| OpenMS 2.5.0

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
- incorporations : SIPPeptide
- 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_coef : ConfidenceScoring::GLM_
- 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 : ConfidenceScoring::GLM_
- 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
- iterator : ConstRefVector< ContainerT >
- Iterator : ConstRefVector< ContainerT >
- iterator : DPosition< D, TCoordinateType >
- Iterator : DPosition< D, TCoordinateType > , EmpiricalFormula
- iterator : EmpiricalFormula , FeatureFinderAlgorithmPickedHelperStructs::MassTraces
- Iterator : FeatureMap
- iterator : HashGrid< Cluster >
- Iterator() : HashGrid< Cluster >::Iterator
- iterator : IMSAlphabet , IsotopeDistribution
- Iterator : IsotopeDistribution , Map< Key, T >
- iterator : MassTrace
- Iterator : Matrix< Value >
- iterator : Matrix< Value >
- Iterator : MSChromatogram , MSExperiment
- iterator : MSExperiment
- Iterator : 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