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

- e -

• e_ : MapAlignmentAlgorithmSpectrumAlignment
• E_ : ProtonDistributionModel
• E_c_term_ : ProtonDistributionModel
• E_n_term_ : ProtonDistributionModel
• E_wrt_h() : EmgGradientDescent
• E_wrt_mu() : EmgGradientDescent
• E_wrt_sigma() : EmgGradientDescent
• E_wrt_tau() : EmgGradientDescent
• ECD : Precursor
• edge : TOPPASVertex::VertexRoundPackage
• edge_ : TOPPASIOMappingDialog
• edge_being_created_ : TOPPASVertex
• EdgeContainer : TOPPASScene , TOPPASVertex
• EdgeIterator : TOPPASScene , TOPPASVertex
• edges_ : TOPPASScene
• edgesBegin() : TOPPASScene
• edgesEnd() : TOPPASScene
• EdgeStatus : TOPPASEdge
• edit() : ParamTree
• editable_ : BaseVisualizerGUI , MetaDataBrowser
• editCurrentItem() : TOPPASInputFilesDialog
• editMetadata() : TOPPViewBase
• editor_ : INIFileEditorWindow , ToolsDialog , TOPPASToolConfigDialog
• editParam() : TOPPASToolVertex
• editText() : Annotation1DItem
• EDTA : FileTypes
• EDTAFile() : EDTAFile
• ef_ : AdductInfo
• efficient_replace_and_optimise() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• egh_tau_location_ : RTSimulation
• egh_tau_scale_ : RTSimulation
• egh_variance_location_ : RTSimulation
• egh_variance_scale_ : RTSimulation
• EGHFitter1D() : EGHFitter1D
• EGHFitterFunctor() : EGHFitter1D::EGHFitterFunctor
• EGHModel() : EGHModel
• EGHTraceFitter() : EGHTraceFitter
• EGHTraceFunctor() : EGHTraceFitter::EGHTraceFunctor
• EgmFitterFunctor() : EmgFitter1D::EgmFitterFunctor
• EI : IonSource
• EIGHTPLEX : ItraqConstants
• EINZEL_LENS : Instrument
• ELECTROMAGNETIC_RADIATION_CHROMATOGRAM : ChromatogramSettings
• ELECTRON_MASS_IN_U : IMSElement
• ELECTRONMULTIPLIER : IonDetector
• ELECTRONMULTIPLIERTUBE : IonDetector
• ELECTROSPRAYINLET : IonSource
• Element() : Element
• element_1_ : FuzzyStringComparator
• element_2_ : FuzzyStringComparator
• element_path_ : CVMappingRule
• element_type : IMSAlphabet
• ElementDB() : ElementDB
• ElementMapping : QTClusterFinder
• ElementNotFound() : ElementNotFound
• elements_ : IMSAlphabet , IMSAlphabetTextParser
• eluents_ : Gradient , GradientVisualizer
• elution_model_ : FeatureFinderIdentificationAlgorithm
• elution_model_fit_score : OpenSwath_Scores
• elution_peak : ProcessData
• elution_peak_list : LCMSCData
• elution_peak_list_ITERATOR : LCMSCData
• elutionModelFit() : EmgScoring
• ElutionModelFitter() : ElutionModelFitter
• ElutionPeakDetection() : ElutionPeakDetection
• elutionPeakExtraInfo : LCElutionPeak
• email : MzTabContactMetaData
• email_ : ContactPerson , ContactPersonVisualizer
• EMC : InstrumentSettings
• emg_ : PeakIntegrator
• emg_gd_ : EmgGradientDescent_friend
• emg_gradient_descent() : EmgGradientDescent
• emg_point() : EmgGradientDescent , EmgGradientDescent_friend
• emg_vector() : EmgGradientDescent , EmgGradientDescent_friend
• EmgFitter1D() : EmgFitter1D
• EmgGradientDescent() : EmgGradientDescent
• EmgGradientDescent_friend : EmgGradientDescent , EmgGradientDescent_friend
• EmgModel() : EmgModel
• EMGPreProcess_() : PeakIntegrator
• EmgScoring() : EmgScoring
• emgscoring_ : MRMFeatureFinderScoring
• EMISSION : InstrumentSettings
• EMISSION_CHROMATOGRAM : ChromatogramSettings
• emitChanged() : TOPPASEdge
• emitToolStarted() : TOPPASToolVertex
• empirical_formula_ : AccurateMassSearchResult
• EmpiricalFormula() : EmpiricalFormula
• empty() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , AASequence , CalibrationData , ConsensusFeature , ConstRefVector< ContainerT > , CVTermList , CVTermListInterface
• EMPTY : DataValue
• empty() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector > , File , HashGrid< Cluster > , IMSIsotopeDistribution , DIntervalBase< D > , BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value > , MetaInfo , MSExperiment , OnDiscMSExperiment , Param , PeptideIdentification , SpectrumLookup
• EMPTY : String , VersionInfo::VersionDetails
• empty_channels : IsobaricQuantifierStatistics
• empty_list_ : TOPPASResources
• empty_rows_ : MzTab
• EMPTY_VALUE : DataValue
• EmptySparseVector : BinnedSpectrum
• EMR : InstrumentSettings
• EMULSION : Sample
• enable_() : ToolsDialog
• enable_binarization : LPWrapper::SolverParam
• enable_clq_cuts : LPWrapper::SolverParam
• enable_cov_cuts : LPWrapper::SolverParam
• enable_feas_pump_heuristic : LPWrapper::SolverParam
• enable_gmi_cuts : LPWrapper::SolverParam
• enable_intensity_filter_ : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• enable_mir_cuts : LPWrapper::SolverParam
• enable_presolve : LPWrapper::SolverParam
• enable_RT_filtering_ : FeatureFindingMetabo
• enable_uis_scoring_ : OpenSwathOSWWriter , OpenSwathTSVWriter
• enabled_trans_ : HiddenMarkovModel
• enableFeatureNumber() : Spectrum2DGoToDialog
• enableLogging_() : TOPPBase
• enableTransition() : HiddenMarkovModel
• enableTransition_() : HiddenMarkovModel
• encloses() : _Region< __K, _Val, _SubVal, _Acc, _Cmp > , ConvexHull2D , DBoundingBox< D > , DRange< D > , Feature
• encode() : Base64
• encodeCompositionVector() : LibSVMEncoder
• encodeCompositionVectors() : LibSVMEncoder
• encodeIntegers() : Base64
• encodeLibSVMProblem() : LibSVMEncoder
• encodeLibSVMProblemWithCompositionAndLengthVectors() : LibSVMEncoder
• encodeLibSVMProblemWithCompositionLengthAndWeightVectors() : LibSVMEncoder
• encodeLibSVMProblemWithCompositionVectors() : LibSVMEncoder
• encodeLibSVMProblemWithOligoBorderVectors() : LibSVMEncoder
• encodeLibSVMVector() : LibSVMEncoder
• encodeLibSVMVectors() : LibSVMEncoder
• encodeNP() : MSNumpressCoder
• encodeNPRaw() : MSNumpressCoder
• encodeOligo() : LibSVMEncoder
• encodeOligoBorders() : LibSVMEncoder
• encodeProblemWithOligoBorderVectors() : LibSVMEncoder
• encoder_ : Base64
• encodeStrings() : Base64
• end() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , AASequence , CalibrationData , ConsensusFeature , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType > , EmpiricalFormula , FeatureFinderIdentificationAlgorithm::RTRegion , HashGrid< Cluster > , IsotopeDistribution , IsotopeWaveletTransform< PeakType >::TransSpectrum , MassTrace , Histogram< ValueType, BinSizeType > , MSExperiment , MzTabPSMSectionRow , Param , ScanWindow , TextFile , XCorrArrayType
• end_ : GUIProgressLoggerImpl , PeptideEvidence , ScanWindowVisualizer
• end_boxes_ : IsotopeWaveletTransform< PeakType >
• end_left_padding_ : ContinuousWaveletTransform
• end_peak_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
• end_point_ : Annotation1DDistanceItem
• end_position_at_10 : PeakIntegrator::PeakShapeMetrics
• end_position_at_5 : PeakIntegrator::PeakShapeMetrics
• end_position_at_50 : PeakIntegrator::PeakShapeMetrics
• end_scan_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
• endElement() : ConsensusXMLFile , CVMappingFile , FeatureXMLFile , IdXMLFile , MascotXMLHandler , MzDataHandler , MzIdentMLHandler , MzMLHandler , MzQuantMLHandler , MzXMLHandler , ParamXMLHandler , PTMXMLHandler , SemanticValidator , ToolDescriptionHandler , TraMLHandler , UnimodXMLHandler , XMLHandler , XQuestResultXMLHandler , OMSSAXMLFile , PepXMLFile , PepXMLFileMascot , ProtXMLFile , QcMLFile , XTandemXMLFile
• endEnzyme() : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• endians_ : MzDataHandler
• EndParsingSoftly() : XMLHandler::EndParsingSoftly
• endPos() : TOPPASEdge
• endProgress() : GUIProgressLoggerImpl , ProgressLogger , ProgressLogger::ProgressLoggerImpl
• endResidue() : ResidueDB
• endRun_() : MascotRemoteQuery
• endScan : MS2ConsensusSpectrum
• endTR : MS2ConsensusSpectrum
• enforced_encoding_ : XMLFile
• enforceEncoding_() : XMLFile
• engine_ : ProteinIdentificationVisualizer
• engine_version_ : ProteinIdentificationVisualizer
• EnhancedTabBar() : EnhancedTabBar
• EnhancedWorkspace() : EnhancedWorkspace
• enhancedWorkspaceWindowChanged() : TOPPViewBase
• enlarge() : DBoundingBox< D >
• enqueueProcess() : TOPPASScene
• ensureAnnotationsWithinDataRange_() : Spectrum1DCanvas
• ensureConvexHulls_() : FeatureFinderIdentificationAlgorithm
• ensureLastChar() : String , StringUtils
• ensureMapsAreFilled_() : CachedSwathFileConsumer , FullSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• ensureUniqueId() : UniqueIdInterface
• ensureWithinDataRange() : Annotation1DCaret , Annotation1DDistanceItem , Annotation1DItem , Annotation1DPeakItem , Annotation1DTextItem
• enterEvent() : SpectrumCanvas , TOPPASTreeView , TOPPASWidget
• entirePipelineFinished() : TOPPASScene
• entries : Param::ParamNode
• entries_ : MzTabDoubleList , MzTabIntegerList , MzTabModificationList , MzTabStringList
• entries_read_ : FASTAFile
• entry : SimProtein
• EntryIterator : Param::ParamNode
• enumerateCrossLinksAndMasses() : OPXLHelper
• enumToName() : MZTrafoModel
• EnzymaticDigestion() : EnzymaticDigestion
• EnzymaticDigestionLogModel() : EnzymaticDigestionLogModel
• enzyme : MzIdentMLDOMHandler::SpectrumIdentificationProtocol
• enzyme_ : Digestion , EnzymaticDigestion , EnzymaticDigestionLogModel , InspectInfile , PeptideIndexing::FoundProteinFunctor , PepXMLFile , ProteinIdentificationVisualizer
• enzyme_info_ : SequestInfile
• enzyme_name_ : PeptideIndexing
• enzyme_names_ : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• enzyme_number_ : SequestInfile
• enzyme_regex_ : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• enzyme_specificity_ : PeptideIndexing
• EnzymeIterator : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• enzymes : XQuestResultXMLHandler
• enzymes_db_ : XQuestResultXMLHandler
• eol_ : CSVWriter
• EPSILON_COEFS_ : EGHTraceFitter
• EQUAL : DataFilters
• equal_() : XMLHandler
• EqualInTolerance() : EqualInTolerance< CompareType >
• equals() : Map< Key, T >
• erase() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConstRefVector< ContainerT > , HashGrid< Cluster > , IMSAlphabet
• erase_exact() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• erase_match_list() : SHFeature
• erase_MZ_cluster_element() : ProcessData
• erase_MZ_LIST_element() : ProcessData
• eraseMinDistance_() : GridBasedClustering< Metric >
• err : MorpheusScore::Result , RNPxlSearch::AnnotatedHit
• error() : XMLHandler , XMLValidator
• error_ : NetworkGetRequest
• error_medians_ : TOFCalibration
• error_message_ : XMLHandler , MascotRemoteQuery
• error_name_ : DefaultParamHandler
• error_occured_ : TOPPASScene
• error_on_unmapped_ : MRMMapping
• error_streams_ : LogConfigHandler
• error_string_ : NetworkGetRequest
• errorIfAlreadyExists() : ExperimentalDesign
• errors_ : SemanticValidator , TOFCalibration
• errorString() : XMLHandler
• ErrorUnit : XTandemInfile
• ertable_ : IntegerMassDecomposer< ValueType, DecompositionValueType >
• ES_FILE_EXT_MISMATCH : TOPPASEdge
• ES_MERGER_EXT_MISMATCH : TOPPASEdge
• ES_MERGER_WITHOUT_TOOL : TOPPASEdge
• ES_NO_SOURCE_PARAM : TOPPASEdge
• ES_NO_TARGET_PARAM : TOPPASEdge
• ES_NOT_READY_YET : TOPPASEdge
• ES_TOOL_API_CHANGED : TOPPASEdge
• ES_UNKNOWN : TOPPASEdge
• ES_VALID : TOPPASEdge
• ESA : MassAnalyzer
• ESCAPE : String
• ESI : IonizationSimulation , IonSource
• esi_adducts_ : IonizationSimulation
• esi_impurity_probabilities_ : IonizationSimulation
• esi_probability_ : IonizationSimulation
• estimate_() : SignalToNoiseEstimator< Container >
• estimate_fixed_point : MSNumpressCoder::NumpressConfig
• estimateBackground() : PeakIntegrator
• estimateBackground_() : PeakIntegrator
• estimateForFragmentFromDNAWeight() : CoarseIsotopePatternGenerator
• estimateForFragmentFromPeptideWeight() : CoarseIsotopePatternGenerator
• estimateForFragmentFromPeptideWeightAndS() : CoarseIsotopePatternGenerator
• estimateForFragmentFromRNAWeight() : CoarseIsotopePatternGenerator
• estimateForFragmentFromWeightAndComp() : CoarseIsotopePatternGenerator
• estimateFromDNAWeight() : CoarseIsotopePatternGenerator
• estimateFromPeptideWeight() : CoarseIsotopePatternGenerator
• estimateFromPeptideWeightAndS() : CoarseIsotopePatternGenerator
• estimateFromRNAWeight() : CoarseIsotopePatternGenerator
• estimateFromWeightAndComp() : CoarseIsotopePatternGenerator , EmpiricalFormula
• estimateFromWeightAndCompAndS() : CoarseIsotopePatternGenerator , EmpiricalFormula
• estimateFWHM() : MassTrace
• estimateNoise() : SignalToNoiseEstimatorMedianRapid
• estimateNoiseFromRandomMS1Scans() : TOPPViewBase
• estimatePeakWidth() : PeakPickerCWT
• estimatePrecursorWeight_() : CompNovoIdentification , CompNovoIdentificationBase
• estimateRTRange() : OpenSwathHelper
• estimateType() : PeakTypeEstimator
• estimateUntrainedTransitions() : HiddenMarkovModel
• ETD : Precursor
• EuclideanSimilarity() : EuclideanSimilarity
• eval() : BSpline2d , CubicSpline2d , GaussFitter , GaussFitter::GaussFitResult , QuadraticRegression , SplinePackage , SplineSpectrum::Navigator , TransformationModelInterpolated::Interpolator
• evaluate() : HiddenMarkovModel , MapAlignmentEvaluationAlgorithm , MapAlignmentEvaluationAlgorithmPrecision , MapAlignmentEvaluationAlgorithmRecall , TransformationModel , TransformationModelBSpline , TransformationModelInterpolated , TransformationModelLinear , TransformationModelLowess
• evaluateEGH_() : EGHModel
• event() : QApplicationTOPP
• evidence : Peptide
• EX_BSPLINE : TransformationModelBSpline
• EX_CONSTANT : TransformationModelBSpline
• EX_GLOBAL_LINEAR : TransformationModelBSpline
• EX_LINEAR : TransformationModelBSpline
• exception : Summary
• exclude_targets_ : TargetedExperiment
• ExclusionListType_ : OfflinePrecursorIonSelection
• execQuery() : MascotRemoteQuery
• executeBlobBind_() : MzMLSqliteHandler
• executeSql_() : MzMLSqliteHandler
• EXECUTION_OK : PeptideIndexing , TOPPBase
• executionFinished() : TOPPASToolVertex
• exist() : IntegerMassDecomposer< ValueType, DecompositionValueType > , MassDecomposer< ValueType, DecompositionValueType >
• exists() : ControlledVocabulary
• EXISTS : DataFilters
• exists() : File , IDFilter::GetMatchingItems< HitType, Entry > , MetaInfo , MultiGradient , Param
• exists_() : ParamEditorDelegate
• existsRun() : QcMLFile
• existsRunQualityParameter() : QcMLFile
• existsSet() : QcMLFile
• existsSetQualityParameter() : QcMLFile
• ExitCodes : PeptideIndexing , TOPPBase
• exp_ : MzDataHandler , MzMLHandler , MzXMLHandler , TraMLHandler , MSDataStoringConsumer , PeakShape
• exp_centroid_ : FeatureFinderMultiplexAlgorithm
• exp_mass_to_charge : MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• exp_masses_ : TOFCalibration
• exp_name_ : PepXMLFile
• exp_picked_ : MultiplexFiltering
• exp_picked_mapping_ : MultiplexFiltering
• exp_picked_white_ : MultiplexFiltering
• exp_profile_ : FeatureFinderMultiplexAlgorithm
• exp_spline_profile_ : MultiplexFilteringProfile
• exp_table_ : IsotopeWavelet
• exp_table_max_index_ : IsotopeWavelet
• expandPrefix_() : LogStreamBuf
• expandToBoundingBox() : ConvexHull2D
• expected_size_ : FeatureXMLFile
• expectList_() : XMLHandler
• experiment_ : MSSim
• experiment_label_ : PepXMLFile
• experiment_type_ : ConsensusMap
• experimental : ProteinResolver::PeptideEntry
• experimental_mass_to_charge_ : IdentificationHit
• ExperimentalDesign() : ExperimentalDesign
• ExperimentalSettings() : ExperimentalSettings
• ExperimentalSettingsVisualizer() : ExperimentalSettingsVisualizer
• ExperimentSharedPtrType : LayerData , Spectrum2DWidget , SpectrumCanvas , TOPPViewBase , TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• ExperimentType : LayerData , SpectrumCanvas , SpectrumWidget , TOPPViewBase , TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• explained_TIC_fraction : SIPPeptide
• explainedintensity : SiriusMzTabWriter::SiriusAdapterHit
• explainedpeaks : SiriusMzTabWriter::SiriusAdapterHit
• explanations_ : MassExplainer
• exponent : FeatureDistance::DistanceParams_
• EXPONENTIAL : MassAnalyzer
• exportAsImage() : TOPPASBase
• exportAttachment() : QcMLFile
• exportEntries_() : SpectraIdentificationViewWidget
• exportIDstats() : QcMLFile
• exportMzTab_() : AccurateMassSearchEngine , MetaboliteSpectralMatching
• exportQP() : QcMLFile
• exportQPs() : QcMLFile
• extend() : DRange< D >
• extendBox_() : IsotopeWaveletTransform< PeakType >
• extendClustersY() : GridBasedClustering< Metric >
• ExtendedIsotopeFitter1D() : ExtendedIsotopeFitter1D
• ExtendedIsotopeModel() : ExtendedIsotopeModel
• extendMassTrace_() : FeatureFinderAlgorithmPicked
• extendMassTraces_() : FeatureFinderAlgorithmPicked
• external_details : ToolDescription
• EXTERNAL_PROGRAM_ERROR : TOPPBase
• extra_rt_extract : ChromExtractParams
• extract_elution_peaks() : ProcessData
• extract_id_() : ChromatogramExtractor
• extract_MS2_elution_features() : FTPeakDetectController
• extract_scan_index() : SiriusMzTabWriter
• extract_value_bartlett() : ChromatogramExtractor
• extract_value_tophat() : ChromatogramExtractor , ChromatogramExtractorAlgorithm
• extractAndTransformScores() : PosteriorErrorProbabilityModel
• extractChannels() : IsobaricChannelExtractor
• extractChromatograms() : ChromatogramExtractor , ChromatogramExtractorAlgorithm
• extractComponents_() : AbsoluteQuantitation
• extractCoverageStrings() : TOPPViewIdentificationViewBehavior
• extractDateTime_() : XQuestResultXMLHandler
• extractFragmentsFromSpectra() : ClusteredMS2ConsensusSpectrum
• extractIncorporationsAtCorrelationMaxima() : TOPPMetaProSIP
• extractIncorporationsAtHeighestDecompositionWeights() : TOPPMetaProSIP
• extractIndexPairsFromBrackets_() : MzTabFile
• extractIntensities_() : ConfidenceScoring
• extractIntensityVectors() : ConsensusMapNormalizerAlgorithmQuantile
• extraction_function : ChromExtractParams
• ExtractionCoordinates : ChromatogramExtractor
• extractIsotopicIntensities() : TOPPMetaProSIP
• extractLabelSet() : MultiplexDeltaMassesGenerator
• extractMarkerIons() : RNPxlMarkerIonExtractor
• extractNumberOfSubSamples_() : MzTabFile
• extractNumPeptides_() : MzTabFile
• extractNumPeptidesDistinct_() : MzTabFile
• extractNumPeptidesUnambiguous_() : MzTabFile
• extractParamsFromLine_() : MRMFeaturePickerFile
• extractPeaks() : FeatureFinderAlgorithmSHCtrl
• extractPeakSpectrum() : TOPPMetaProSIP
• extractPeptideModifications_() : MzTabFile
• extractPeptideSequences() : IDFilter
• extractProteinAccession_() : MzTabFile
• extractProteinAccessionsSet() : PeptideHit
• extractRunFromLine_() : AbsoluteQuantitationStandardsFile
• extractScanNumber() : SpectrumLookup
• extractSpectra() : TargetedSpectraExtractor
• extractTrainingSet() : EmgGradientDescent , EmgGradientDescent_friend
• extractXICs() : MetaProSIPXICExtraction
• extractXICsOfIsotopeTraces() : MetaProSIPXICExtraction
• extraMSPeakInfo : MSPeak
• extraPeakInfo_ : CentroidPeak
• extrapolate_ : TransformationModelBSpline