- a -

• AAIndex() : AAIndex
• AASequence() : AASequence
• AASequenceIdentity() : MRMDecoy
• abort_() : FeatureFinderAlgorithmPicked
• abortPipeline() : TOPPASBase , TOPPASScene
• abortTOPPTool() : TOPPViewBase
• aboutToBeDestroyed() : SpectrumWidget , TOPPASWidget
• aboutToCloseId() : EnhancedTabBar , TOPPASTabBar
• absolutePath() : File
• AbsoluteQuantitation() : AbsoluteQuantitation
• AbsoluteQuantitationMethodFile() : AbsoluteQuantitationMethodFile
• AbsoluteQuantitationStandards() : AbsoluteQuantitationStandards
• AbsoluteQuantitationStandardsFile() : AbsoluteQuantitationStandardsFile
• accession() : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_
• accessionEqual_() : ConsensusMapMergerAlgorithm , IDMergerAlgorithm
• accessionHash_() : ConsensusMapMergerAlgorithm , IDMergerAlgorithm
• accumulateFilterValues() : MRMFeatureFilter
• AccurateMassSearchEngine() : AccurateMassSearchEngine
• AccurateMassSearchResult() : AccurateMassSearchResult
• acidic() : AAIndex
• Acquisition() : Acquisition
• AcquisitionInfo() : AcquisitionInfo
• AcquisitionInfoVisualizer() : AcquisitionInfoVisualizer
• AcquisitionVisualizer() : AcquisitionVisualizer
• AcqusHandler() : AcqusHandler
• actionModeChange() : Spectrum3DOpenGLCanvas , SpectrumCanvas
• activate1DSpectrum() : TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• activateAsPrecursorPeak() : MSPeak
• activateBehavior() : TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• activateCache() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• activateLayer() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas
• activatePrecalculationMode() : MultiGradient
• activateSpectrum() : Spectrum1DCanvas
• activeLayerIndex() : SpectrumCanvas
• activeSubWindow_() : TOPPASBase
• adaptPenScaling_() : Spectrum2DCanvas
• add() : Compomer , DataFilters , AveragePosition< D > , MetaDataBrowser , MSSpectrum::Chunks , QTCluster , TOPPASResources
• add1DSignal_() : RawMSSignalSimulation
• add2Buttons_() : BaseVisualizerGUI
• add2DSignal_() : RawMSSignalSimulation
• add_() : MetaInfoVisualizer
• add_alignment_error() : LCMS
• add_feature() : LCMS
• add_LC_elution_peak() : LCMSCData
• add_matched_feature() : SHFeature
• add_modification() : MS2Info
• add_MS2_info() : SHFeature
• add_raw_peak_to_LC_MS_run() : FTPeakDetectController
• add_raw_spec_name() : LCMS
• add_raw_spec_name_map() : LCMS
• add_scan_raw_data() : ProcessData
• addAbundantImmoniumIons_() : TheoreticalSpectrumGenerator
• addAMinusBPeaks_() : NucleicAcidSpectrumGenerator
• addAnalysisResults() : PeptideHit
• addBaseLine_() : RawMSSignalSimulation
• addBetaAccessions() : OPXLHelper
• addBooleanComboBox_() : BaseVisualizerGUI
• addButton_() : BaseVisualizerGUI
• addChargedSpectrum_() : NucleicAcidSpectrumGenerator
• addCheckboxItemToBottomRow_() : SpectraIdentificationViewWidget
• addChromatogram() : MRMTransitionGroup< ChromatogramType, TransitionType > , MSExperiment
• addChromatograms() : OpenSwathCalibrationWorkflow , OpenSwathWorkflowSonar
• addCluster() : ClusteringGrid
• addClusterElements_() : QTClusterFinder
• addColumn() : LPWrapper
• addComboBox_() : BaseVisualizerGUI
• addCOMETFeatures() : PercolatorFeatureSetHelper
• addCompound() : TargetedExperiment
• addCONCATSEFeatures() : PercolatorFeatureSetHelper
• addConfiguration() : IncludeExcludeTarget , TraMLProduct
• addConsensusFeature_() : FeatureGroupingAlgorithmKD
• addConsensusMap() : MSQuantifications
• addConstraint_() : MRMFeatureSelector
• addContact() : TargetedExperiment
• addCV() : TargetedExperiment
• addCVReference() : CVMappings
• addCVTerm() : CVMappingRule , CVTermList , CVTermListInterface
• addData() : LinearRegressionWithoutIntercept , TOPPViewBase
• addData_() : MSExperiment::ContainerAdd_< ContainerValueType, addMassTraces > , MSExperiment::ContainerAdd_< ContainerValueType, false > , MSExperiment::ContainerAdd_< ContainerValueType, true >
• addDataFile() : TOPPViewBase
• addDataProcessing() : MSDataWritingConsumer
• addDataProcessing_() : SpectrumCanvas , TOPPBase
• addDetectorNoise_() : RawMSSignalSimulation
• addDoubleItemToBottomRow_() : SpectraIdentificationViewWidget
• addDoubleLineEdit_() : BaseVisualizerGUI
• addEdge() : TOPPASScene
• addEluent() : Gradient
• addEluent_() : GradientVisualizer
• addEmptyLine_() : TOPPBase
• addEntry_() : SpectrumLookup
• addEnzyme_() : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• addEnzymeInfo() : SequestInfile
• addExcludeTarget() : TargetedExperiment
• addExternalType() : ToolDescription
• addFakeMSMSToFeature() : FTPeakDetectController
• addFeature() : KDTreeFeatureMaps , MRMFeature , MRMTransitionGroup< ChromatogramType, TransitionType >
• addFile() : FileWatcher
• addFiles_() : InputFileList
• addFragmentPeaks_() : NucleicAcidSpectrumGenerator
• addHit() : PeptideIndexing::FoundProteinFunctor , SpectrumIdentification
• addHits_() : PeptideIndexing
• addHoveringEdge() : TOPPASScene
• addIncludeTarget() : TargetedExperiment
• addInEdge() : TOPPASVertex
• addInstrument() : TargetedExperiment
• addIntensity() : BackgroundIntensityBin
• addIntermediateProduct() : ReactionMonitoringTransition
• addInterpretation() : IncludeExcludeTarget , TraMLProduct
• addIntItemToBottomRow_() : SpectraIdentificationViewWidget
• addIntLineEdit_() : BaseVisualizerGUI
• addIonMatchStatistics() : SpectrumAnnotator
• addIsotopeCluster_() : TheoreticalSpectrumGenerator
• addIsotopeTrace() : ConsensusIsotopePattern
• addKLinkedIonPeaks_() : SimpleTSGXLMS , TheoreticalSpectrumGeneratorXLMS
• addLabel_() : BaseVisualizerGUI
• addLabelAnnotation_() : Spectrum1DCanvas
• addLabelToProteinHits_() : ICPLLabeler
• addLayer() : SpectrumCanvas
• addLCelutionProfile() : FTPeakDetectController
• addLine() : TextFile
• addLinearIonLosses_() : TheoreticalSpectrumGeneratorXLMS
• addLinearPeaks_() : SimpleTSGXLMS , TheoreticalSpectrumGeneratorXLMS
• addLineEdit_() : BaseVisualizerGUI
• addLineEditButton_() : BaseVisualizerGUI
• addListView_() : BaseVisualizerGUI
• addLosses_() : SimpleTSGXLMS , TheoreticalSpectrumGenerator
• addLossesFaster_() : TheoreticalSpectrumGenerator
• addLossFormula() : Residue
• addLossName() : Residue
• addMappingRule() : CVMappings
• addMaps() : KDTreeFeatureMaps
• addMASCOTFeatures() : PercolatorFeatureSetHelper
• addMassTrace() : FeatureHypothesis
• addMatches_() : ModificationDefinitionsSet
• addMaxInclusionListSizeConstraints_() : PSLPFormulation
• addMetaDataMetricsToMzTab() : Ms2IdentificationRate , TIC
• addMetaInfoToOptionalColumns() : MzTab
• addMetaValues() : MetaInfoInterface
• addMetaValues_() : XQuestResultXMLHandler
• addMissingRTsToPeptideIDs() : SpectrumMetaDataLookup
• addMissingSpectrumReferences() : SpectrumMetaDataLookup
• addModification() : ModificationDefinitionsSet , ModificationsDB
• addModification_() : TransitionTSVFile
• addModificationsSequences_() : MRMAssay
• addModificationToPeptideHit_() : ICPLLabeler , ITRAQLabeler , O18Labeler , SILACLabeler
• addMS1elutionSignal() : FeatureLCProfile
• addMS1Map_() : CachedSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• addMS2ConsensusSpectrum() : ClusteredMS2ConsensusSpectrum
• addMS2Feature() : SHFeature
• addMS2FeatureToMS1Feature() : FTPeakDetectController
• addMS2Fragment() : MS2ConsensusSpectrum
• addMSGFFeatures() : PercolatorFeatureSetHelper
• addMSLevel() : PeakFileOptions
• addMSPeak() : BackgroundIntensityBin
• addMSRunMetaData_() : MzTab
• addMULTISEFeatures() : PercolatorFeatureSetHelper
• addMzMetaValues_() : MzCalibration
• addMzTabMoleculeParentContext_() : IdentificationDataConverter
• addMzTabSEScores_() : IdentificationDataConverter
• addNewState() : HiddenMarkovModel
• addNewSwathMap_() : CachedSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• addNTermLossFormula() : Residue
• addNTermLossName() : Residue
• addOptionalColumnsToSectionRow_() : MzTabFile
• addOutEdge() : TOPPASVertex
• addOutsideMS1elutionSignal() : FeatureLCProfile
• addPeak() : MultiplexFilteredMSExperiment
• addPeak_() : PeakPickerCWT , TheoreticalSpectrumGeneratorXLMS
• addPeakAnnotation() : Spectrum1DCanvas
• addPeakAnnotations_() : TOPPViewIdentificationViewBehavior
• addPeakAnnotationsFromID_() : TOPPViewIdentificationViewBehavior
• addPeakMSScan() : BackgroundControl
• addPeaks_() : TheoreticalSpectrumGenerator
• addPepEvidenceToRows() : MzTab
• addPeptide() : TargetedExperiment
• addPeptideAndAssociatedProteinsWithRunInfo_() : IDBoostGraph
• addPeptideEvidence() : PeptideHit
• addPeptideIDWithAssociatedProteins_() : IDBoostGraph
• addPeptideRT_() : FeatureFinderIdentificationAlgorithm
• addPeptideSequences_() : MapAlignmentAlgorithmTreeGuided
• addPeptideToMap_() : FeatureFinderIdentificationAlgorithm
• addPercolatorFeatureList() : OPXLHelper
• addPoint() : ConvexHull2D
• addPoints() : ConvexHull2D
• addPrecursorAcquisitionNumberConstraint_() : PSLPFormulation
• addPrecursorChromatogram() : MRMTransitionGroup< ChromatogramType, TransitionType >
• addPrecursorCVTerm() : IncludeExcludeTarget , ReactionMonitoringTransition
• addPrecursorFeature() : MRMFeature
• addPrecursorLabels1D_() : TOPPViewIdentificationViewBehavior
• addPrecursorPeaks_() : SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• addPredecessorState() : HMMState
• addPredictionTerm() : IncludeExcludeTarget , ReactionMonitoringTransition
• addPrimaryMSRunPath() : ProteinIdentification
• addProcessingStep() : ScoredProcessingResult
• addProductCVTerm() : IncludeExcludeTarget , ReactionMonitoringTransition
• addProtein() : TargetedExperiment
• addProteinCoverageConstraint_() : PSLPFormulation
• addProteinGroups_() : ConsensusXMLFile , IdXMLFile
• addProteinPositionMetaValues() : OPXLHelper
• addProteinToILP_() : PSLPFormulation
• addPublication() : TargetedExperiment
• addRatio() : ConsensusFeature
• addRecentFile_() : TOPPViewBase
• addReferenceFormat() : SpectrumLookup
• addResidue_() : ResidueDB
• addResidueSet() : Residue
• addRow() : CsvFile , LPWrapper
• addRTBinCapacityConstraint_() : PSLPFormulation
• addRTFitData() : MapAlignmentAlgorithmKD
• addRunAttachment() : QcMLFile
• addRunQualityParameter() : QcMLFile
• addSample() : ExperimentalDesign::SampleSection
• addSatellite() : MultiplexFilteredPeak
• addSatelliteProfile() : MultiplexFilteredPeak
• addScore() : IdentificationData , ScoredProcessingResult , MRMFeature
• addSearchMetaData_() : MzTab
• addSection() : Param
• addSeparator_() : BaseVisualizerGUI
• addSetAttachment() : QcMLFile
• addSetQualityParameter() : QcMLFile
• addShiftedPeakFragmentAnnotation_() : RNPxlFragmentAnnotationHelper
• addShotNoise_() : RawMSSignalSimulation
• addSingleChargedIons_() : CompNovoIonScoringBase
• addSoftware() : TargetedExperiment
• addSourceFile() : TargetedExperiment
• addSpectrum() : MSExperiment
• addSpectrumIdentification() : Identification
• addSpectrumMetaData_() : MzMLHandler
• addSpectrumToLibrary() : MSPGenericFile , MSPGenericFile_friend
• addStepSizeConstraint_() : PSLPFormulation
• addSuccessorState() : HMMState
• addSynonym() : DigestionEnzyme , Residue , ResidueModification
• addSynonymTransition() : HiddenMarkovModel
• addTab() : EnhancedTabBar , TOPPASTabBar
• addTag() : Param
• addTags() : Param
• addTargetCVTerm() : TargetedExperiment
• addText_() : TOPPBase
• addTextEdit_() : BaseVisualizerGUI
• addTextItemToBottomRow_() : SpectraIdentificationViewWidget
• addTheoreticalSpectrumLayer_() : TOPPViewIdentificationViewBehavior
• addTimepoint() : Gradient
• addTimepoint_() : GradientVisualizer
• addToCache_() : LogStreamBuf
• addToGroup() : FeatureGroupingAlgorithmUnlabeled
• addTOPPASFile() : TOPPASBase
• addTransition() : MRMTransitionGroup< ChromatogramType, TransitionType > , TargetedExperiment
• addTreatment() : Sample
• Adduct() : Adduct
• AdductInfo() : AdductInfo
• addUpSpectra() : SpectrumAddition
• addUserLabelAnnotation_() : Spectrum1DCanvas
• addUserPeakAnnotation_() : Spectrum1DCanvas
• addValue() : BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value >
• addVariable_() : MRMFeatureSelector
• addVertex() : TOPPASScene
• addVertexWithLookup_() : IDBoostGraph
• addVSpacer_() : BaseVisualizerGUI
• addWhiteNoise_() : RawMSSignalSimulation
• addXLinkIonLosses_() : TheoreticalSpectrumGeneratorXLMS
• addXLinkIonPeaks_() : SimpleTSGXLMS , TheoreticalSpectrumGeneratorXLMS
• addXLTargetDecoyMV() : OPXLHelper
• addXTANDEMFeatures() : PercolatorFeatureSetHelper
• adjustBuffer_() : SpectrumCanvas
• adjustCorrectToMS1Precursor() : ProcessData
• advanceFollowUp() : IsobaricChannelExtractor::PuritySate_
• advanceTarget_() : MatchedIterator< CONT_T, TRAIT, CONST_T >
• affineGapalign_() : MapAlignmentAlgorithmSpectrumAlignment
• after() : SysInfo::MemUsage
• aggregateInfo_() : MSstatsFile
• AhoCorasickAmbiguous() : AhoCorasickAmbiguous
• align() : MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering , MapAlignmentAlgorithmSpectrumAlignment
• aliphatic() : AAIndex
• allInputsReady() : TOPPASVertex
• allowedTol() : DaTrait , PpmTrait , ValueTrait
• allParentsAreDecoys() : IdentifiedSequence< SeqType >
• allSameMolecule() : QueryMatchGroup
• allSameQuery() : QueryMatchGroup
• AminoAcidModification() : PepXMLFile::AminoAcidModification
• AnalysisSummary() : MSQuantifications::AnalysisSummary
• analyzeHeader_() : QuantitativeExperimentalDesign
• analyzeLCElutionPeak() : LCElutionPeak
• annotate() : IDMapper , RNPxlReport
• annotate_() : AccurateMassSearchEngine
• annotate_feature_() : MetaboliteFeatureDeconvolution
• annotateBestPerPeptide() : IDFilter
• annotateBestPerPeptidePerRun() : IDFilter
• annotateBestPerPeptidePerRunWithData() : IDFilter
• annotateBestPerPeptideWithData() : IDFilter
• annotateFeatures_() : FeatureFinderIdentificationAlgorithm
• annotateFeaturesFinalizeAssay_() : FeatureFinderIdentificationAlgorithm
• annotateIndistProteins() : IDBoostGraph
• annotateIndistProteins_() : IDBoostGraph
• annotateIon() : MRMIonSeries
• annotateMatches() : SpectrumAnnotator
• annotateMS1FromMassFingerprinting_() : TOPPViewBase
• annotateQuantificationsToProteins() : PeptideAndProteinQuant
• annotateSpectra() : TargetedSpectraExtractor
• annotateSwathMapsFromFile() : SwathWindowLoader
• annotateTransition() : MRMIonSeries
• annotateTransitionCV() : MRMIonSeries
• annotateWithID() : TOPPViewBase
• Annotation1DCaret() : Annotation1DCaret
• Annotation1DDistanceItem() : Annotation1DDistanceItem
• Annotation1DItem() : Annotation1DItem
• Annotation1DPeakItem() : Annotation1DPeakItem
• Annotation1DTextItem() : Annotation1DTextItem
• Annotations1DContainer() : Annotations1DContainer
• AnnotationStatistics() : AnnotationStatistics
• annotationToCV_() : MRMIonSeries
• annotationToCVTermList_() : MRMIonSeries
• append() : ToolDescription , TOPPASVertex::TOPPASFilenames
• appendASCII() : StringManager
• appendChromatogram() : IChromatogramsWriter
• appendColumns() : ConsensusMap
• appendConsumer() : MSDataChainingConsumer
• appendRows() : ConsensusMap
• appendSpectrum() : ISpectraWriter
• AppliedProcessingStep() : AppliedProcessingStep
• apply() : ComplementFilter , ComplementMarker , ConsensusIDAlgorithm , DeNovoPostScoring , FalseDiscoveryRate , FilterFunctor , GoodDiffFilter , IDDecoyProbability , IntensityBalanceFilter , IsotopeDiffFilter , IsotopeMarker , NeutralLossDiffFilter , NeutralLossMarker , PeakMarker , TICFilter , TransformationDescription
• apply_() : ConsensusIDAlgorithm , ConsensusIDAlgorithmIdentity , ConsensusIDAlgorithmSimilarity , IDDecoyProbability
• applyAtMostOneVariableModification_() : ModifiedNASequenceGenerator , ModifiedPeptideGenerator
• applyBasic() : FalseDiscoveryRate
• applyCalibration() : AbsoluteQuantitation
• applyDesign2Resolver() : QuantitativeExperimentalDesign
• applyDilation_() : MorphologicalFilter
• applyDilationSimple_() : MorphologicalFilter
• applyErosion_() : MorphologicalFilter
• applyErosionSimple_() : MorphologicalFilter
• applyEstimated() : FalseDiscoveryRate
• applyEstimatedParameters() : EmgGradientDescent , EmgGradientDescent_friend
• applyEvaluateProteinIDs() : FalseDiscoveryRate
• applyFixedModifications() : ModifiedNASequenceGenerator , ModifiedPeptideGenerator
• applyFunctionOnPeptideHits() : MapUtilities< MapType >
• applyFunctionOnPeptideHits_() : MapUtilities< MapType >
• applyFunctionOnPeptideIDs() : MapUtilities< MapType >
• applyFunctionOnPeptideIDs_() : MapUtilities< MapType >
• applyFunctorOnCCs() : IDBoostGraph
• applyFunctorOnCCsST() : IDBoostGraph
• applyLabelToProteinHit_() : SILACLabeler
• applyLogTransformation() : Histogram< ValueType, BinSizeType >
• applyMemberFunction() : ConsensusMap , Feature , FeatureMap
• applyToBaseFeature_() : MapAlignmentTransformer
• applyToConsensusFeature_() : MapAlignmentTransformer
• applyTOFConversion_() : TOFCalibration
• applyToFeature_() : MapAlignmentTransformer
• applyToQueryMatches() : FalseDiscoveryRate
• applyTransformation() : InternalCalibration
• applyTransformation_() : InternalCalibration
• applyTransformations() : KDTreeFeatureMaps
• applyVariableModifications() : ModifiedNASequenceGenerator , ModifiedPeptideGenerator
• areaBegin() : MSExperiment
• areaBeginConst() : MSExperiment
• areaEnd() : MSExperiment
• areaEndConst() : MSExperiment
• AreaIterator() : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
• asBool_() : XMLHandler
• AScore() : AScore
• asDateTime_() : XMLHandler
• asDouble_() : XMLHandler
• asFloat_() : XMLHandler
• asInt_() : XMLHandler
• askForOutputDir() : TOPPASScene
• asMass() : AccurateMassSearchEngine::CompareEntryAndMass_
• asMutable() : FeatureHandle
• Assay() : MSQuantifications::Assay
• assembleInclusionListForProteinBasedLP_() : PSLPFormulation
• assembleRunMap_() : MSstatsFile
• assign() : ConstRefVector< ContainerT > , DIntervalBase< D >
• assignDeltaScore_() : PercolatorFeatureSetHelper
• assignMS2IndexToFeature() : FeatureMapping
• assignRanks() : PeptideIdentification , ProteinIdentification
• assignTypes_() : XFDRAlgorithm
• assignUIDs() : MSQuantifications
• associateMS2FeatureToMS1Feature() : FTPeakDetectController
• asUInt_() : XMLHandler
• asVector() : Matrix< Value >
• AsymmetricStatistics() : AsymmetricStatistics< RealT >
• at() : QCBase::SpectraMap
• atEnd() : FASTAFile
• Attachment() : QcMLFile::Attachment
• attributeAsDouble_() : XMLHandler
• attributeAsDoubleList_() : XMLHandler
• attributeAsInt_() : XMLHandler
• attributeAsIntList_() : XMLHandler
• attributeAsString_() : XMLHandler
• attributeAsStringList_() : XMLHandler
• AUC() : ROCCurve
• autoUpdateProjections() : Spectrum2DWidget
• average() : SpectraMerger
• averageCentroidSpectra_() : SpectraMerger
• averageCoefficients_() : TOFCalibration
• averageErrors_() : TOFCalibration
• AverageLinkage() : AverageLinkage
• averageMass() : IsotopeDistribution
• averagePopulationAberration() : ClusterAnalyzer
• AveragePosition() : AveragePosition< D >
• averageProfileSpectra_() : SpectraMerger
• averageSilhouetteWidth() : ClusterAnalyzer
• AxisPainter() : AxisPainter
• AxisTickCalculator() : AxisTickCalculator
• AxisWidget() : AxisWidget