSLevels() : PeakFileOptions
setMSmallMoleculeEvidenceSectionRows() : MzTabM
setMSmallMoleculeFeatureSectionRows() : MzTabM
setMSmallMoleculeSectionRows() : MzTabM
setMulticharge() : InspectInfile
setMZ() : MobilityPeak2D, Peak1D, Peak2D, PeptideIdentification, Product, TraMLProduct
setMz32Bit() : PeakFileOptions
setMZArray() : Spectrum, OSSpectrum
setMZErrorPPM() : AccurateMassSearchResult
setMZRange() : FeatureFileOptions, PeakFileOptions
setName() : ContactPerson, CVReference, CVTerm, DefaultParamHandler, DigestionEnzyme, Element, GlobalExceptionHandler, IMSElement, IncludeExcludeTarget, Instrument, IdentificationHit, LayerDataBase, MetaInfoDescription, ModelDescription< D >, MSChromatogram, MSSpectrum, MzTabParameter, ReactionMonitoringTransition, Residue, ResidueModification, Ribonucleotide, Sample, Software
setNameAttribute() : SemanticValidator
setNameOfFile() : SourceFile
setNameSuffix() : LayerDataBase
setNaN() : MzTabDouble, MzTabInteger
setNativeID() : ChromatogramSettings, ReactionMonitoringTransition, SpectrumSettings
setNativeIDType() : SourceFile
setNativeIDTypeAccession() : SourceFile
setNeutralLossAverageMasses() : ResidueModification
setNeutralLossDiffFormulas() : ResidueModification
setNeutralLossesForIons() : SequestInfile
setNeutralLossMonoMasses() : ResidueModification
setNewCode() : Ribonucleotide
setNoiseSuppression() : XTandemInfile
setNominalMass() : IMSIsotopeDistribution
setNormalizedIntensityValues() : ConsensusMapNormalizerAlgorithmQuantile
setNormalizeXcorr() : SequestInfile
setNPoints() : AbsoluteQuantitationMethod
setNrMS1Spectra() : SwathQC
setNTermGain() : DigestionEnzymeProtein
setNTerminalModification() : AASequence
setNTerminalModificationByDiffMonoMass() : AASequence
setNTermLossFormulas() : Residue
setNTermLossNames() : Residue
setNucleicAcidSectionRows() : MzTab
setNucleotideReadingFrame() : SequestInfile
setNull() : MzTabBoolean, MzTabDouble, MzTabDoubleList, MzTabInteger, MzTabIntegerList, MzTabModification, MzTabModificationList, MzTabParameter, MzTabParameterList, MzTabSpectraRef, MzTabString, MzTabStringList
setNumber() : Sample
setNumberOfMissedCleavages() : XTandemInfile
setNumberOfThreads() : XTandemInfile
setNumpressConfigurationFloatDataArray() : PeakFileOptions
setNumpressConfigurationIntensity() : PeakFileOptions
setNumpressConfigurationMassTime() : PeakFileOptions
setObjective() : LPWrapper
setObjectiveSense() : LPWrapper
setObservedIntensity() : AccurateMassSearchResult
setObservedMZ() : AccurateMassSearchResult
setObservedPrecursorMass() : SpectralMatch
setObservedPrecursorRT() : SpectralMatch
setObservedRT() : AccurateMassSearchResult
setObservedSpectrumIndex() : SpectralMatch
setObservedSpectrumNativeID() : SpectralMatch
setOffset() : BiGaussModel, EmgModel, ExtendedIsotopeModel, GaussModel, InterpolationModel, IsotopeModel, LinearInterpolation< Key, Value >
setOffset_0() : BilinearInterpolation< Key, Value >
setOffset_1() : BilinearInterpolation< Key, Value >
setOligonucleotideSectionRows() : MzTab
setOMSSAID() : DigestionEnzymeProtein
setOnDiscPeakData() : LayerDataChrom, LayerDataPeak
setOneLetterCode() : Residue
setOpenMPNumThreads() : OpenMSBuildInfo
setOptions() : FeatureXMLFile, FileHandler, IndexedMzMLFileLoader, ConsensusXMLHandler, FeatureXMLHandler, MzDataHandler, MzMLHandler, MzXMLHandler, MzDataFile, MzMLFile, MzXMLFile, OnDiscMSExperiment
setOrder() : IonDetector, IonSource, MassAnalyzer
setOrganism() : Sample
setOrigin() : ResidueModification, Ribonucleotide
setOriginalSpectrum() : DeconvolvedSpectrum
setOriginAnnotationMode_() : IDRipper
setOSMSectionRows() : MzTab
setOutDir() : TOPPASScene
setOutputFilename() : XTandemInfile
setOutputFolderName() : TOPPASOutputVertex
setOutputLines() : SequestInfile
setOutputResults() : XTandemInfile
setOverallQuality() : Feature
setPairValue_() : MRMFeatureQCFile
setParam() : TOPPViewPrefDialog, ModelDescription< D >, TOPPASToolVertex
setParameters() : DefaultParamHandler, PeakPickerIM
setParameters_() : QTClusterFinder
setParseUnknownScores() : PepXMLFile
setPartialSequence() : SequestInfile
setPassThreshold() : IdentificationHit
setPathToFile() : SourceFile
setPeakAnnotations() : PeptideHit
setPeakData() : LayerDataPeak
setPeakGroups() : DeconvolvedSpectrum
setPeakMassTolerance() : InspectInfile, SequestInfile
setPen() : Annotations1DContainer
setPenalty() : NeedlemanWunsch
setPeptideEvidence_() : XQuestResultXMLHandler
setPeptideEvidences() : PeptideHit
setPeptideGroupLabel() : Peptide
setPeptideIdentifications() : AnnotatedMSRun, BaseFeature
setPeptideIds() : IPeptideIds, LayerDataFeature, LayerDataIdent
setPeptideMassUnit() : SequestInfile
setPeptideRef() : IncludeExcludeTarget, ReactionMonitoringTransition
setPeptides() : TargetedExperiment
setPeptideScoresForMap_() : IDScoreGetterSetter
setPeptideScoresFromMap_() : IDScoreGetterSetter
setPeptideSectionRows() : MzTab
setPercentage() : Gradient
setPipelineRunning() : TOPPASScene
setPka() : Residue
setPkb() : Residue
setPkc() : Residue
setPlotWidget() : PlotCanvas
setPluginPath() : TVToolDiscovery
setPolarity() : InstrumentSettings, IonSource
setPos() : ChromatogramPeak, MobilityPeak1D, Peak1D
setPosition() : Annotation1DCaret< DataPoint >, Annotation1DPeakItem< DataPoint >, Annotation1DTextItem, Annotation1DVerticalLineItem, ChromatogramPeak, FASTAFile, MobilityPeak1D, MobilityPeak2D, Peak1D, Peak2D
setPositionsAndParameters() : MzTabModification
setPossibleChargeStates() : Precursor
setPrechosenItems() : ListFilterDialog
setPrecision() : Weights
setPrecursor() : ChromatogramSettings, DeconvolvedSpectrum
setPrecursorAdduct() : SpectralMatch
setPrecursorCVTermList() : IncludeExcludeTarget, ReactionMonitoringTransition
setPrecursorErrorType() : XTandemInfile
setPrecursorImWindow() : SwathMapMassCorrection
setPrecursorMassErrorUnit() : XTandemInfile
setPrecursorMassTolerance() : InspectInfile, SequestInfile
setPrecursorMassToleranceMinus() : XTandemInfile
setPrecursorMassTolerancePlus() : XTandemInfile
setPrecursorMZ() : IncludeExcludeTarget, ReactionMonitoringTransition
setPrecursorMZRange() : PeakFileOptions
setPrecursorMZSelectedIon() : PeakFileOptions
setPrecursorMzWindow() : SwathMapMassCorrection
setPrecursorPeakGroup() : DeconvolvedSpectrum
setPrecursors() : SpectrumSettings
setPrecursorScanNumber() : DeconvolvedSpectrum
setPrediction() : IncludeExcludeTarget, ReactionMonitoringTransition
setPreferredFixedModifications() : PepXMLFile
setPreferredVariableModifications() : PepXMLFile
setPrefix() : LogStream
setPresenceAndScanEventNumber_() : Ms2SpectrumStats
setPressure() : HPLC
setPrimaryID() : BaseFeature
setPrimaryIdentifier() : SpectralMatch
setPrimaryMSRunPath() : ConsensusMap, FeatureMap, ProteinIdentification
setPrintDuplicateReferences() : SequestInfile
setProcessingActions() : DataProcessing
setProduct() : ChromatogramSettings, ReactionMonitoringTransition
setProductCVTermList() : IncludeExcludeTarget
setProductMZ() : IncludeExcludeTarget, ReactionMonitoringTransition
setProducts() : SpectrumSettings
setProgress() : GUIProgressLoggerImpl, ProgressLogger::ProgressLoggerImpl, ProgressLogger
setProtein() : OSWData
setProteinAccession() : PeptideEvidence
setProteinIdentifications() : AnnotatedMSRun, ConsensusMap, FeatureMap
setProteinMassFilter() : SequestInfile
setProteins() : TargetedExperiment
setProteinSectionRows() : MzTab
setPSIID() : DigestionEnzymeProtein
setPSIMODAccession() : ResidueModification
setPSMSectionRows() : MzTab
setPublications() : TargetedExperiment
setQscore() : PeakGroup
setQscore2D() : PeakGroup
setQuality() : BaseFeature, Feature
setQualityAts_ : QcMLFile
setQualityQPs_ : QcMLFile
setQualityQPs_members_ : QcMLFile
setQuantifyingTransition() : ReactionMonitoringTransition, LightTransition
setQuantities() : DeconvolvedSpectrum
setQuantMethod() : MassTrace
setQuantMethods() : AbsoluteQuantitation
setQuery() : ACTrieState
setQueryMass() : AccurateMassSearchResult
setQuerySpectra() : MascotRemoteQuery
setQvalue() : PeakGroup
setRange() : DimBase, DimIM, DimINT, DimMZ, DimRT, MRMFeatureFilter, Plot1DGoToDialog, Plot2DGoToDialog
setRank() : IdentificationHit, PeptideHit, ProteinHit
setRANSACParams() : MZTrafoModel
setRANSACSeed() : MZTrafoModel
setRatios() : ConsensusFeature
setRecycling() : TOPPASVertex
setReference() : FeatureGroupingAlgorithmUnlabeled, MapAlignmentAlgorithmIdentification, MapAlignmentAlgorithmPoseClustering
setReflectronState() : MassAnalyzer
setRegEx() : DigestionEnzyme
setRegExDescription() : DigestionEnzyme
setRemovePrecursorNearPeaks() : SequestInfile
setRepAbsCharge() : PeakGroup
setRequiredModules() : PythonModuleRequirement
setRequirementLevel() : CVMappingRule
setResidueSets() : Residue
setResiduesInUpperCase() : SequestInfile
setResolution() : IonDetector, MassAnalyzer
setResolutionMethod() : MassAnalyzer
setResolutionType() : MassAnalyzer
setRestrictions() : ListEditorDelegate
setRetentionTime() : IncludeExcludeTarget, ReactionMonitoringTransition
setRichText() : Annotation1DCaret< DataPoint >
setRightSplitter() : HistogramDialog, HistogramWidget
setRoundMasses() : CoarseIsotopePatternGenerator
setRowBounds() : LPWrapper
setRowName() : LPWrapper
setRT() : ChromatogramPeak, Mobilogram, MSSpectrum, Peak2D, PeptideIdentification, RetentionTime
setRTRange() : FeatureFileOptions, PeakFileOptions
setRunID() : OSWData
setSample() : ExperimentalSettings
setSamples() : BiGaussModel, EmgModel, ExtendedIsotopeModel, GaussModel, InterpolationModel, IsotopeModel
setSampleSection() : ExperimentalDesign
setSaveFileName() : TOPPASScene
setScale() : EuclideanSimilarity, LinearInterpolation< Key, Value >
setScale_0() : BilinearInterpolation< Key, Value >
setScale_1() : BilinearInterpolation< Key, Value >
setScalingFactor() : InterpolationModel
setScanDirection() : MassAnalyzer
setScanEventNumber_() : Ms2SpectrumStats
setScanLaw() : MassAnalyzer
setScanMode() : InstrumentSettings
setScanNumber() : PeakGroup
setScanRate() : MassAnalyzer
setScanRegExp_() : SpectrumLookup
setScanTime() : MassAnalyzer
setScanWindows() : InstrumentSettings
setScopePath() : CVMappingRule
setScore() : FeatureHypothesis, PeptideHit, ProteinHit
setScore_() : IDScoreGetterSetter
setScoreAndMoveIfTarget_() : IDScoreGetterSetter
setScoreHigherWorse_() : IDScoreGetterSetter
setScoreHigherWorseAndMoveIfTarget_() : IDScoreGetterSetter
setScores() : MRMFeature
setScores_() : IDScoreGetterSetter
setScoresAndRemoveDecoys_() : IDScoreGetterSetter
setScoresHigherWorse_() : IDScoreGetterSetter
setScoresHigherWorseAndRemoveDecoys_() : IDScoreGetterSetter
setScoreType() : PeptideIdentification, ProteinIdentification
setScoreType_() : IDScoreGetterSetter
setScoreTypeAndSettings_() : BayesianProteinInferenceAlgorithm
setSearchEngine() : ProteinIdentification
setSearchEngineVersion() : ProteinIdentification
setSearchParameters() : ProteinIdentification
setSecondaryIdentifier() : SpectralMatch
setSectionDescription() : Param
setSeed() : DecoyGenerator, RANSAC< TModelType >, UniqueIdGenerator
setSeeds() : FeatureFinderAlgorithm, FeatureFinderAlgorithmPicked
setSelected() : Annotation1DItem
setSelectedPen() : Annotations1DContainer
setSemiCleavage() : XTandemInfile
setSeparator() : MzTabStringList
setSequence() : IMSElement, NASequence, PeptideHit, ProteinHit
setSequenceHeaderFilter() : SequestInfile
setShowFragmentIons() : SequestInfile
setSideChainBasicity() : Residue
setSignificanceThreshold() : PeptideIdentification, ProteinIdentification
setSingleMass() : Adduct
setSize() : SaveImageDialog
setSizeOnly() : FeatureFileOptions, FeatureXMLHandler
setSizeRatio_() : SaveImageDialog
setSkipChromatograms() : PeakFileOptions
setSkipXMLChecks() : IndexedMzMLHandler, MzMLSpectrumDecoder, OnDiscMSExperiment, PeakFileOptions
setSmallMoleculeSectionRows() : MzTab
setSMILESString() : SpectralMatch
setSmoothedIntensities() : MassTrace
setSNR() : PeakGroup
setSoftware() : DataProcessing, Instrument, TargetedExperiment
setSortChromatogramsByRT() : PeakFileOptions
setSortSpectraByMZ() : PeakFileOptions
setSourceClassification() : ResidueModification
setSourceFeatureIndex() : AccurateMassSearchResult
setSourceFile() : ChromatogramSettings, SpectrumSettings
setSourceFiles() : ExperimentalSettings, TargetedExperiment
setSourceOutParam() : TOPPASEdge
setSourceVertex() : TOPPASEdge
setSpecificity() : EnzymaticDigestion
setSpecRef() : MzTabSpectraRef
setSpecRefFile() : MzTabSpectraRef
setSpectra() : InspectInfile, MSExperiment
setSpectraDataRef() : SpectrumMetaDataLookup
setSpectraProcessingFunc() : MSDataTransformingConsumer
setSpectrumIdentifications() : Identification
setSpectrumReference() : PeptideIdentification
setSqlRunID() : MSExperiment
setSqlSourceFile() : OSWData
setStandardEnzymeInfo_() : SequestInfile
setStart() : PeptideEvidence
setState() : Sample
setStatus() : MetaDataBrowser
setStrictFlag() : MRMFeatureFinderScoring
setStringDataArrays() : Mobilogram, MSChromatogram, MSSpectrum, ProteinIdentification::ProteinGroup
setSubordinates() : Feature
setSubsamples() : Sample
setSum() : BasicStatistics< RealT >
setSumFormula() : SpectralMatch
setSymbol() : Element
setSynonyms() : DigestionEnzyme, Residue, ResidueModification
setTabText() : EnhancedTabBar
setTabWidth() : FuzzyStringComparator
setTag() : SemanticValidator
setTagCount() : InspectInfile
setTargetCVTerms() : TargetedExperiment
setTargetDecoyType() : PeakGroup, PeptideHit, ProteinHit, SpectralDeconvolution
setTargeted() : PeakGroup
setTargetInParam() : TOPPASEdge
setTargetMasses() : SpectralDeconvolution
setTargetMetaValue() : TargetedExperiment
setTargetPrecursorCharge_() : SpectralDeconvolution
setTargetVertex() : TOPPASEdge
setTaxon() : XTandemInfile
setTaxonomyFilename() : XTandemInfile
setTemperature() : HPLC
setTermName() : CVMappingTerm
setTermSpecificity() : ResidueModification, Ribonucleotide
setText() : Annotation1DItem
setTextBox() : Plot1DCanvas
setTextOffset() : Annotation1DVerticalLineItem
setThreeLetterCode() : Residue
setThreePrimeGain() : DigestionEnzymeRNA
setThreePrimeMod() : NASequence
setThreshold() : ClusterHierarchical, FineIsotopePatternGenerator
setTickLevel() : AxisWidget
setTicks() : Annotation1DDistanceItem
setTime() : DateTime
setTimeArray() : Chromatogram, OSChromatogram
setting : MzTabSoftwareMetaData
settings_ : FullSwathFileConsumer, MSDataWritingConsumer
setTitle() : PythonModuleRequirement
setToEnd_() : MatchedIterator< CONT_T, TRAIT, CONST_T >
setTOFTotalPathLength() : MassAnalyzer
setToleranceEstimation() : SpectralDeconvolution
setTool_() : ToolsDialog
setToolDescriptions() : ToolDescriptionHandler
setTopoNr() : TOPPASOutputVertex, TOPPASToolVertex, TOPPASVertex
setTopoSortMarked() : TOPPASVertex
setToString() : FuzzyStringComparator::InputLine
setTotalProbability() : FineIsotopePatternGenerator
setTransformationModel() : AbsoluteQuantitationMethod
setTransformationModelParams() : AbsoluteQuantitationMethod
setTransitionGroupID() : MRMTransitionGroup< ChromatogramType, TransitionType >
setTransitions() : TargetedExperiment
setType() : ListEditorDelegate, IonDetector, MassAnalyzer, SpectrumSettings
setTypeName() : ListEditorDelegate, ListEditor
setULOD() : AbsoluteQuantitationMethod
setULOQ() : AbsoluteQuantitationMethod
setUnassignedPeptideIdentifications() : ConsensusMap, FeatureMap
setUniModRecordId() : ResidueModification
setUniqueId() : UniqueIdInterface
setUnit() : CVTerm, DataValue, MetaInfoRegistry
setUnitAccessionAttribute() : SemanticValidator
setUnitNameAttribute() : SemanticValidator
setUnitType() : DataValue
setup() : SimpleSVM
setURL() : ContactPerson
setUrl() : NetworkGetRequest
setUsePPM() : CalibrationData
setUseTerm() : CVMappingTerm
setUseTermName() : CVMappingTerm
setValidFormats_() : TOPPBase
setValidStrings() : Param
setValidStrings_() : TOPPBase
setValue() : CVTerm, DistanceMatrix< Value >, Matrix< Value >, MetaInfo, MzTabParameter, Param
setValueAttribute() : SemanticValidator
setValueFromFile() : DigestionEnzyme, DigestionEnzymeProtein, DigestionEnzymeRNA
setValueQuick() : DistanceMatrix< Value >
setVariance() : BasicStatistics< RealT >
setVendor() : Instrument
setVerbose() : TVToolDiscovery
setVerboseLevel() : FuzzyStringComparator
setVersion() : Software
setVisibleArea() : PlotCanvas
setVisibleArea1D() : TVIdentificationViewController
setVisibleAreaX() : PlotCanvas
setVisibleAreaY() : PlotCanvas
setVolume() : Sample
setWhitelist() : FuzzyStringComparator
setWidgetsfromFDDefaultParam_() : FLASHDeconvTabWidget
setWidth() : BaseFeature, FeatureHandle
setWriteIndex() : PeakFileOptions
setWriteSupplementalData() : PeakFileOptions
setX() : DPosition< D, TCoordinateType >
setXLabel() : Plot3DOpenGLCanvas
setXTandemID() : DigestionEnzymeProtein
setY() : DPosition< D, TCoordinateType >
setYLabel() : Plot3DOpenGLCanvas
setZLabel() : Plot3DOpenGLCanvas
setZoomScan() : InstrumentSettings
sf_accession : SiriusMSFile::AccessionInfo
sf_filename : SiriusMSFile::AccessionInfo
sf_path : SiriusMSFile::AccessionInfo
sf_type : SiriusMSFile::AccessionInfo
sgfilter_ : FIAMSDataProcessor
sgolay_ : PeakPickerChromatogram, PeakPickerMobilogram
sgolay_frame_length_ : PeakPickerChromatogram, PeakPickerIM, PeakPickerMobilogram
sgolay_polynomial_order_ : PeakPickerChromatogram, PeakPickerIM, PeakPickerMobilogram
SHA1 : SourceFile
SHADE_FLAT : Plot3DCanvas
SHADE_SMOOTH : Plot3DCanvas
ShadeModes : Plot3DCanvas
shape() : TOPPASEdge, TOPPASVertex
shared_xerces_ptr() : shared_xerces_ptr< T >
shift : NuXLFragmentAnnotationHelper::FragmentAnnotationDetail_, RangeBase
shiftedIonsToString() : NuXLFragmentAnnotationHelper
shiftedToPHFA() : NuXLFragmentAnnotationHelper
short_name : MultiplexDeltaMassesGenerator::Label
shortDimensionName() : MobilityPeak2D, Peak2D
shortDimensionNameIM() : MobilityPeak2D
shortDimensionNameMZ() : MobilityPeak2D, Peak2D
shortDimensionNameRT() : Peak2D
shortDimensionUnit() : MobilityPeak2D, Peak2D
shortDimensionUnitIM() : MobilityPeak2D
shortDimensionUnitMZ() : MobilityPeak2D, Peak2D
shortDimensionUnitRT() : Peak2D
SHOULD : CVMappingRule
shouldThrowForMissingIM_() : Biosaur2Algorithm
show() : EnhancedTabBar
show_alignment_ : Plot1DCanvas
show_fragment_ions_ : SequestInfile
show_grid_ : PlotCanvas
show_legend_ : AxisWidget
show_splitters_ : HistogramWidget
show_timing_ : PlotCanvas
showAboutDialog() : FLASHDeconvWizardBase, QApplicationTOPP, SwathWizardBase, TOPPASBase
showAllHits_() : MetaDataBrowser
showAsWindow_() : TOPPASBase
showChromatograms() : TVDIATreeTabController
showChromatogramsAsNew1D() : DataSelectionTabs, Plot2DCanvas, Plot2DWidget, SpectraTreeTab, TVDIATreeTabController, TVSpectraViewController
showChromatogramsInCanvas_() : TVDIATreeTabController
showContextMenu() : HistogramWidget
showCurrentLayerPreferences() : Plot1DCanvas, Plot2DCanvas, Plot3DCanvas, PlotCanvas
showCurrentPeaksAs2D() : Plot1DCanvas, Plot1DWidget, Plot3DCanvas, Plot3DWidget, TOPPViewBase
showCurrentPeaksAs3D() : Plot1DCanvas, Plot1DWidget, Plot2DCanvas, Plot2DWidget, TOPPViewBase
showCurrentPeaksAsDIA() : Plot1DCanvas, Plot1DWidget, TOPPViewBase
showCurrentPeaksAsIonMobility() : Plot1DCanvas, Plot1DWidget, Plot2DCanvas, Plot2DWidget, TOPPViewBase
showCursorStatus() : TOPPASBase, TOPPViewBase
showDetails_() : MetaDataBrowser
showDocumentation() : ParamEditor
showFileDialog() : InputFile, InputFileList, OutputDirectory, TOPPASOutputFilesDialog
showFileDialog_() : PythonSelector
showFilesDialog() : TOPPASInputFileListVertex
showGoToDialog() : Plot1DWidget, Plot2DWidget, Plot3DWidget, PlotWidget, TOPPViewBase
showGridLines() : PlotCanvas
showIntensityDistribution() : PlotWidget
showIOMappingDialog() : TOPPASEdge
showLegend() : AxisWidget, Plot1DWidget, Plot3DCanvas, Plot3DWidget, PlotWidget
showMetaData() : PlotCanvas
showMetaDistribution() : PlotWidget
showPipelineFinishedLogMessage() : TOPPASBase
showPlotWidgetInWindow() : TOPPViewBase
showPreferences() : TOPPViewBase
showProjections() : Plot2DCanvas
showProjections_() : Plot2DWidget
showRange() : Plot2DGoToDialog
showSpectrumAlignmentDialog() : TOPPViewBase
showSpectrumAsNew1D() : DataSelectionTabs, Plot2DCanvas, Plot2DWidget, SpectraTreeTab, TVIdentificationViewController, TVSpectraViewController
showSpectrumBrowser() : TOPPViewBase
showSpectrumGenerationDialog() : TOPPViewBase
showSpectrumMetaData() : SpectraTreeTab, TOPPViewBase
showSplitters() : HistogramWidget
showStatistics() : PlotWidget
showStatusMessage() : TOPPASBase, TOPPViewBase
showTOPPDialog() : TOPPViewBase
showTOPPDialog_() : TOPPViewBase
showURL() : TOPPASBase
showWindow() : TOPPViewBase
shrink_to_fit() : ExposedVector< VectorElement >
shuffle() : DecoyGenerator
shufflePeptide() : MRMDecoy
shufflePeptideLight() : MRMDecoy
shufflePeptides() : DecoyGenerator
shuffler_ : ConfidenceScoring, DecoyGenerator, RANSAC< TModelType >
si_map_ : MzIdentMLDOMHandler
si_pro_map_ : MzIdentMLDOMHandler
SIDE : Compomer
sidx_ : SpectrumAccessSqMass
sigma : GaussFitter::GaussFitResult
sigma_ : EGHTraceFitter, GaussFilterAlgorithm, GaussTraceFitter
sigma_5_bound_ : EGHTraceFitter
signal_decoy : PeakGroup
signal_not_unique : ChannelQC
signal_proportion : PrecursorPurity::PurityScores
signal_to_noise_ : FeatureFinderAlgorithmMetaboIdent, FeatureFinderIdentificationAlgorithm, PeakPickerChromatogram, PeakPickerHiRes, PeakPickerIterative, PeakPickerMobilogram
SignalToNoiseEstimator() : SignalToNoiseEstimator< Container >
SignalToNoiseEstimatorMeanIterative() : SignalToNoiseEstimatorMeanIterative< Container >
SignalToNoiseEstimatorMedian() : SignalToNoiseEstimatorMedian< Container >
SignalToNoiseEstimatorMedianRapid() : SignalToNoiseEstimatorMedianRapid
SignalToNoiseOpenMS() : SignalToNoiseOpenMS< ContainerT >
sil_2_sdat_ : MzIdentMLHandler
sil_2_sdb_ : MzIdentMLHandler
sil_2_sip_ : MzIdentMLHandler
SIM : InstrumentSettings
similarities_ : ConsensusIDAlgorithmSimilarity
SimilarityCache : ConsensusIDAlgorithmSimilarity
simpleExtractChromatograms_() : OpenSwathCalibrationWorkflow
simpleFindBestFeature() : OpenSwathHelper
SimplePeak() : SimpleTSGXLMS::SimplePeak
SimpleSearchEngineAlgorithm() : SimpleSearchEngineAlgorithm
SimpleSVM() : SimpleSVM
SimpleTSGXLMS() : SimpleTSGXLMS
simplify() : String
simpson_() : PeakIntegrator
simulateNoReRanking() : DBSuitability::SuitabilityData
single_mobilogram_ : LayerDataIonMobility
SingleLinkage() : SingleLinkage
singleMass_ : Adduct
SiriusExportAlgorithm() : SiriusExportAlgorithm
SiriusTargetDecoySpectra() : SiriusFragmentAnnotation::SiriusTargetDecoySpectra
site : MzTabModificationMetaData
sites_ : UnimodXMLHandler
size() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >, AASequence, ACTrie, CalibrationData, ConsensusFeature, ConsensusMap::ColumnHeader, ConstRefVector< ContainerT >, DataFilters
SIZE : DataFilters
size() : DeconvolvedSpectrum, DPosition< D, TCoordinateType >, ExposedVector< VectorElement >, FASTAContainer< TFI_File >, FASTAContainer< TFI_Vector >, FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern, HashGrid< Cluster >, IMSAlphabet
SIZE : IMSIsotopeDistribution
size() : IMSIsotopeDistribution, Weights, IDBoostGraph::ProteinGroup, MzMLHandlerHelper::BinaryData, IsotopeDistribution, KDTreeFeatureMaps, Histogram< ValueType, BinSizeType >, Matrix< Value >, Mobilogram, MRMFeatureOpenMS, MRMTransitionGroup< ChromatogramType, TransitionType >, MSExperiment, MultiGradient, MultiplexFilteredMSExperiment, MultiplexFilteredPeak, NASequence, OnDiscMSExperiment, Param::ParamNode, Param, PeakGroup, QCBase::SpectraMap, QTCluster, SplineInterpolatedPeaks, StringView, TOPPASVertex::TOPPASFilenames, TransitionGroupOpenMS< SpectrumT, TransitionT >, IMRMFeature, ITransitionGroup, MockMRMFeature, MockTransitionGroup
size_ : ClusterProxyKD, StringView
SIZE_OF_ANALYZERTYPE : MassAnalyzer
SIZE_OF_ANNOTATIONSTATE : BaseFeature
SIZE_OF_CHECKSUMTYPE : SourceFile
SIZE_OF_CHROMATOGRAM_TYPE : ChromatogramSettings
SIZE_OF_DATATYPE : DataValue
SIZE_OF_FLAGS : LayerDataDefs
SIZE_OF_FLOATINDICES : PeakPickerChromatogram, PeakPickerMobilogram
SIZE_OF_IONOPTICSTYPE : Instrument
SIZE_OF_ITRAQ_TYPES : ItraqConstants
SIZE_OF_LABEL_TYPE : LayerDataDefs
SIZE_OF_MODELTYPE : MZTrafoModel
SIZE_OF_MT_QUANTMETHOD : MassTrace
SIZE_OF_NAMES : ColorBrewer::Distinct
SIZE_OF_NUMPRESSCOMPRESSION : MSNumpressCoder
SIZE_OF_ORIGIN_ANNOTATION_FORMAT : IDRipper
SIZE_OF_PEAKMASSTYPE : ProteinIdentification
SIZE_OF_PROCESSINGACTION : DataProcessing
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_SPECTRUMTYPE : SpectrumSettings
SIZE_OF_TAB_INDEX : DataSelectionTabs
SIZE_OF_TYPE : FileTypes
SIZE_OF_VALUES : OSWHierarchy
size_only_ : FeatureFileOptions, FeatureXMLHandler
size_proportions_ : SaveImageDialog
size_ratio_ : SaveImageDialog
size_type : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >, ConstRefVector< ContainerT >, ExposedVector< VectorElement >, HashGrid< Cluster >, IMSAlphabet, IMSElement, IMSIsotopeDistribution, IntegerMassDecomposer< ValueType, DecompositionValueType >, Weights
size_x_ : SaveImageDialog
size_y_ : SaveImageDialog
sizeHint() : ColorSelector
SizeOfNASFragmentType : NASequence
SizeOfResidueType : Residue
sizeProfile() : MultiplexFilteredPeak
SizeType : ConvexHull2D, DistanceMatrix< Value >, String
SizeUnderflow() : SizeUnderflow
skip_chromatogram_ : MzMLHandler
skip_chromatograms_ : PeakFileOptions
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_abundance_assay : MzTabMSmallMoleculeSectionRow
small_molecule_abundance_study_variable : MzTabMSmallMoleculeSectionRow
small_molecule_abundance_variation_study_variable : MzTabMSmallMoleculeSectionRow
small_molecule_data_ : MzTab
small_molecule_feature_abundance_assay : MzTabMSmallMoleculeFeatureSectionRow
small_molecule_feature_quantification_unit : MzTabMMetaData
small_molecule_identification_reliability : MzTabMMetaData
small_molecule_quantification_unit : MzTabMetaData, MzTabMMetaData
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
sme_id_ref_ambiguity_code : MzTabMSmallMoleculeFeatureSectionRow
sme_id_refs : MzTabMSmallMoleculeFeatureSectionRow
sme_identifier : MzTabMSmallMoleculeEvidenceSectionRow
sme_optional_column_names_ : MzTabM
smf_id_refs : MzTabMSmallMoleculeSectionRow
smf_identifier : MzTabMSmallMoleculeFeatureSectionRow
smf_optional_column_names_ : MzTabM
smile : IdentifiedCompound
smiles : MzTabMSmallMoleculeEvidenceSectionRow, MzTabMSmallMoleculeSectionRow, MzTabSmallMoleculeSectionRow
SMILES : TransitionTSVFile::TSVTransition
smiles : LightCompound
smiles_string : Compound
smiles_string_ : SpectralMatch
sml_identifier : MzTabMSmallMoleculeSectionRow
sml_optional_column_names_ : MzTabM
smoothData() : ElutionPeakDetection, LowessSmoothing
smoothDeltaMassHistogram_() : OpenSearchModificationAnalysis
smoothed_intensities_ : MassTrace
SMOOTHING : DataProcessing
sn_ : SignalToNoiseOpenMS< ContainerT >
sn_bin_count_ : MRMFeatureFinderScoring, PeakPickerChromatogram, PeakPickerIterative, PeakPickerMobilogram
sn_ratio : OpenSwath_Scores
SN_statistics_ : SpectrumAnnotator
sn_win_len_ : MRMFeatureFinderScoring, PeakPickerChromatogram, PeakPickerIterative, PeakPickerMobilogram
snap_factors_ : PlotCanvas
snapShot_() : StopWatch
snapToGrid() : TOPPASScene
snd_database_ : SequestInfile
snr_ : PeakGroup
snr_mul_factor_ : FLASHHelperClasses::PrecalculatedAveragine
snr_weight_ : TargetedSpectraExtractor
snt_ : PeakPickerChromatogram
software : MzTabMetaData, MzTabMMetaData, MzTabSoftwareMetaData
Software() : Software
software_ : DataProcessing, Instrument, MzMLHandler, TargetedExperiment
software_name_ : SoftwareVisualizer
software_ref : ProcessingStep, Prediction, RetentionTime
software_version_ : SoftwareVisualizer
SoftwareVisualizer() : SoftwareVisualizer
SOLID : Sample
SOLUTION : Sample
solve() : BSpline2d, LPWrapper, NonNegativeLeastSquaresSolver
SOLVED : NonNegativeLeastSquaresSolver
solveNNLS_() : IsobaricIsotopeCorrector
SOLVER : LPWrapper
solver_ : LPWrapper
SOLVER_GLPK : LPWrapper
SolverParam() : LPWrapper::SolverParam
SolverStatus : LPWrapper
somethingHasChanged() : TOPPASEdge, TOPPASVertex
sort() : DeconvolvedSpectrum, ROCCurve, MSSpectrum, PeakGroup, 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, Mobilogram, MSChromatogram, MSSpectrum
sortByIonMobility() : MSSpectrum
sortByMaps() : ConsensusMap
sortByMass() : IsotopeDistribution
sortByMZ() : ConsensusMap, FeatureMap
sortByNames() : IMSAlphabet
sortByOverallQuality() : FeatureMap
sortByPosition() : ConsensusMap, ConstRefVector< ContainerT >, FeatureMap, Mobilogram, MSChromatogram, MSSpectrum
sortByPositionPresorted() : MSSpectrum
sortByPrecursorInt() : MetaboTargetedAssay
sortByQscore() : DeconvolvedSpectrum
sortByQuality() : ConsensusMap
sortByRT() : CalibrationData, ConsensusMap, FeatureMap
sortBySize() : ConsensusMap
sortByUnique_() : ProteinInference
sortByValues() : IMSAlphabet
sortChromatograms() : MSExperiment
Sorted : IsotopeDistribution
sorted_ : ROCCurve
SortExtractionCoordinatesByMZ() : ChromatogramExtractorAlgorithm::ExtractionCoordinates
SortExtractionCoordinatesReverseByMZ() : ChromatogramExtractorAlgorithm::ExtractionCoordinates
sortPeptideIdentifications() : BaseFeature
sortPeptideIdentificationsByMapIndex() : ConsensusMap
sortPSM_() : MzTabFile
sortSpectra() : MSExperiment
sortSpectrumByMZ() : SpectrumAddition
sortTransitionsByName() : TargetedExperiment
sortTransitionsByProductMZ() : TargetedExperiment
source : MzTabInstrumentMetaData
source_feature_index_ : AccurateMassSearchResult
source_file : SiriusMSFile::CompoundInfo
source_file_ : ChromatogramSettings, OSWData, SpectrumSettings
source_files_ : ExperimentalSettings, MzMLHandler, TargetedExperiment
source_format : SiriusMSFile::CompoundInfo
source_out_param_ : TOPPASEdge
SourceClassification : ResidueModification
SourceFile() : SourceFile
SourceFileVisualizer() : SourceFileVisualizer
sourceHasChanged() : TOPPASEdge
sp_ : EnhancedTabBarWidgetInterface
sp_map_ : MzIdentMLDOMHandler
spacer_ : Plot1DWidget
spacing_ : GaussFilter, GaussFilterAlgorithm, LinearResampler
spacing_difference_ : PeakPickerHiRes, PeakPickerIterative
spacing_difference_gap_ : PeakPickerHiRes
spacing_for_spectra_resampling_ : MRMFeatureFinderScoring, OpenSwathScoring
sparse_window_percent_ : SignalToNoiseEstimatorMedian< Container >
SparseVectorType : BinnedSpectrum
spatiallyGreaterEqual() : DPosition< D, TCoordinateType >
spatiallyLessEqual() : DPosition< D, TCoordinateType >
spec_ : DeconvolvedSpectrum, MzDataHandler, MzMLHandler, MSSpectrum::Chunks, TheoreticalSpectrumGenerationDialog
SPEC_FULL : EnzymaticDigestion
spec_gen_ : NeighborSeq
spec_gen_dialog_ : TOPPViewBase
spec_id_ : MzMLSqliteHandler, MzMLSqliteSwathHandler
spec_id_view_ : TVIdentificationViewController
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
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_ : DIATreeTab, SpectraTreeTab
spectra_data : IDRipper::IdentificationRuns
spectra_data_ref : MzIdentMLDOMHandler::SpectrumIdentification, SpectrumMetaDataLookup
spectra_expected_ : MSDataWritingConsumer
SPECTRA_IDX : DataSelectionTabs
spectra_index_ : CachedmzML, CachedMzMLHandler
spectra_linear_peaks : OPXLDataStructs::PreprocessedPairSpectra
spectra_merge_method_type_ : OpenSwathScoring
spectra_meta_ : SpectrumAccessOpenMSInMemory
spectra_native_ids_ : IndexedMzMLHandler, OnDiscMSExperiment
spectra_offsets_ : IndexedMzMLHandler, MzMLHandler
spectra_ref : MzTabMSmallMoleculeEvidenceSectionRow, MzTabOSMSectionRow, MzTabPeptideSectionRow, MzTabPSMSectionRow, MzTabSmallMoleculeSectionRow
spectra_search_box_ : DIATreeTab, SpectraTreeTab
spectra_treewidget_ : SpectraTreeTab
spectra_view_widget_ : DataSelectionTabs
spectra_written_ : MSDataCachedConsumer, MSDataWritingConsumer
spectra_xlink_peaks : OPXLDataStructs::PreprocessedPairSpectra
SpectraDistance_() : SpectraMerger::SpectraDistance_
SpectraIDViewTab() : SpectraIDViewTab
SpectralDeconvolution() : SpectralDeconvolution
SpectralMatch() : SpectralMatch
SpectraMap() : QCBase::SpectraMap
SpectraMerger() : SpectraMerger
spectrastAnnotationExtract() : TransitionTSVFile
spectrastRTExtract() : TransitionTSVFile
SpectraSTSimilarityScore() : SpectraSTSimilarityScore
SpectraTreeTab() : SpectraTreeTab
spectraview_controller_ : DataSelectionTabs
spectrum : FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern, FeatureFinderAlgorithmPickedHelperStructs::Seed
Spectrum() : Spectrum
spectrum : MzMLHandler::SpectrumData, MzXMLHandler::SpectrumData, MetaboTargetedAssay::CompoundSpectrumPair, PeakIndex, TargetedSpectraExtractor::Match
spectrum_addition_method_ : MRMFeatureFinderScoring
spectrum_data_ : MzMLHandler, MzXMLHandler
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_merge_method_type_ : MRMFeatureFinderScoring
spectrum_ranges_ : MSExperiment
spectrum_widget_ : LayerListView, PlotCanvas
SpectrumAccessOpenMS() : SpectrumAccessOpenMS
SpectrumAccessOpenMSCached() : SpectrumAccessOpenMSCached
SpectrumAccessOpenMSInMemory() : SpectrumAccessOpenMSInMemory
SpectrumAccessQuadMZTransforming() : SpectrumAccessQuadMZTransforming
SpectrumAccessSqMass() : SpectrumAccessSqMass
SpectrumAccessTransforming() : SpectrumAccessTransforming
SpectrumAdditionMethod : OpenSwathScoring
SpectrumAlignment() : SpectrumAlignment
SpectrumAlignmentDialog() : SpectrumAlignmentDialog
SpectrumAlignmentScore() : SpectrumAlignmentScore
SpectrumAnnotator() : SpectrumAnnotator
SpectrumCheapDPCorr() : SpectrumCheapDPCorr
SpectrumConstIteratorType : PlotCanvas
spectrumContextMenu_() : SpectraTreeTab
SpectrumCount() : SpectrumCount
spectrumDeselected() : SpectraIDViewTab
spectrumDoubleClicked() : SpectraTreeTab
SpectrumIdentification() : SpectrumIdentification
SpectrumIdRef : AnnotatedMSRun
SpectrumIteratorType : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
SpectrumLookup() : SpectrumLookup
SpectrumMatchesTopN() : FragmentIndex::SpectrumMatchesTopN
SpectrumMergeMethodType : OpenSwathScoring
SpectrumMeta() : SpectrumMeta
SpectrumMetaData() : SpectrumMetaDataLookup::SpectrumMetaData
SpectrumMetaDataLookup() : SpectrumMetaDataLookup
SpectrumPrecursorComparator() : SpectrumPrecursorComparator
SpectrumPtrType : DIAScoring
SpectrumRangeManager() : SpectrumRangeManager
SpectrumRangeManagerType : MSExperiment
spectrumRanges() : MSExperiment
spectrumSearchText_() : DIATreeTab, SpectraTreeTab
spectrumSelected() : SpectraIDViewTab, SpectraTreeTab
SpectrumSettings() : SpectrumSettings
SpectrumSettingsVisualizer() : SpectrumSettingsVisualizer
SpectrumT : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
SpectrumType : AnnotatedMSRun, CachedSwathFileConsumer, FeatureFinderAlgorithmPicked, FullSwathFileConsumer, IMSDataConsumer, CachedMzMLHandler, MzDataHandler, MzMLHandler, MzXMLHandler, LayerDataPeak, MSDataCachedConsumer, MSDataSqlConsumer, MSDataWritingConsumer, MSExperiment, MzMLSwathFileConsumer, PlotCanvas, PlotWidget, RegularSwathFileConsumer, SpectrumSettings, TOPPViewBase, TVControllerBase, MRMScoring
spectrumTypeToString() : SpectrumSettings
SPECXML : FileTypes
SPLIB : FileTypes
spline_ : BSpline2d, SplinePackage, TransformationModelBSpline
SplineInterpolatedPeaks() : SplineInterpolatedPeaks
SplinePackage() : SplinePackage
split() : ConsensusMap, String
split_quoted() : String
splitByFAIMSCV() : IMDataConverter
splitByMiddle() : XQuestResultXMLHandler
splitByNth() : XQuestResultXMLHandler
splitExperimentByIonMobility() : IMDataConverter
splitHills_() : Biosaur2Algorithm
splitIntoPeptidesAndXLs() : NuXLFDR
SplitMeta : ConsensusMap
splitModificationBySpecifiedAA() : MascotXMLHandler
splitTransitionGroupsDetection_() : MRMFeatureFinderScoring
splitTransitionGroupsIdentification_() : MRMFeatureFinderScoring
sptr : SwathMap
sptr_ : SpectrumAccessTransforming
sql_batch_size_ : MzMLSqliteHandler
SqliteConnector() : SqliteConnector
SqlOpenMode : SqliteConnector
SqlOperationFailed() : SqlOperationFailed
SQMASS : FileTypes
SqMassFile() : SqMassFile
sqrt2pi : EmgFitter1D::EgmFitterFunctor, BasicStatistics< RealT >
sqrt_2 : EmgFitter1D::EgmFitterFunctor
SqrtScaler() : SqrtScaler
squared_difference_counted() : squared_difference_counted< _Tp, _Dist >
sr_map_ : MzIdentMLDOMHandler
src : RangeStatsType
SRM : InstrumentSettings
ss_ : SVOutStream
st_ : Annotation1DCaret< DataPoint >
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 : ParentMatch
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() : CVMappingFile, IdXMLFile, ConsensusXMLHandler, FeatureXMLHandler, MascotXMLHandler, MzDataHandler, MzIdentMLHandler, MzMLHandler, MzMLValidator, MzXMLHandler, ParamXMLHandler, PTMXMLHandler, SemanticValidator, ToolDescriptionHandler, TraMLHandler, UnimodXMLHandler, XMLHandler, XQuestResultXMLHandler, OMSSAXMLFile, PepXMLFile, PepXMLFileMascot, ProtXMLFile, QcMLFile, TransformationXMLFile, XTandemXMLFile
startPos() : TOPPASEdge
startProgress() : GUIProgressLoggerImpl, ProgressLogger::ProgressLoggerImpl, ProgressLogger
state : TheoreticalSpectrumGenerationDialog::CheckBox
state_ : MzTabDouble, MzTabInteger, Sample
states : AnnotationStatistics
STATIC_FIELD : Instrument
static_for_each_base_() : RangeManager< RangeBases >
Statistics() : PeptideAndProteinQuant::Statistics
statistics1_ : BiGaussFitter1D, BiGaussModel
statistics2_ : BiGaussFitter1D, BiGaussModel
statistics_ : EmgModel, FeatureFinderIdentificationAlgorithm, Fitter1D, GaussModel, PeptideProteinResolution
stats : LayerDataDefs::ProjectionData
stats_ : IsobaricQuantifier, LayerStatisticsDialog, PeptideAndProteinQuant
Status : QCBase
status_ : PepXMLFile, TOPPASToolVertex
status_list_ : MetaDataBrowser
std::hash< MetaInfo > : MetaInfo
stddev() : mean_and_stddev
stdev_ : SignalToNoiseEstimatorMeanIterative< Container >
SteinScottImproveScore() : SteinScottImproveScore
StepOpt : IdentificationDataConverter
stepPrimary_() : ACTrie
steps_and_scores : ScoredProcessingResult
stepScout_() : ACTrie
stickdata_ : Plot3DOpenGLCanvas
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
storage_formats_ : LayerStoreData
store() : AbsoluteQuantitationMethodFile, AcquisitionInfoVisualizer, AcquisitionVisualizer, BaseVisualizerGUI, CachedmzML, ConsensusXMLFile, ContactPersonVisualizer, CsvFile, DataProcessingVisualizer, DocumentIdentifierVisualizer, DTA2DFile, DTAFile, EDTAFile, ExperimentalSettingsVisualizer, FASTAFile, FeatureXMLFile, GNPSMetaValueFile, GNPSMGFFile, GNPSQuantificationFile, GradientVisualizer, HPLCVisualizer, IBSpectraFile, IdXMLFile, IndexedMzMLFileLoader, InspectInfile, InstrumentSettingsVisualizer, InstrumentVisualizer, OMSFileStore
STORE : XMLHandler
store() : IonDetectorVisualizer, IonSourceVisualizer, KroenikFile, MascotGenericFile, MassAnalyzerVisualizer, MetaInfoDescriptionVisualizer, MetaInfoVisualizer, MRMFeatureQCFile, MsInspectFile, MSPFile, MSPGenericFile, MzDataFile, MzIdentMLFile, MzMLFile, MzQCFile, MzTabFile, MzTabMFile, MzXMLFile, OMSFile, ParamCTDFile, ParamCWLFile, ParamEditor, ParamJSONFile, ParamXMLFile, PepNovoInfile, PeptideHitVisualizer, PeptideIdentificationVisualizer, PepXMLFile, PercolatorInfile, PrecursorVisualizer, ProductVisualizer, ProteinHitVisualizer, ProteinIdentificationVisualizer, ProtXMLFile, PTMXMLFile, QcMLFile, QuantmsIO, SampleVisualizer, ScanWindowVisualizer, SequestInfile, SiriusMSFile, SoftwareVisualizer, SourceFileVisualizer, SpecArrayFile, SpectrumSettingsVisualizer, SqMassFile, 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
storeAdducts_() : OMSFileStore
storeAppliedProcessingStep_() : OMSFileStore
storeBaseFeature_() : OMSFileStore
storeBuffer() : MzMLFile
storeConsensusColumnHeaders_() : OMSFileStore
storeConsensusFeatures() : FileHandler
storeConsensusFeatures_() : OMSFileStore
storeCVTerm_() : OMSFileStore
storeDataProcessing_() : OMSFileStore
storeDBSearchParams_() : OMSFileStore
storeElements_() : ElementDB
storeExperiment() : FileHandler
storeFeatureAndSubordinates_() : OMSFileStore
storeFeatures() : FileHandler
storeFeatures_() : OMSFileStore
storeFullCM() : LayerStoreDataConsensusMapAll
storeFullData() : LayerData1DChrom, LayerData1DIonMobility, LayerData1DPeak, LayerDataBase, LayerDataChrom, LayerDataConsensus, LayerDataFeature, LayerDataIdent, LayerDataIonMobility, LayerDataPeak
storeFullExperiment() : LayerStoreDataPeakMapAll
storeFullFM() : LayerStoreDataFeatureMapAll
storeFullIdent() : LayerStoreDataIdentAll
storeIdentifications() : FileHandler
storeIdentifiedCompounds_() : OMSFileStore
storeIdentifiedSequences_() : OMSFileStore
storeINI_() : ToolsDialog, TOPPASToolConfigDialog
storeInputFiles_() : OMSFileStore
storeISO() : MSstatsFile
storeIsotopes_() : ElementDB
storeJSON() : SwathQC
storeLFQ() : MSstatsFile, TriqlerFile
storeMapMetaData_() : OMSFileStore
storeMetaInfo_() : OMSFileStore
storeMetaInfos_() : OMSFileStore
storeObservationMatches_() : OMSFileStore
storeObservations_() : OMSFileStore
storeOriginalRT_() : MapAlignmentTransformer
storeParentGroupSets_() : OMSFileStore
storeParentMatches_() : OMSFileStore
storeParentSequences_() : OMSFileStore
storePeptideReliabilityColumn() : MzTabFile
storePeptideUriColumn() : MzTabFile
storeProcessingSoftwares_() : OMSFileStore
storeProcessingSteps_() : OMSFileStore
storeProteinGoTerms() : MzTabFile
storeProteinReliabilityColumn() : MzTabFile
storeProteinUriColumn() : MzTabFile
storePSMReliabilityColumn() : MzTabFile
storePSMUriColumn() : MzTabFile
storeQC() : FileHandler
storeRecursive_() : ParamEditor
storeRotationAndZoom() : Plot3DOpenGLCanvas
storeScoredProcessingResults_() : OMSFileStore
storeScoreTypes_() : OMSFileStore
storeSmallMoleculeReliabilityColumn() : MzTabFile
storeSmallMoleculeUriColumn() : MzTabFile
storeSpectraMSP() : TargetedSpectraExtractor
storeSpectrum() : FileHandler
storeSpectrum_() : FIAMSDataProcessor
storeTIC() : DTA2DFile
storeTransformations() : FileHandler
storeTransitions() : FileHandler
storeVersionAndDate_() : OMSFileStore
storeVisibleChromatogram() : LayerStoreDataPeakMapVisible
storeVisibleCM() : LayerStoreDataConsensusMapVisible
storeVisibleData() : LayerData1DChrom, LayerData1DIonMobility, LayerData1DPeak, LayerDataBase, LayerDataChrom, LayerDataConsensus, LayerDataFeature, LayerDataIdent, LayerDataIonMobility, LayerDataPeak
storeVisibleExperiment() : LayerStoreDataPeakMapVisible
storeVisibleFM() : LayerStoreDataFeatureMapVisible
storeVisibleIdent() : LayerStoreDataIdentVisible
storeVisibleSpectrum() : LayerStoreDataPeakMapVisible
strarray_ : TransitionTSVFile
stream : LogStreamBuf::StreamStruct
stream_ : IndentedStream, 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
StreamManipulator : IndentedStream
streamPQPToLightTargetedExperiment_() : TransitionPQPFile
StreamStruct() : LogStreamBuf::StreamStruct
streamTSVToLightTargetedExperiment_() : TransitionTSVFile
StreamType : StreamHandler
strict_ : MRMFeatureFinderScoring
STRING : ListEditor, ParameterInformation, StreamHandler
String() : String
string_data_arrays_ : Mobilogram, MSChromatogram, MSSpectrum, ProteinIdentification::ProteinGroup
STRING_LIST : DataValue, ParamValue
STRING_VALUE : DataValue, ParamValue
StringDataArray : Mobilogram, MSChromatogram, MSSpectrum, ProteinIdentification::ProteinGroup
StringDataArrays : Mobilogram, MSChromatogram, MSSpectrum, ProteinIdentification::ProteinGroup
STRINGLIST : ParameterInformation
stringListToIsotopeCorrectionMatrix_() : IsobaricQuantitationMethod
StringListUtils() : StringListUtils
StringManager() : StringManager
stringSimdDecoder_() : Base64
stringSimdEncoder_() : Base64
StringView() : StringView
strip_namespaces_ : CVMappingFile
stripExtension() : FileHandler
strLength() : StringManager
struct_size_in_datapoints_ : MorphologicalFilter
study_variable : MzTabMetaData, MzTabMMetaData
stw_ : WizardGUILock< TWidgetClass >
su_ : MRMFeatureFinderScoring, OpenSwathScoring
sub_index : FeatureFinderAlgorithmMetaboIdent::MassTraceBounds
sub_scores : PeptideHit::PepXMLAnalysisResult
subordinate_feature_level_ : FeatureXMLHandler
subordinates_ : Feature
subquery_score_ : OMSFileLoad
subsamples_ : Sample
subsections_ : DefaultParamHandler, TOPPBase
subsections_TOPP_ : TOPPBase
subset() : MRMTransitionGroup< ChromatogramType, TransitionType >
subsetDependent() : MRMTransitionGroup< ChromatogramType, TransitionType >
substitute() : String
substr() : String, StringView
SUBSTREESTATUS : TOPPASVertex
subvalue_type : _Region< __K, _Val, _SubVal, _Acc, _Cmp >, KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
success : DecoyHelper::Result, FalseDiscoveryRate::DecoyStringHelper::Result
suffix : ACNode, Param::ParamNode, String
suffix_fraction : PeptideSearchEngineFIAlgorithm::AnnotatedHit_, SimpleSearchEngineAlgorithm::AnnotatedHit_
suit_ : DBSuitability_friend
suitability : DBSuitability::SuitabilityData
suitability_corr : DBSuitability::SuitabilityData
suitability_corr_no_rerank : DBSuitability::SuitabilityData
suitability_no_rerank : DBSuitability::SuitabilityData
sum() : BasicStatistics< RealT >
sum_ : BasicStatistics< RealT >, RangeStats< VALUE_TYPE >
sum_formula : LightCompound
sum_formula_ : SpectralMatch
sum_intensity : LayerDataDefs::ProjectionData::Summary
sum_tolerance_im_ : PeakPickerIM
sum_tolerance_mz_ : PeakPickerIM
sum_xx_ : LinearRegressionWithoutIntercept
sum_xy_ : LinearRegressionWithoutIntercept
SumFormula : TransitionTSVFile::TSVTransition
sumFrame_() : PeakPickerIM
sumIntensity_() : MSstatsFile, TriqlerFile
Summary() : Summary
SummaryStatistics() : SummaryStatistics< T >
superimposer_ : MapAlignmentAlgorithmPoseClustering
support : ConsensusIDAlgorithm::HitInfo
supported_schemes : TOPPASResource
supported_types_ : LayerAnnotatorBase
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 : NuXLRTPrediction
svm_feat_centers_ : FeatureFindingMetabo
svm_feat_scales_ : FeatureFindingMetabo
svm_min_prob_ : FeatureFinderIdentificationAlgorithm, FFIDAlgoExternalIDHandler
svm_n_parts_ : FeatureFinderIdentificationAlgorithm, FFIDAlgoExternalIDHandler
svm_n_samples_ : FeatureFinderIdentificationAlgorithm, FFIDAlgoExternalIDHandler
svm_predictor_names_ : FeatureFinderIdentificationAlgorithm, FFIDAlgoExternalIDHandler
svm_probs_external_ : FeatureFinderIdentificationAlgorithm, FFIDAlgoExternalIDHandler
svm_probs_internal_ : FeatureFinderIdentificationAlgorithm, FFIDAlgoExternalIDHandler
svm_quality_cutoff : FeatureFinderIdentificationAlgorithm, FFIDAlgoExternalIDHandler
svm_xval_out_ : FeatureFinderIdentificationAlgorithm, FFIDAlgoExternalIDHandler
SVOutStream() : SVOutStream
swap() : ConsensusMap, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >, ConstRefVector< ContainerT >, DocumentIdentifier, DPosition< D, TCoordinateType >, ExposedVector< VectorElement >, FeatureMap, Gravitator, IdentificationData, Weights, unique_xerces_ptr< T >, MetaInfoInterface, Mobilogram, MSExperiment, PeakGroup, UniqueIdIndexer< T >, UniqueIdInterface
swapDimensions() : DRange< D >
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
switchBackScoreType() : IDScoreSwitcherAlgorithm
switchKR() : MRMDecoy
switchKRLight() : MRMDecoy
switchOrientation_() : SpectraIDViewTab
switchScores() : IDScoreSwitcherAlgorithm
switchToGeneralScoreType() : IDScoreSwitcherAlgorithm
switchToScoreType() : IDScoreSwitcherAlgorithm
symbol_ : Element
symbols_ : ElementDB
symmetric_ : LevMarqFitter1D, TransformationModelLinear
symmetry_ : EmgFitter1D, EmgModel
sync() : LogStreamBuf
sync_() : RecentFilesMenu
synchronizePeakAnnotations() : LayerData1DPeak
syncLF_() : LogStreamBuf
synonyms : ControlledVocabulary::CVTerm
synonyms_ : DigestionEnzyme, MSPGenericFile, Residue, ResidueModification
synonyms_separator_ : MSPGenericFile