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• IBSpectraFile() : IBSpectraFile
• ICPLLabeler() : ICPLLabeler
• IDBoostGraph() : IDBoostGraph
• IDDecoyProbability() : IDDecoyProbability
• Identification() : Identification
• IdentificationData() : IdentificationData
• IdentificationHit() : IdentificationHit
• IdentifiedCompound() : IdentifiedCompound
• IdentifiedSequence() : IdentifiedSequence< SeqType >
• identifyCharge() : IsotopeWaveletTransform< PeakType >
• IDFilter() : IDFilter
• IDMapper() : IDMapper
• IDMergerAlgorithm() : IDMergerAlgorithm
• IDRipper() : IDRipper
• IDScoresAsMetaValue() : MRMFeature
• IdXMLFile() : IdXMLFile
• IEWindow() : InclusionExclusionList::IEWindow
• IllegalArgument() : IllegalArgument
• IllegalKey() : Map< Key, T >::IllegalKey
• IllegalPosition() : IllegalPosition
• IllegalSelfOperation() : IllegalSelfOperation
• IllegalTreeOperation() : IllegalTreeOperation
• ILPDCWrapper() : ILPDCWrapper
• importDBSearchParameters_() : IdentificationDataConverter
• importExperimentalSettings() : XMassFile
• importIDs() : IdentificationDataConverter
• importSequences() : IdentificationDataConverter
• IMSAlphabet() : IMSAlphabet
• IMSElement() : IMSElement
• IMSIsotopeDistribution() : IMSIsotopeDistribution
• inc() : Histogram< ValueType, BinSizeType >
• incFrom() : Histogram< ValueType, BinSizeType >
• include() : TOPPASScene
• IncludeExcludeTarget() : IncludeExcludeTarget
• includeMSMSPeptides_() : ProteinResolver
• includePipeline() : TOPPASBase
• InclusionExclusionList() : InclusionExclusionList
• incomingEdgesCount() : TOPPASVertex
• IncompatibleIterators() : IncompatibleIterators
• increase_LC_elution_peak_counter() : ProcessData
• increaseBoundingBox_() : IDMapper
• incUntil() : Histogram< ValueType, BinSizeType >
• index() : HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator , Matrix< Value >
• index2key() : LinearInterpolation< Key, Value >
• index2key_0() : BilinearInterpolation< Key, Value >
• index2key_1() : BilinearInterpolation< Key, Value >
• IndexedMzMLFileLoader() : IndexedMzMLFileLoader
• IndexedMzMLHandler() : IndexedMzMLHandler
• IndexOverflow() : IndexOverflow
• indexPair() : Matrix< Value >
• IndexUnderflow() : IndexUnderflow
• inEdgeHasChanged() : TOPPASOutputFileListVertex , TOPPASToolVertex , TOPPASVertex
• inEdgesBegin() : TOPPASVertex
• inEdgesEnd() : TOPPASVertex
• infer() : ProteinInference
• infer_() : ProteinInference
• inferFromPeptides() : ModificationDefinitionsSet
• inferMoreEdges_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• inferPosteriorProbabilities() : BayesianProteinInferenceAlgorithm
• inferPosteriorProbabilities_() : BayesianProteinInferenceAlgorithm
• INIFileEditorWindow() : INIFileEditorWindow
• InIntensityRange() : InIntensityRange< PeakType >
• init() : AccurateMassSearchEngine , BackgroundControl , ContinuousWaveletTransform , ContinuousWaveletTransformNumIntegration , IsotopeWavelet , IsotopicDist , SignalToNoiseEstimator< Container > , TargetedSpectraExtractor::BinnedSpectrumComparator , TargetedSpectraExtractor::Comparator , TransformationModelInterpolated::Interpolator , Pattern< TNeedle, FuzzyAC >
• init_() : CubicSpline2d , GridBasedClustering< Metric > , MzDataHandler , MzXMLHandler , MassExplainer , NLargest , SplineInterpolatedPeaks , UniqueIdGenerator
• initBins_() : Histogram< ValueType, BinSizeType >
• initChannelMap() : ItraqConstants
• initDataStructures_() : XFDRAlgorithm
• initGridSearchFromParams_() : BayesianProteinInferenceAlgorithm
• initialize() : ConfidenceScoring , GaussFilterAlgorithm , OpenSwathScoring , SimRandomNumberGenerator
• initializeCluster() : QTCluster
• initializeDefaultParameters_() : TOPPViewBase
• initializeGL() : Spectrum3DOpenGLCanvas
• initializeGlm() : ConfidenceScoring
• initializeLookup() : MascotXMLFile
• initializeMap_() : FileTypes
• initializeMaps_() : SvmTheoreticalSpectrumGenerator
• initializeMIContrastMatrix() : MRMScoring
• initializeMIMatrix() : MRMScoring
• initializeMIPrecursorCombinedMatrix() : MRMScoring
• initializeMIPrecursorContrastMatrix() : MRMScoring
• initializeMIPrecursorMatrix() : MRMScoring
• initializeModificationsDB() : ModificationsDB
• initializeMZMLMap_() : FileTypes
• initializeScan() : IsotopeWaveletTransform< PeakType >
• initializeWT_() : PeakPickerCWT
• initializeXCorrContrastMatrix() : MRMScoring
• initializeXCorrMatrix() : MRMScoring
• initializeXCorrPrecursorCombinedMatrix() : MRMScoring
• initializeXCorrPrecursorContrastMatrix() : MRMScoring
• initializeXCorrPrecursorMatrix() : MRMScoring
• initIsotopeDistributions_() : CompNovoIdentificationBase , CompNovoIonScoringBase
• initModificationMassesRNA() : RNPxlModificationsGenerator
• initParam_() : RawTandemMSSignalSimulation , TOPPASToolVertex
• initParameters_() : SVMWrapper
• initParams() : FeatureFinderAlgorithmSHCtrl
• initPattern() : AhoCorasickAmbiguous
• initPlots() : PosteriorErrorProbabilityModel
• initvec() : Chromatogram , Spectrum , OSChromatogram , OSSpectrum
• INIUpdater() : INIUpdater
• InMSLevelRange() : InMSLevelRange< SpectrumType >
• InMzRange() : InMzRange< PeakType >
• InPrecursorMZRange() : InPrecursorMZRange< SpectrumType >
• inputFileReadable_() : TOPPBase
• InputLine() : FuzzyStringComparator::InputLine
• inputs() : LevMarqFitter1D::GenericFunctor , GumbelMaxLikelihoodFitter::Functor< _Scalar, NX, NY > , OptimizePick::OptPeakFunctor , TraceFitter::GenericFunctor , TwoDOptimization::TwoDOptFunctor
• InRTRange() : InRTRange< SpectrumType >
• insert() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , HashGrid< Cluster > , IsotopeDistribution , LogStream , MultiGradient , Param , Param::ParamNode
• insert_MZ_cluster_element() : ProcessData
• insert_new_observed_mz() : ProcessData
• insert_observed_mz() : ProcessData
• insertCalibrationPoint() : CalibrationData
• insertHit() : PeptideIdentification , ProteinIdentification
• insertIndistinguishableProteins() : ProteinIdentification
• insertIntoMultiIndex_() : IdentificationData
• insertmarker() : MarkerMower
• insertNewVertex_() : TOPPASBase
• insertNewVertexInCenter_() : TOPPASBase
• insertNotification() : LogStream
• insertPair() : ROCCurve
• insertProteinGroup() : ProteinIdentification
• insertProteinIDs_() : IDMergerAlgorithm
• insertRuns() : IDMergerAlgorithm
• insideBand_() : MapAlignmentAlgorithmSpectrumAlignment
• InspectInfile() : InspectInfile
• InspectOutfile() : InspectOutfile
• instance() : SuperHirnParameters
• instance_() : Factory< FactoryProduct > , SingletonRegistry
• Instrument() : Instrument
• InstrumentSettings() : InstrumentSettings
• InstrumentSettingsVisualizer() : InstrumentSettingsVisualizer
• InstrumentVisualizer() : InstrumentVisualizer
• InsufficientInput() : ClusterFunctor::InsufficientInput
• IntegerMassDecomposer() : IntegerMassDecomposer< ValueType, DecompositionValueType >
• integrate_() : ContinuousWaveletTransformNumIntegration , GaussFilterAlgorithm
• integratePeak() : PeakIntegrator
• integratePeak_() : PeakIntegrator
• integratePeaks_() : PeakPickerMRM
• intensity() : KDTreeFeatureMaps
• IntensityBalanceFilter() : IntensityBalanceFilter
• intensityFilterPassed_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• IntensityIteratorWrapper() : IntensityIteratorWrapper< IteratorT >
• intensityLess_() : MetaboTargetedAssay
• intensityModeChange_() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas , SpectrumWidget
• intensityScore_() : FeatureFinderAlgorithmPicked
• InternalCalibration() : InternalCalibration
• interpolatedColorAt() : MultiGradient
• InterpolationModel() : InterpolationModel
• Interpretation() : Interpretation
• interpretRetentionTime_() : TransitionTSVFile
• intersection_() : FeatureFinderAlgorithmPicked
• intersects() : DBoundingBox< D > , DRange< D >
• intersects_with() : _Region< __K, _Val, _SubVal, _Acc, _Cmp >
• invalidate_() : HistogramWidget
• InvalidIterator() : InvalidIterator
• InvalidParameter() : InvalidParameter
• InvalidRange() : InvalidRange
• InvalidSize() : InvalidSize
• InvalidValue() : InvalidValue
• invert() : TransformationDescription , TransformationModelLinear
• invertRecylingMode() : TOPPASToolVertex , TOPPASVertex
• IOException() : IOException
• IOInfo() : TOPPASToolVertex::IOInfo
• IonDetector() : IonDetector
• IonDetectorVisualizer() : IonDetectorVisualizer
• IonizationSimulation() : IonizationSimulation
• ionize() : IonizationSimulation
• ionizeEsi_() : IonizationSimulation
• ionizeMaldi_() : IonizationSimulation
• IonMobilityScoring() : IonMobilityScoring
• IonScore() : CompNovoIonScoringBase::IonScore , DeNovoIonScoring::IonScore
• IonSource() : IonSource
• IonSourceVisualizer() : IonSourceVisualizer
• IonType() : SvmTheoreticalSpectrumGenerator::IonType
• iRpropPlus() : EmgGradientDescent , EmgGradientDescent_friend
• isActive() : ChargePair , DataFilters , OpenSwathOSWWriter , OpenSwathTSVWriter
• isAmbiguous() : Ribonucleotide
• isAnyList() : TOPPASToolVertex::IOInfo
• isBetterScore() : IdentificationData
• isCharged() : EmpiricalFormula
• isChildOf() : ControlledVocabulary
• isCleavageSite_() : EnzymaticDigestionLogModel
• isCompatible() : AdductInfo , BinnedSpectrum , ModificationDefinitionsSet
• isConflicting() : Compomer
• isConsensusFeatureVisible_() : Spectrum2DCanvas
• isContained() : BaseModel< D >
• isCutoffEnabled() : TOPPViewOpenDialog
• isDataDIA() : TOPPViewOpenDialog
• isDetectingTransition() : ReactionMonitoringTransition , LightTransition
• isDIAData() : LayerData
• isDirectory() : File
• isDrawInterestingMZs() : Spectrum1DCanvas
• isDryRun() : TOPPASScene
• isEdgeAllowed_() : TOPPASScene
• isEditable() : BaseVisualizerGUI , MetaDataBrowser
• isEmpty() : DataValue , DBoundingBox< D > , DRange< D > , EmpiricalFormula
• IsEmptySpectrum() : IsEmptySpectrum< SpectrumType >
• isEnd_() : MatchedIterator< CONT_T, TRAIT, CONST_T >
• isExperimentCached() : SimpleOpenMSSpectraFactory
• isFeatureValid_() : IonizationSimulation
• isFinished() : TOPPASVertex
• isFixedModification() : ModificationDefinition
• isFractionated() : ExperimentalDesign
• isGUIMode() : TOPPASScene
• isHidden() : HMMState
• isHigherBetterScore() : ControlledVocabulary::CVTerm
• isHigherScoreBetter() : PeptideIdentification , ProteinIdentification
• isIdentifyingTransition() : ReactionMonitoringTransition , LightTransition
• isInCache_() : LogStreamBuf
• IsInCollisionEnergyRange() : IsInCollisionEnergyRange< SpectrumType >
• isInf() : MzTabNullNaNAndInfAbleBase , MzTabNullNaNAndInfAbleInterface
• IsInIsolationWindow() : IsInIsolationWindow< SpectrumType >
• IsInIsolationWindowSizeRange() : IsInIsolationWindowSizeRange< SpectrumType >
• isInitIsotopeDist() : SuperHirnParameters
• isInPackage() : SplinePackage
• isInResidueSet() : Residue
• isInstantiated() : ModificationsDB
• isInSwath_() : MRMAssay
• isInternallyConsistent() : MRMTransitionGroup< ChromatogramType, TransitionType >
• isIntersected() : DRange< D >
• isInvalid() : QTCluster
• isIonLadderVisible() : Spectrum1DCanvas
• isIonMobilityData() : LayerData
• isLegalIsotopePattern_() : FeatureFindingMetabo
• isLegendShown() : AxisWidget , Spectrum3DCanvas , Spectrum3DWidget , SpectrumWidget
• isLogScale() : AxisWidget
• isMapConsistent() : ConsensusMap
• isMappingConsistent_() : MRMTransitionGroup< ChromatogramType, TransitionType >
• isMatch_() : IDMapper
• isMetaEmpty() : MetaInfoInterface
• isModified() : AASequence , ParamEditor , Residue , Ribonucleotide
• isMzToXAxis() : SpectrumCanvas
• isNaN() : MzTabNullNaNAndInfAbleBase , MzTabNullNaNAndInfAbleInterface
• isNonEmptyCell() : ClusteringGrid
• isNull() : MzTabDoubleList , MzTabIntegerList , MzTabModification , MzTabModificationList , MzTabNullAbleBase , MzTabNullAbleInterface , MzTabNullNaNAndInfAbleBase , MzTabParameter , MzTabParameterList , MzTabSpectraRef , MzTabString , MzTabStringList
• IsobaricChannelExtractor() : IsobaricChannelExtractor
• IsobaricChannelInformation() : IsobaricQuantitationMethod::IsobaricChannelInformation
• IsobaricNormalizer() : IsobaricNormalizer
• IsobaricQuantifier() : IsobaricQuantifier
• IsobaricQuantifierStatistics() : IsobaricQuantifierStatistics
• IsobaricQuantitationMethod() : IsobaricQuantitationMethod
• isOneTableFile_() : ExperimentalDesignFile
• isoPeakMeans() : OPXLHelper
• isOpen() : Bzip2Ifstream , GzipIfstream
• isOpenMSDataPath_() : File
• IsoSpecOrderedGeneratorWrapper() : IsoSpecOrderedGeneratorWrapper
• IsoSpecThresholdGeneratorWrapper() : IsoSpecThresholdGeneratorWrapper
• IsoSpecThresholdWrapper() : IsoSpecThresholdWrapper
• IsoSpecTotalProbGeneratorWrapper() : IsoSpecTotalProbGeneratorWrapper
• IsoSpecTotalProbWrapper() : IsoSpecTotalProbWrapper
• IsotopeCluster() : IsotopeCluster
• IsotopeDiffFilter() : IsotopeDiffFilter
• IsotopeDistribution() : IsotopeDistribution
• IsotopeDistributionCache() : IsotopeDistributionCache
• IsotopeFitter1D() : IsotopeFitter1D
• IsotopeMarker() : IsotopeMarker
• IsotopeModel() : IsotopeModel
• IsotopePattern() : FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern
• IsotopePatternGenerator() : IsotopePatternGenerator
• isotopeScore_() : FeatureFinderAlgorithmPicked
• IsotopeWavelet() : IsotopeWavelet
• IsotopeWaveletTransform() : IsotopeWaveletTransform< PeakType >
• isPeptide() : TransitionTSVFile::TSVTransition , LightCompound
• isPipelineRunning() : TOPPASScene
• isPPM() : SpectrumAlignmentDialog
• isPrefix() : PeptideIndexing
• isProductChargeStateSet() : ReactionMonitoringTransition , LightTransition
• isProteinInMinimalList() : PSProteinInference
• isQuantifyable_() : MSstatsFile
• isQuantifyingTransition() : ReactionMonitoringTransition , LightTransition
• isReachable() : TOPPASVertex
• isRecyclingEnabled() : TOPPASVertex
• isRegistered() : Factory< FactoryProduct > , SingletonRegistry
• isRTColumnOn() : RTSimulation
• isRTset() : RetentionTime
• isRunning() : StopWatch
• isSameHandle() : MapAlignmentEvaluationAlgorithm
• isSameProtein_() : XFDRAlgorithm
• isSelected() : Annotation1DItem
• isSemanticallyValid() : MzDataFile , MzIdentMLFile , MzMLFile , MzQuantMLFile , TraMLFile
• isSingleAdduct() : Compomer
• isSorted() : MSChromatogram , MSExperiment , MSSpectrum
• isSortedByRT() : OnDiscMSExperiment
• isSubsampledSpectrum_() : SwathQC
• isSuperSetOf() : QCBase::Status
• isSupported() : FileHandler
• isToolReady() : TOPPASToolVertex
• isTopoSortMarked() : TOPPASVertex
• isTrained() : MZTrafoModel
• isUpstreamFinished() : TOPPASVertex
• isUserDefined() : ResidueModification
• isValid() : ClusterProxyKD , FeatureFinderAlgorithmPickedHelperStructs::MassTrace , FeatureFinderAlgorithmPickedHelperStructs::MassTraces , Gradient , XMLFile , MzMLFile , Param::ParamEntry , PeakIndex , UniqueIdInterface , XMLValidator
• isValid_() : ExperimentalDesign
• isValidHashedReference_() : IdentificationData
• isValidModel() : MZTrafoModel
• isValidPrecursor_() : IsobaricChannelExtractor
• isValidProduct() : EnzymaticDigestion , ProteaseDigestion
• isValidProduct_() : EnzymaticDigestion
• isValidReference_() : IdentificationData
• IsZoomSpectrum() : IsZoomSpectrum< SpectrumType >
• itemChanged() : TheoreticalSpectrumGenerationDialog
• itemClicked() : TOPPASScene
• itemDragged() : TOPPASVertex
• itemReleased() : TOPPASScene
• iterateFeatureMap() : QCBase
• Iterator() : AASequence::Iterator , HashGrid< Cluster >::Iterator , NASequence::Iterator
• iteratorsSet() : PeakShape
• IteratorWrapper() : IteratorWrapper< Iterator >
• ItraqEightPlexQuantitationMethod() : ItraqEightPlexQuantitationMethod
• ItraqFourPlexQuantitationMethod() : ItraqFourPlexQuantitationMethod
• ITRAQLabeler() : ITRAQLabeler