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

- i -

• i : Base64::Reinterpreter32_ , Base64::Reinterpreter64_ , IsotopeWavelet::fi_
• I_LABELS : LayerData
• I_PEPTIDEMZ : LayerData
• IBSpectraFile() : IBSpectraFile
• ICP : IonSource
• ICPLLabeler() : ICPLLabeler
• id : ChromatogramExtractorAlgorithm::ExtractionCoordinates , ControlledVocabulary::CVTerm , ChromatogramMeta , SpectrumMeta , IsobaricQuantitationMethod::IsobaricChannelInformation , ItraqConstants::ChannelInfo
• ID : MS2Feature , MS2Info
• id : QcMLFile::Attachment , QcMLFile::QualityParameter , Contact , CV , Instrument , PeptideCompound , Protein , Publication , LightCompound , LightProtein , OSChromatogramMeta , OSSpectrumMeta , Peptide , Protein
• id_ : Compomer , DocumentIdentifier , Identification , IdentificationHit , IDMergerAlgorithm , IdXMLFile , MzIdentMLHandler , PeptideIdentification , ProteinIdentification , ResidueModification , SpectrumIdentification
• id_count : PeptideAndProteinQuant::PeptideData , PeptideAndProteinQuant::ProteinData
• id_data_ : MascotXMLHandler
• id_format : MzTabMSRunMetaData
• id_identifier_ : ConsensusXMLFile , FeatureXMLFile
• IDBoostGraph() : IDBoostGraph
• IDDecoyProbability() : IDDecoyProbability
• idec : MzIdentMLDOMHandler::PeptideEvidence
• Identification() : Identification
• identification_ : SpectrumSettings
• identification_date_ : ProteinIdentificationVisualizer
• IDENTIFICATION_MAPPING : DataProcessing
• identification_rate : Ms2IdentificationRate::IdentificationRateData
• identification_threshold_ : PeptideIdentificationVisualizer , ProteinIdentificationVisualizer
• IdentificationData() : IdentificationData
• IdentificationHit() : IdentificationHit
• identifications : CsiFingerIdMzTabWriter::CsiAdapterRun , SiriusMzTabWriter::SiriusAdapterRun
• identificationview_behavior_ : TOPPViewBase
• identified : IDMapper::SpectraIdentificationState
• identified_compound_lookup_ : IdentificationData
• identified_compounds_ : IdentificationData
• identified_molecule_ref : MoleculeQueryMatch
• identified_oligo_lookup_ : IdentificationData
• identified_oligos_ : IdentificationData
• identified_peptide_lookup_ : IdentificationData
• identified_peptides_ : IdentificationData
• IdentifiedCompound : IdentificationData , IdentifiedCompound
• IdentifiedCompoundRef : IdentificationData
• IdentifiedCompounds : IdentificationData
• IdentifiedMoleculeRef : IdentificationData
• IdentifiedOligo : IdentificationData
• IdentifiedOligoRef : IdentificationData
• IdentifiedOligos : IdentificationData
• IdentifiedPeptide : IdentificationData
• IdentifiedPeptideRef : IdentificationData
• IdentifiedPeptides : IdentificationData
• IdentifiedSequence() : IdentifiedSequence< SeqType >
• identifier : FASTAFile::FASTAEntry , IdentifiedCompound , MzTabSmallMoleculeSectionRow , ProteinResolver::ResolverResult
• identifier_ : Acquisition , CVMappingRule , CVReference , DocumentIdentifierVisualizer , MascotXMLHandler , PeptideIdentificationVisualizer , ProteinIdentificationVisualizer
• identifier_id_ : ConsensusXMLFile , FeatureXMLFile
• identifyCharge() : IsotopeWaveletTransform< PeakType >
• identifying_transition : TransitionTSVFile::TSVTransition , LightTransition
• IDFilter : IdentificationData , IDFilter
• IDINITIALUNTITLED : TOPPASBase
• IDMapper() : IDMapper
• IDMergerAlgorithm() : IDMergerAlgorithm
• IDPointer : IDBoostGraph
• IDPointerConst : IDBoostGraph
• IDRipper() : IDRipper
• ids : FeatureFinderIdentificationAlgorithm::RTRegion
• ids_ : SpectrumLookup
• IDScoresAsMetaValue() : MRMFeature
• idsToRemove : MS1FeatureMerger
• idx_ : KDTreeFeatureNode
• IDX_ABUNDANCE : PeakPickerMRM
• IDX_FWHM : PeakPickerMRM
• IDX_LEFTBORDER : PeakPickerMRM
• IDX_RIGHTBORDER : PeakPickerMRM
• IDXML : FileTypes
• IdXMLFile() : IdXMLFile
• IEWindow() : InclusionExclusionList::IEWindow
• ifs_ : CachedmzML
• ignore_adduct_ : FeatureDistance
• ignore_charge_ : FeatureDistance , IDMapper
• ignore_missed_cleavages_ : IDFilter::DigestionFilter
• ignore_update : SpectraIdentificationViewWidget
• IL_equivalent_ : PeptideIndexing
• ILG : IsoSpecTotalProbGeneratorWrapper , IsoSpecTotalProbWrapper
• ILLEGAL_PARAMETERS : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , PeptideIndexing , TOPPBase , XFDRAlgorithm
• IllegalArgument() : IllegalArgument
• IllegalKey() : Map< Key, T >::IllegalKey
• IllegalPosition() : IllegalPosition
• IllegalSelfOperation() : IllegalSelfOperation
• IllegalTreeOperation() : IllegalTreeOperation
• ILP_IPS : PrecursorIonSelection
• ILPDCWrapper() : ILPDCWrapper
• im : RawMSSignalSimulation::ContaminantInfo
• IM_ALL : RawMSSignalSimulation
• im_correction_function_ : SwathMapMassCorrection
• im_delta_score : OpenSwath_Scores
• im_drift : OpenSwath_Scores
• im_drift_extra_pcnt_ : OpenSwathScoring
• im_drift_weighted : OpenSwath_Scores
• IM_ESI : RawMSSignalSimulation
• im_extra_drift_ : MRMFeatureFinderScoring
• im_extraction_window : ChromExtractParams
• im_extraction_window_ : SwathMapMassCorrection
• IM_LINEAR : MultiGradient
• IM_LOG : SpectrumCanvas
• IM_MALDI : RawMSSignalSimulation
• im_ms1_contrast_coelution : OpenSwath_Scores
• im_ms1_contrast_shape : OpenSwath_Scores
• im_ms1_delta_score : OpenSwath_Scores
• im_ms1_sum_contrast_coelution : OpenSwath_Scores
• im_ms1_sum_contrast_shape : OpenSwath_Scores
• IM_MS_AXIS_TITLE : SpectrumWidget
• IM_NONE : SpectrumCanvas
• IM_ONEKZERO_AXIS_TITLE : SpectrumWidget
• IM_PERCENTAGE : SpectrumCanvas
• IM_SNAP : SpectrumCanvas
• IM_STAIRS : MultiGradient
• im_xcorr_coelution_score : OpenSwath_Scores
• im_xcorr_shape_score : OpenSwath_Scores
• IMD : Precursor
• importDBSearchParameters_() : IdentificationDataConverter
• importExperimentalSettings() : XMassFile
• importIDs() : IdentificationDataConverter
• importSequences() : IdentificationDataConverter
• IMSAlphabet() : IMSAlphabet
• IMSElement() : IMSElement
• IMSIsotopeDistribution() : IMSIsotopeDistribution
• in_description_ : FeatureXMLFile
• in_edges_ : TOPPASVertex
• in_ini_section_ : ToolDescriptionHandler
• in_spectrum_list_ : MzMLHandler
• inc() : Histogram< ValueType, BinSizeType >
• incFrom() : Histogram< ValueType, BinSizeType >
• inchi : CsiFingerIdMzTabWriter::CsiAdapterHit , IdentifiedCompound
• inchi_key : MzTabSmallMoleculeSectionRow
• inchi_string_ : SpectralMatch
• inchikey2D : CsiFingerIdMzTabWriter::CsiAdapterHit
• include() : TOPPASScene
• include_targets_ : TargetedExperiment
• IncludeExcludeTarget() : IncludeExcludeTarget
• includeMSMSPeptides_() : ProteinResolver
• includePipeline() : TOPPASBase
• InclusionExclusionList() : InclusionExclusionList
• incomingEdgesCount() : TOPPASVertex
• INCOMPATIBLE_INPUT_DATA : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , TOPPBase
• IncompatibleIterators() : IncompatibleIterators
• incomplete_line_ : LogStreamBuf
• incorrectly_assigned_fit_gumbel_param_ : PosteriorErrorProbabilityModel
• incorrectly_assigned_fit_param_ : PosteriorErrorProbabilityModel
• increase_LC_elution_peak_counter() : ProcessData
• increaseBoundingBox_() : IDMapper
• incUntil() : Histogram< ValueType, BinSizeType >
• ind_apex_intensity : OpenSwath_Ind_Scores
• ind_area_intensity : OpenSwath_Ind_Scores
• ind_intensity_ratio : OpenSwath_Ind_Scores
• ind_intensity_score : OpenSwath_Ind_Scores
• ind_isotope_correlation : OpenSwath_Ind_Scores
• ind_isotope_overlap : OpenSwath_Ind_Scores
• ind_log_intensity : OpenSwath_Ind_Scores
• ind_log_sn_score : OpenSwath_Ind_Scores
• ind_massdev_score : OpenSwath_Ind_Scores
• ind_mi_ratio : OpenSwath_Ind_Scores
• ind_mi_score : OpenSwath_Ind_Scores
• ind_num_transitions : OpenSwath_Ind_Scores
• ind_total_area_intensity : OpenSwath_Ind_Scores
• ind_total_mi : OpenSwath_Ind_Scores
• ind_transition_names : OpenSwath_Ind_Scores
• ind_xcorr_coelution_score : OpenSwath_Ind_Scores
• ind_xcorr_shape_score : OpenSwath_Ind_Scores
• index : DeNovoIonScoring::IonScore , HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator , ChromatogramMeta , SpectrumMeta , Matrix< Value > , PeakCandidate , ProteinResolver::ISDGroup , ProteinResolver::MSDGroup , ProteinResolver::PeptideEntry , ProteinResolver::ProteinEntry , OSChromatogramMeta , OSSpectrumMeta
• index2key() : LinearInterpolation< Key, Value >
• index2key_0() : BilinearInterpolation< Key, Value >
• index2key_1() : BilinearInterpolation< Key, Value >
• index_ : FeatureFinderDefs::NoSuccessor , FidHandler
• index_offset_ : IndexedMzMLHandler
• index_to_description_ : MetaInfoRegistry
• index_to_name_ : MetaInfoRegistry
• index_to_unit_ : MetaInfoRegistry
• index_to_value_ : MetaInfo
• indexed_mzml_file_ : OnDiscMSExperiment
• indexed_schema_location_ : MzMLFile
• IndexedMzMLFileLoader() : IndexedMzMLFileLoader
• IndexedMzMLHandler() : IndexedMzMLHandler
• IndexMap_ : PeptideProteinResolution
• IndexOverflow() : IndexOverflow
• IndexPair : FeatureFinderDefs , IsotopeCluster
• indexPair() : Matrix< Value >
• IndexPosMappingType : PepNovoOutfile
• IndexScorePair : HyperScore
• IndexSet : FeatureFinderDefs , Fitter1D , IsotopeCluster
• IndexTriple : OfflinePrecursorIonSelection
• IndexType : MRMDecoy
• IndexUnderflow() : IndexUnderflow
• indices_ : IsotopeWaveletTransform< PeakType >
• indis : ProteinResolver::ProteinEntry
• indist_prot_grp_to_pep_ : PeptideProteinResolution
• indistinguishable_proteins_ : ProteinIdentification
• individual_intensities_ : AccurateMassSearchResult
• INDUCTIVEDETECTOR : IonDetector
• INDUCTIVELYCOUPLEDPLASMA : IonSource
• inEdgeHasChanged() : TOPPASOutputFileListVertex , TOPPASToolVertex , TOPPASVertex
• inEdgesBegin() : TOPPASVertex
• inEdgesEnd() : TOPPASVertex
• inf_ : SVOutStream
• infer() : ProteinInference
• infer_() : ProteinInference
• inferFromPeptides() : ModificationDefinitionsSet
• inferMoreEdges_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• inferPosteriorProbabilities() : BayesianProteinInferenceAlgorithm
• inferPosteriorProbabilities_() : BayesianProteinInferenceAlgorithm
• infile_ : FASTAFile
• infinity : FeatureDistance
• info_ : SpectrumCheapDPCorr
• info_streams_ : LogConfigHandler
• infty_ : IntegerMassDecomposer< ValueType, DecompositionValueType >
• INFUSION : IonSource
• INI : FileTypes
• ini_file_ : ToolsDialog
• ini_location_ : TOPPBase
• 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
• init_param_ : GammaDistributionFitter , GaussFitter , GumbelDistributionFitter , GumbelMaxLikelihoodFitter
• init_prob_ : HiddenMarkovModel
• init_size_ : DistanceMatrix< Value >
• initBins_() : Histogram< ValueType, BinSizeType >
• initChannelMap() : ItraqConstants
• initDataStructures_() : XFDRAlgorithm
• initGridSearchFromParams_() : BayesianProteinInferenceAlgorithm
• initialize() : ConfidenceScoring , GaussFilterAlgorithm , OpenSwathScoring , SimRandomNumberGenerator
• initializeCluster() : QTCluster
• initializeDefaultParameters_() : TOPPViewBase
• initializedMaps_ : SvmTheoreticalSpectrumGenerator
• 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
• initialTrTolerance_ : SuperHirnParameters
• initIsotopeDist_ : SuperHirnParameters
• initIsotopeDistributions_() : CompNovoIdentificationBase , CompNovoIonScoringBase
• initModificationMassesRNA() : RNPxlModificationsGenerator
• initParam_() : RawTandemMSSignalSimulation , TOPPASToolVertex
• initParameters_() : SVMWrapper
• initParams() : FeatureFinderAlgorithmSHCtrl
• initPattern() : AhoCorasickAmbiguous
• initPlots() : PosteriorErrorProbabilityModel
• initvec() : Chromatogram , Spectrum , OSChromatogram , OSSpectrum
• INIUpdater() : INIUpdater
• inlet_type_ : IonSource , IonSourceVisualizer
• INLETNULL : IonSource
• InletType : IonSource
• InMSLevelRange() : InMSLevelRange< SpectrumType >
• InMzRange() : InMzRange< PeakType >
• InPrecursorMZRange() : InPrecursorMZRange< SpectrumType >
• input_1_name_ : FuzzyStringComparator
• input_2_name_ : FuzzyStringComparator
• input_combo_ : ToolsDialog
• INPUT_FILE : ListEditor , ParameterInformation
• INPUT_FILE_CORRUPT : TOPPBase
• INPUT_FILE_EMPTY : TOPPBase
• INPUT_FILE_LIST : ParameterInformation
• INPUT_FILE_NOT_FOUND : TOPPBase
• INPUT_FILE_NOT_READABLE : TOPPBase
• input_file_opt : DataQuery
• input_file_refs : DataProcessingStep
• input_filename_ : OpenSwathOSWWriter , OpenSwathTSVWriter , XTandemInfile
• input_files_ : IdentificationData
• input_line_1_ : FuzzyStringComparator
• input_line_2_ : FuzzyStringComparator
• input_type : ProteinResolver::ResolverResult
• inputFileReadable_() : TOPPBase
• InputFileRef : IdentificationData
• InputFiles : IdentificationData
• InputLine() : FuzzyStringComparator::InputLine
• inputs() : LevMarqFitter1D::GenericFunctor , GumbelMaxLikelihoodFitter::Functor< _Scalar, NX, NY > , OptimizePick::OptPeakFunctor , TraceFitter::GenericFunctor , TwoDOptimization::TwoDOptFunctor
• InputsAtCompileTime : GumbelMaxLikelihoodFitter::Functor< _Scalar, NX, NY >
• InputType : GumbelMaxLikelihoodFitter::Functor< _Scalar, NX, NY >
• 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
• Inside : DRange< D >
• inside_ : LinearInterpolation< Key, Value >
• inside_0_ : BilinearInterpolation< Key, Value >
• inside_1_ : BilinearInterpolation< Key, Value >
• insideBand_() : MapAlignmentAlgorithmSpectrumAlignment
• InspectInfile() : InspectInfile
• InspectOutfile() : InspectOutfile
• instance() : SuperHirnParameters
• instance_() : Factory< FactoryProduct > , LogConfigHandler , SingletonRegistry , SuperHirnParameters , UniqueIdGenerator
• instance_number_ : TOPPBase
• instance_ptr_ : Factory< FactoryProduct >
• institution_ : ContactPerson , ContactPersonVisualizer
• Instrument() : Instrument
• instrument : MzTabMetaData
• Instrument : TargetedExperiment , Instrument
• instrument_ : ExperimentalSettings , HPLC , InspectInfile , MascotInfile
• instrument_ref : Configuration
• instrument_settings_ : ChromatogramSettings , SpectrumSettings
• instruments_ : MzMLHandler , TargetedExperiment
• InstrumentSettings() : InstrumentSettings
• instrumentsettings_polarity_ : InstrumentSettingsVisualizer
• instrumentsettings_scan_mode_ : InstrumentSettingsVisualizer
• InstrumentSettingsVisualizer() : InstrumentSettingsVisualizer
• InstrumentVisualizer() : InstrumentVisualizer
• InsufficientInput() : ClusterFunctor::InsufficientInput
• INT : ListEditor , ParameterInformation
• int_ : PrecursorVisualizer
• int_32_bit_ : PeakFileOptions
• INT_LIST : DataValue
• int_max : PeakPickerMaxima::PeakCandidate
• int_range_ : RangeManager< D >
• int_scale_ : Spectrum3DOpenGLCanvas
• int_sum : OPXLDataStructs::CrossLinkSpectrumMatch
• INT_VALUE : DataValue
• INTEGER : LPWrapper
• integer_data_arrays_ : MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
• integer_decomposer_type : RealMassDecomposer
• integer_value_type : RealMassDecomposer
• IntegerDataArray : MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
• IntegerDataArrays : MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
• IntegerMassDecomposer() : IntegerMassDecomposer< ValueType, DecompositionValueType >
• integrate_() : ContinuousWaveletTransformNumIntegration , GaussFilterAlgorithm
• integrated_intensities_ : PeakPickerMRM
• integrated_intensity : PeakCandidate
• integratePeak() : PeakIntegrator
• integratePeak_() : PeakIntegrator
• integratePeaks_() : PeakPickerMRM
• integration_type_ : PeakIntegrator
• INTEGRATION_TYPE_INTENSITYSUM : PeakIntegrator
• INTEGRATION_TYPE_SIMPSON : PeakIntegrator
• INTEGRATION_TYPE_TRAPEZOID : PeakIntegrator
• intens : FeatureFinderAlgorithmIsotopeWavelet::BoxElement , IsotopeWaveletTransform< PeakType >::BoxElement
• intens_signals : LCElutionPeak
• intensIsotopesStDev_ : ConsensusIsotopePattern
• INTENSITY : DataFilters
• intensity : FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern , FeatureFinderAlgorithmPickedHelperStructs::Seed , FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern , RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_
• INTENSITY : IsotopeDistribution
• intensity() : KDTreeFeatureMaps , MS1Signal
• INTENSITY : MSPeak
• Intensity : MSstatsFile
• intensity : OpenSwath_Scores , PeptideHit::PeakAnnotation , ProteinResolver::MSDGroup , ProteinResolver::PeptideEntry , RawMSSignalSimulation::ContaminantInfo
• intensity_ : CentroidPeak , ChromatogramPeak , MultiplexSatelliteProfile , Peak1D , Peak2D
• INTENSITY_AXIS_TITLE : SpectrumWidget
• intensity_bin_boarders : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• intensity_bin_values : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• intensity_bins_ : FeatureFinderAlgorithmPicked
• intensity_button_group_ : TOPPViewBase
• intensity_cutoff_ : MultiplexFiltering
• intensity_l : MRMFeatureQC::ComponentGroupQCs , MRMFeatureQC::ComponentQCs
• intensity_mode_ : SpectrumCanvas
• intensity_mz_step_ : FeatureFinderAlgorithmPicked
• intensity_percentage_ : FeatureFinderAlgorithmPicked
• intensity_percentage_optional_ : FeatureFinderAlgorithmPicked
• intensity_range_ : FeatureFileOptions , PeakFileOptions
• intensity_rt_step_ : FeatureFinderAlgorithmPicked
• intensity_scale_ : RawMSSignalSimulation
• intensity_scale_stddev_ : RawMSSignalSimulation
• intensity_threshold_ : FeatureFinderAlgorithmIsotopeWavelet
• intensity_thresholds_ : FeatureFinderAlgorithmPicked
• intensity_type_ : FeatureFinderAlgorithmIsotopeWavelet
• intensity_u : MRMFeatureQC::ComponentGroupQCs , MRMFeatureQC::ComponentQCs
• intensityArea : MS2Fragment
• IntensityBalanceFilter() : IntensityBalanceFilter
• intensityBinMap : BackgroundControl
• intensityCV_ : SuperHirnParameters
• intensityFilterPassed_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• intensityFloor_ : SuperHirnParameters
• intensityHist_ : BackgroundIntensityBin
• IntensityIteratorWrapper() : IntensityIteratorWrapper< IteratorT >
• intensityLess_() : MetaboTargetedAssay
• IntensityMap : SvmTheoreticalSpectrumGenerator
• intensityMap_ : BackgroundIntensityBin
• intensityModeChange_() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas , SpectrumWidget
• IntensityModes : SpectrumCanvas
• IntensityRangeType : RangeManager< D >
• intensityScore_() : FeatureFinderAlgorithmPicked
• intensityThreshold_ : SuperHirnParameters
• IntensityThresholdCalculation : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• IntensityType : Annotation1DItem , BaseModel< D > , ChromatogramPeak , ExtendedIsotopeModel , FeatureFinderAlgorithm , InterpolationModel , IsotopeModel , MSExperiment , Peak1D , Peak2D , ProductModel< 2 > , ProteinInference
• intenstype_ : IsotopeWaveletTransform< PeakType >
• intercept_ : LinearRegression , TransformationModelLinear
• intermediate_products_ : ReactionMonitoringTransition
• Internal : NASequence
• INTERNAL : OPXLDataStructs
• Internal : Residue
• Internal::ClassTest::isFileSimilar : FuzzyStringComparator
• Internal::ClassTest::testStringSimilar : FuzzyStringComparator
• INTERNAL_ERROR : TOPPBase
• internal_formula_ : Residue
• internal_to_a_monoweight_ : Residue
• internal_to_b_monoweight_ : Residue
• internal_to_c_monoweight_ : Residue
• internal_to_cterm_monoweight_ : Residue
• internal_to_full_monoweight_ : Residue
• internal_to_nterm_monoweight_ : Residue
• internal_to_x_monoweight_ : Residue
• internal_to_y_monoweight_ : Residue
• internal_to_z_monoweight_ : Residue
• InternalCalibration() : InternalCalibration
• interp_ : TransformationModelInterpolated
• interpol_xs_ : IsotopeWaveletTransform< PeakType >
• interpol_ys_ : IsotopeWaveletTransform< PeakType >
• interpolate_precursor_purity_ : IsobaricChannelExtractor
• interpolatedColorAt() : MultiGradient
• interpolation_ : InterpolationModel
• interpolation_mode_ : MultiGradient
• interpolation_step_ : Fitter1D , InterpolationModel
• InterpolationMode : MultiGradient
• InterpolationModel : GaussModel , InterpolationModel
• Interpretation : TargetedExperiment , Interpretation
• interpretation_list_ : IncludeExcludeTarget , TraMLProduct
• interpretRetentionTime_() : TransitionTSVFile
• intersection_() : FeatureFinderAlgorithmPicked
• intersects() : DBoundingBox< D >
• Intersects : DRange< D >
• intersects() : DRange< D >
• intersects_with() : _Region< __K, _Val, _SubVal, _Acc, _Cmp >
• INTLIST : ParameterInformation
• ints_32 : MzMLHandlerHelper::BinaryData
• ints_64 : MzMLHandlerHelper::BinaryData
• intsum_alpha : OPXLDataStructs::CrossLinkSpectrumMatch
• intsum_beta : OPXLDataStructs::CrossLinkSpectrumMatch
• IntType : CachedMzMLHandler
• inv_table_steps_ : IsotopeWavelet
• INVALID : UniqueIdInterface
• invalidate_() : HistogramWidget
• InvalidIterator() : InvalidIterator
• InvalidParameter() : InvalidParameter
• InvalidRange() : InvalidRange
• InvalidSize() : InvalidSize
• InvalidValue() : InvalidValue
• inventory_ : Factory< FactoryProduct > , SingletonRegistry
• invert() : TransformationDescription , TransformationModelLinear
• invertRecylingMode() : TOPPASToolVertex , TOPPASVertex
• IOException() : IOException
• IOG : IsoSpecOrderedGeneratorWrapper
• IOInfo() : TOPPASToolVertex::IOInfo
• ion_cutoff_percentage_ : SequestInfile
• ion_detectors_ : Instrument
• ion_ladder_visible_ : Spectrum1DCanvas
• ion_mass_tolerance_ : MascotInfile
• ion_mobility : ChromatogramExtractorAlgorithm::ExtractionCoordinates
• ion_mode_ : AccurateMassSearchEngine , MetaboliteSpectralMatching
• ion_optics_ : Instrument , InstrumentVisualizer
• ion_ratio_feature_name : MRMFeatureQC::ComponentGroupQCs
• ion_ratio_l : MRMFeatureQC::ComponentGroupQCs
• ion_ratio_pair_name_1 : MRMFeatureQC::ComponentGroupQCs
• ion_ratio_pair_name_2 : MRMFeatureQC::ComponentGroupQCs
• ion_ratio_u : MRMFeatureQC::ComponentGroupQCs
• ion_series_weights_ : SequestInfile
• ion_sources_ : Instrument
• ion_tree_ : SiriusAdapterAlgorithm
• ion_types : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• IonDetector() : IonDetector
• IonDetectorVisualizer() : IonDetectorVisualizer
• ionization : SiriusMSFile::CompoundInfo
• ionization_method_ : IonSource , IonSourceVisualizer
• ionization_type_ : IonizationSimulation
• IonizationMethod : IonSource
• IONIZATIONMETHOD : RawMSSignalSimulation
• IonizationSimulation() : IonizationSimulation
• IonizationType : IonizationSimulation
• ionize() : IonizationSimulation
• ionizeEsi_() : IonizationSimulation
• ionizeMaldi_() : IonizationSimulation
• IonMapT : MRMAssay
• IONMETHODNULL : IonSource
• IonMobilityScoring() : IonMobilityScoring
• IonOpticsType : Instrument
• IonScore : CompNovoIdentification , CompNovoIdentificationBase , CompNovoIdentificationCID , CompNovoIonScoring , CompNovoIonScoringBase::IonScore , CompNovoIonScoringCID , DeNovoIonScoring::IonScore
• IonSeries : MRMAssay , MRMIonSeries
• IonSource() : IonSource
• IonSourceVisualizer() : IonSourceVisualizer
• IONSTORAGE : MassAnalyzer
• IONTOPHOTONDETECTOR : IonDetector
• IonType() : SvmTheoreticalSpectrumGenerator::IonType , SvmTheoreticalSpectrumGeneratorTrainer , TargetedExperiment
• iontype : Interpretation
• IonType : Interpretation
• IOT_FILE : TOPPASToolVertex::IOInfo
• IOT_LIST : TOPPASToolVertex::IOInfo
• IOType : TOPPASToolVertex::IOInfo
• IPS : PrecursorIonSelection
• iRpropPlus() : EmgGradientDescent , EmgGradientDescent_friend
• is_absdiff_small_ : FuzzyStringComparator
• is_active_ : ChargePair , DataFilters
• IS_actual_concentration : AbsoluteQuantitationStandards::featureConcentration , AbsoluteQuantitationStandards::runConcentration
• IS_component_name : AbsoluteQuantitationStandards::runConcentration
• is_decoy : ParentMolecule , IDFilter::HasDecoyAnnotation< HitType >
• is_end_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , MatchedIterator< CONT_T, TRAIT, CONST_T >
• IS_feature : AbsoluteQuantitationStandards::featureConcentration
• is_initialized_ : AccurateMassSearchEngine
• is_instantiated_ : ModificationsDB
• is_internal : ToolDescriptionInternal
• is_inverse_orientation_ : AxisWidget
• is_isotope_1_mono : CompNovoIonScoringBase::IonScore
• is_log_ : AxisWidget
• is_ms1_shown_ : SpectraIdentificationViewWidget
• IS_name_ : AbsoluteQuantitationMethod
• is_number : FuzzyStringComparator::StreamElement_
• is_openpepxl_ : XQuestResultXMLHandler
• is_prefix : DecoyHelper::Result
• is_protein_note_ : XTandemXMLFile
• is_repeatable_ : CVMappingTerm
• is_result_valid_ : SignalToNoiseEstimator< Container >
• is_running_ : StopWatch
• is_space : FuzzyStringComparator::StreamElement_
• is_spectrum_note_ : XTandemXMLFile
• is_status_success_ : FuzzyStringComparator
• is_swapped_ : Spectrum1DCanvas
• 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
• isd_group : ProteinResolver::MSDGroup , ProteinResolver::PeptideEntry , ProteinResolver::ProteinEntry
• isDataDIA() : TOPPViewOpenDialog
• isDetectingTransition() : ReactionMonitoringTransition , LightTransition
• isDIAData() : LayerData
• isDirectory() : File
• isDrawInterestingMZs() : Spectrum1DCanvas
• isDryRun() : TOPPASScene
• isds : ProteinResolver::ResolverResult
• 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
• ISI : IonSource
• 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
• iso_ : MassAnalyzerVisualizer
• iso_map_ : TwoDOptimization
• iso_map_iter : TwoDOptimization::Data
• iso_number_ms2_negative : IsobaricQuantifierStatistics
• iso_number_reporter_different : IsobaricQuantifierStatistics
• iso_number_reporter_negative : IsobaricQuantifierStatistics
• iso_pattern_ : FeatureHypothesis
• iso_similarity_ : AccurateMassSearchEngine
• iso_solution_different_intensity : IsobaricQuantifierStatistics
• iso_total_intensity_negative : IsobaricQuantifierStatistics
• IsobaricChannelExtractor() : IsobaricChannelExtractor
• IsobaricChannelInformation() : IsobaricQuantitationMethod::IsobaricChannelInformation
• IsobaricChannelList : IsobaricQuantitationMethod
• IsobaricNormalizer() : IsobaricNormalizer
• IsobaricQuantifier() : IsobaricQuantifier
• IsobaricQuantifierStatistics() : IsobaricQuantifierStatistics
• IsobaricQuantitationMethod() : IsobaricQuantitationMethod
• isolation_width_ : MassAnalyzer
• isOneTableFile_() : ExperimentalDesignFile
• isoPeakMeans() : OPXLHelper
• ISOPEAKS : MSPeak
• isOpen() : Bzip2Ifstream , GzipIfstream
• isOpenMSDataPath_() : File
• isoscore : SiriusMzTabWriter::SiriusAdapterHit
• IsoSpecOrderedGeneratorWrapper() : IsoSpecOrderedGeneratorWrapper
• IsoSpecThresholdGeneratorWrapper() : IsoSpecThresholdGeneratorWrapper
• IsoSpecThresholdWrapper() : IsoSpecThresholdWrapper
• IsoSpecTotalProbGeneratorWrapper() : IsoSpecTotalProbGeneratorWrapper
• IsoSpecTotalProbWrapper() : IsoSpecTotalProbWrapper
• isotope : NucleicAcidSearchEngine::PrecursorInfo
• isotope_ : SiriusAdapterAlgorithm
• isotope_correction_enabled_ : IsobaricQuantifier
• isotope_corrections_ : ITRAQLabeler
• isotope_correlation : OpenSwath_Scores
• isotope_distance_ : ExtendedIsotopeModel , IsotopeModel
• isotope_distribution_ : IsotopeModel
• isotope_distributions_ : CompNovoIdentificationBase , CompNovoIonScoringBase , FeatureFinderAlgorithmPicked , IsotopeDistributionCache
• isotope_filt_svm_ : FeatureFindingMetabo
• isotope_filtering_model_ : FeatureFindingMetabo
• isotope_label_type_ : MSstatsFile::MSstatsLine_
• isotope_lorentz_fwhm_ : IsotopeModel
• isotope_model_ : TheoreticalSpectrumGenerator
• isotope_overlap : OpenSwath_Scores
• isotope_pattern_iterations_ : SiriusAdapterAlgorithm
• isotope_pmin_ : FeatureFinderIdentificationAlgorithm
• isotope_probs_ : FeatureFinderIdentificationAlgorithm
• isotope_stdev_ : ExtendedIsotopeFitter1D , ExtendedIsotopeModel , IsotopeFitter1D , IsotopeModel
• IsotopeCluster() : IsotopeCluster
• ISOTOPECORRECTIONS_EIGHTPLEX : ItraqConstants
• ISOTOPECORRECTIONS_FOURPLEX : ItraqConstants
• ISOTOPECORRECTIONS_TMT_SIXPLEX : ItraqConstants
• IsotopeDiffFilter() : IsotopeDiffFilter
• IsotopeDistribution() : IsotopeDistribution
• IsotopeDistributionCache() : IsotopeDistributionCache
• IsotopeFitter1D() : IsotopeFitter1D
• IsotopeMarker() : IsotopeMarker
• IsotopeMatrices : ItraqConstants , ITRAQLabeler
• IsotopeModel() : IsotopeModel
• IsotopePattern : FeatureFinderAlgorithmPicked , FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern
• isotopePattern : LCElutionPeak
• IsotopePatternGenerator() : IsotopePatternGenerator
• isotopes_ : Element , IMSElement
• isotopes_per_peptide_max_ : FeatureFinderMultiplexAlgorithm , MultiplexFiltering
• isotopes_per_peptide_min_ : FeatureFinderMultiplexAlgorithm , MultiplexFiltering
• isotopes_sim_score_ : AccurateMassSearchResult
• isotopes_type : IMSElement
• isotopeScore_() : FeatureFinderAlgorithmPicked
• isotopesTrace_ : ConsensusIsotopePattern
• IsotopeType : CompNovoIdentification , CompNovoIdentificationCID , CompNovoIonScoring , CompNovoIonScoringBase , CompNovoIonScoringCID
• IsotopeVariant : Tagging
• IsotopeWavelet() : IsotopeWavelet
• IsotopeWaveletTransform() : IsotopeWaveletTransform< PeakType > , IsotopeWaveletTransform< PeakType >::TransSpectrum
• ISOTOPIC_LABEL : ResidueModification
• isotopicPeaks_ : DeconvPeak
• isotopIdx_ : CentroidPeak
• 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 >
• IT : MassAnalyzer
• it_ : ConsensusXMLFile
• it_ref_ : MatchedIterator< CONT_T, TRAIT, CONST_T >
• it_tgt_ : MatchedIterator< CONT_T, TRAIT, CONST_T >
• itemChanged() : TheoreticalSpectrumGenerationDialog
• itemClicked() : TOPPASScene
• itemDragged() : TOPPASVertex
• itemenclosed_ : CsvFile
• ItemMap : IDFilter::GetMatchingItems< HitType, Entry >
• itemReleased() : TOPPASScene
• items : IDFilter::GetMatchingItems< HitType, Entry >
• itemseperator_ : CsvFile
• iterateFeatureMap() : QCBase
• ITERATION_EXCEEDED : NonNegativeLeastSquaresSolver
• iterator : _Iterator< _Val, _Ref, _Ptr > , KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• Iterator() : AASequence::Iterator , Annotations1DContainer
• iterator : ConsensusFeature
• Iterator : ConsensusMap , ConstRefVector< ContainerT >
• iterator : ConstRefVector< ContainerT > , DPosition< D, TCoordinateType >
• Iterator : DPosition< D, TCoordinateType > , EmpiricalFormula
• iterator : EmpiricalFormula , FeatureFinderAlgorithmPickedHelperStructs::MassTraces
• Iterator : FeatureMap
• iterator : HashGrid< Cluster >
• Iterator() : HashGrid< Cluster >::Iterator
• iterator : IMSAlphabet
• Iterator : IsotopeDistribution
• iterator : IsotopeDistribution
• Iterator : Map< Key, T >
• iterator : MassTrace
• Iterator : Matrix< Value >
• iterator : Matrix< Value >
• Iterator : MSChromatogram
• iterator : MSExperiment
• Iterator : MSExperiment , MSSpectrum , NASequence::Iterator , String , StringListUtils , TextFile
• iterator : XCorrArrayType
• iterator_category : _Iterator< _Val, _Ref, _Ptr > , AASequence::ConstIterator , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , MatchedIterator< CONT_T, TRAIT, CONST_T > , NASequence::ConstIterator
• iteratorsSet() : PeakShape
• IteratorWrapper() : IteratorWrapper< Iterator >
• ITG : IsoSpecThresholdGeneratorWrapper , IsoSpecThresholdWrapper
• itraq_type_ : ITRAQLabeler
• ITRAQ_TYPES : ItraqConstants
• ItraqEightPlexQuantitationMethod() : ItraqEightPlexQuantitationMethod
• ItraqFourPlexQuantitationMethod() : ItraqFourPlexQuantitationMethod
• ITRAQLabeler() : ITRAQLabeler