| OpenMS 2.5.0

### - 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
- 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 , 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
- 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
- addLossFormula() : Residue
- addLossName() : Residue
- addMappingRule() : CVMappings
- addMaps() : KDTreeFeatureMaps
- addMASCOTFeatures() : PercolatorFeatureSetHelper
- addMassTrace() : FeatureHypothesis
- addMatches_() : ModificationDefinitionsSet
- addMaxInclusionListSizeConstraints_() : PSLPFormulation
- addMetaInfoToOptionalColumns() : MzTab
- 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
- 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_() : 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
- 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
- align_() : UTILProteomicsLFQ
- alignAndLink_() : UTILProteomicsLFQ
- 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() : ConsensusMap
- applyFunctionOnPeptideHits_() : ConsensusMap
- applyFunctionOnPeptideIDs() : ConsensusMap
- applyFunctionOnPeptideIDs_() : ConsensusMap
- 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