- i -

i : Base64::Reinterpreter32_ , Base64::Reinterpreter64_ , IsotopeWavelet::fi_
i_ : Index
id : ChromatogramExtractorAlgorithm::ExtractionCoordinates , ControlledVocabulary::CVTerm , ChromatogramMeta , SpectrumMeta , IsobaricQuantitationMethod::IsobaricChannelInformation , ItraqConstants::ChannelInfo , QcMLFile::Attachment , QcMLFile::QualityParameter , Contact , CV , Instrument , PeptideCompound , Protein , Publication , LightCompound , LightProtein , OSChromatogramMeta , OSSpectrumMeta , Peptide , Protein
id_ : MQEvidence , MQMsms , Compomer , DocumentIdentifier , FASTAFile , Identification , IdentificationHit , IDMergerAlgorithm , IdXMLFile , MzIdentMLHandler , OSWProtein , OSWTransition , PeptideIdentification , ProteinIdentification , QTCluster::BulkData , ResidueModification , SpectrumIdentification
id_confidence_measure : MzTabMMetaData , MzTabMSmallMoleculeEvidenceSectionRow
id_data_ : ConsensusMap , FeatureMap , MascotXMLHandler
id_format : MzTabMMSRunMetaData , MzTabMSRunMetaData
id_identifier_ : ConsensusXMLHandler , FeatureXMLHandler
id_matches_ : BaseFeature
id_view_widget_ : DataSelectionTabs
idec : MzIdentMLDOMHandler::PeptideEvidence
ident_run_idx : IDRipper::RipFileIdentifier
identification_ : SpectrumSettings
identification_date_ : ProteinIdentificationVisualizer
identification_method : MzTabMSmallMoleculeEvidenceSectionRow
identification_rate : Ms2IdentificationRate::IdentificationRateData
identification_threshold_ : PeptideIdentificationVisualizer , ProteinIdentificationVisualizer
identifications : CsiFingerIdMzTabWriter::CsiAdapterRun , SiriusMzTabWriter::SiriusAdapterRun
identified : IDMapper::SpectraIdentificationState
identified_compound_keys_ : OMSFileStore
identified_compound_lookup_ : IdentificationData
identified_compound_refs : IdentificationData::RefTranslator
identified_compounds_ : IdentificationData
identified_molecule_var : ObservationMatch
identified_molecule_vars_ : OMSFileLoad
identified_oligo_keys_ : OMSFileStore
identified_oligo_lookup_ : IdentificationData
identified_oligo_refs : IdentificationData::RefTranslator
identified_oligos_ : IdentificationData
identified_peptide_keys_ : OMSFileStore
identified_peptide_lookup_ : IdentificationData
identified_peptide_refs : IdentificationData::RefTranslator
identified_peptides_ : IdentificationData
identifier : FASTAFile::FASTAEntry , IdentifiedCompound , MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping , MzTabSmallMoleculeSectionRow , ProteinResolver::ResolverResult
identifier_ : Acquisition , CVMappingRule , CVReference , DocumentIdentifierVisualizer , MascotXMLHandler , PeptideIdentificationVisualizer , ProteinIdentificationVisualizer
identifier_id_ : ConsensusXMLHandler , FeatureXMLHandler
identifier_to_msrunpath : ProteinIdentification::Mapping
identifying_transition : TransitionTSVFile::TSVTransition , LightTransition
idrunid_2_idrunindex_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
ids : FeatureFinderIdentificationAlgorithm::RTRegion
ids_ : LayerStatisticsIdent , LayerStoreDataIdentVisible , SpectrumLookup
idview_controller_ : DataSelectionTabs
idx_ : KDTreeFeatureNode
idx_feat : OSWIndexTrace
idx_pep : OSWIndexTrace
idx_prot : OSWIndexTrace
idx_trans : OSWIndexTrace
ifl_ : TOPPASInputFilesDialog
ifs_ : CachedmzML
ignore_adduct_ : FeatureDistance
ignore_charge_ : FeatureDistance , IDMapper
ignore_missed_cleavages_ : IDFilter::DigestionFilter
ignore_update : SpectraIDViewTab
IL_equivalent_ : PeptideIndexing
ILG : IsoSpecTotalProbGeneratorWrapper , IsoSpecTotalProbWrapper
im : RawMSSignalSimulation::ContaminantInfo
im_correction_function_ : SwathMapMassCorrection
im_delta : OpenSwath_Scores
im_delta_score : OpenSwath_Scores
im_drift : OpenSwath_Scores
im_drift_extra_pcnt_ : OpenSwathScoring
im_drift_weighted : OpenSwath_Scores
im_extra_drift_ : MRMFeatureFinderScoring
im_extraction_window : ChromExtractParams
im_extraction_window_ : SwathMapMassCorrection
im_ms1_contrast_coelution : OpenSwath_Scores
im_ms1_contrast_shape : OpenSwath_Scores
im_ms1_delta : OpenSwath_Scores
im_ms1_delta_score : OpenSwath_Scores
im_ms1_drift : OpenSwath_Scores
im_ms1_sum_contrast_coelution : OpenSwath_Scores
im_ms1_sum_contrast_shape : OpenSwath_Scores
IM_MS_AXIS_TITLE : PlotWidget
IM_ONEKZERO_AXIS_TITLE : PlotWidget
im_xcorr_coelution_score : OpenSwath_Scores
im_xcorr_shape_score : OpenSwath_Scores
imLower : SwathMap
imUpper : SwathMap
in_description_ : FeatureXMLHandler
in_edges_ : TOPPASVertex
in_ini_section_ : ToolDescriptionHandler
in_spectrum_list_ : MzMLHandler
inchi : CsiFingerIdMzTabWriter::CsiAdapterHit , IdentifiedCompound , MzTabMSmallMoleculeEvidenceSectionRow , MzTabMSmallMoleculeSectionRow
inchi_key : MzTabSmallMoleculeSectionRow
inchi_string_ : SpectralMatch
inchikey2D : CsiFingerIdMzTabWriter::CsiAdapterHit
include_targets_ : TargetedExperiment
incomplete_line_ : LogStreamBuf
incorrectly_assigned_fit_gumbel_param_ : PosteriorErrorProbabilityModel
incorrectly_assigned_fit_param_ : PosteriorErrorProbabilityModel
ind2prot_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
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
indentation_ : IndentedStream
index : DeNovoIonScoring::IonScore , ChromatogramMeta , SpectrumMeta , PeakCandidate , ProteinResolver::ISDGroup , ProteinResolver::MSDGroup , ProteinResolver::PeptideEntry , ProteinResolver::ProteinEntry , OSChromatogramMeta , OSSpectrumMeta
index_ : FeatureFinderDefs::NoSuccessor , FidHandler , PeakGroup
index_map : IDRipper::IdentificationRuns
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
indices_ : IsotopeWaveletTransform< PeakType >
indis : ProteinResolver::ProteinEntry
indist_prot_grp_to_pep_ : PeptideProteinResolution
indistinguishable_proteins_ : ProteinIdentification
individual_intensities_ : AccurateMassSearchResult
inf_ : SVOutStream
infile_ : FASTAFile
infinity : FeatureDistance
info_ : SpectrumCheapDPCorr
info_streams_ : LogConfigHandler
info_text_ : PythonModuleRequirement
infty_ : IntegerMassDecomposer< ValueType, DecompositionValueType >
ini_file_ : ToolsDialog
ini_location_ : TOPPBase
init_param_ : GammaDistributionFitter , GaussFitter , GumbelDistributionFitter , GumbelMaxLikelihoodFitter
init_prob_ : HiddenMarkovModel
init_size_ : DistanceMatrix< Value >
initializedMaps_ : SvmTheoreticalSpectrumGenerator
inlet_type_ : IonSource , IonSourceVisualizer
input_ : Colorizer
input_1_name_ : FuzzyStringComparator
input_2_name_ : FuzzyStringComparator
input_combo_ : ToolsDialog
input_file : Observation
input_file_keys_ : OMSFileStore
input_file_refs : IdentificationData::RefTranslator , ProcessingStep
input_file_refs_ : OMSFileLoad
input_filename_ : OpenSwathOSWWriter , OpenSwathTSVWriter , XTandemInfile
input_files_ : IdentificationData
input_line_1_ : FuzzyStringComparator
input_line_2_ : FuzzyStringComparator
input_type : ProteinResolver::ResolverResult
insert_pos : Args
inside_ : LinearInterpolation< Key, Value >
inside_0_ : BilinearInterpolation< Key, Value >
inside_1_ : BilinearInterpolation< Key, Value >
instance_ : LogConfigHandler , UniqueIdGenerator
instance_number_ : TOPPBase
instance_ptr_ : Factory< FactoryProduct >
institution_ : ContactPerson , ContactPersonVisualizer
instrument : MzTabMetaData , MzTabMMetaData
instrument_ : ExperimentalSettings , HPLC , InspectInfile , MascotInfile
instrument_ref : MzTabMMSRunMetaData , Configuration
instrument_settings_ : ChromatogramSettings , SpectrumSettings
instruments_ : MzMLHandler , TargetedExperiment
instrumentsettings_polarity_ : InstrumentSettingsVisualizer
instrumentsettings_scan_mode_ : InstrumentSettingsVisualizer
int_ : PrecursorVisualizer
int_32_bit_ : PeakFileOptions
int_coef : ConfidenceScoring::GLM_
int_max : PeakPickerMaxima::PeakCandidate
int_scale_ : Plot3DOpenGLCanvas
int_sum : OPXLDataStructs::CrossLinkSpectrumMatch
integer_data_arrays_ : MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
integrated_intensities_ : PeakPickerMRM
integrated_intensity : PeakCandidate
integration_type_ : PeakIntegrator
INTEGRATION_TYPE_INTENSITYSUM : PeakIntegrator
INTEGRATION_TYPE_SIMPSON : PeakIntegrator
INTEGRATION_TYPE_TRAPEZOID : PeakIntegrator
intens : FeatureFinderAlgorithmIsotopeWavelet::BoxElement , IsotopeWaveletTransform< PeakType >::BoxElement
intensities : TIC::Result
intensity : FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern , FeatureFinderAlgorithmPickedHelperStructs::Seed , FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern , FLASHDeconvHelperStructs::LogMzPeak , RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ , MassTraceDetection::Apex , OpenSwath_Scores , PeptideHit::PeakAnnotation , ProteinResolver::MSDGroup , ProteinResolver::PeptideEntry , RawMSSignalSimulation::ContaminantInfo
intensity_ : ChromatogramPeak , MobilityPeak1D , MobilityPeak2D , MultiplexSatelliteProfile , Peak1D , Peak2D , PeakGroup , TriqlerFile::TriqlerLine_
INTENSITY_AXIS_TITLE : PlotWidget
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_ : PlotCanvas
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 , FLASHDeconvAlgorithm
intensity_thresholds_ : FeatureFinderAlgorithmPicked
intensity_type_ : FeatureFinderAlgorithmIsotopeWavelet
intensity_u : MRMFeatureQC::ComponentGroupQCs , MRMFeatureQC::ComponentQCs
intenstype_ : IsotopeWaveletTransform< PeakType >
intercept : ConfidenceScoring::GLM_
intercept_ : LinearRegression , TransformationModelLinear
intermediate_products_ : ReactionMonitoringTransition
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
interp_ : TransformationModelInterpolated
interpol_xs_ : IsotopeWaveletTransform< PeakType >
interpol_ys_ : IsotopeWaveletTransform< PeakType >
interpolate_precursor_purity_ : IsobaricChannelExtractor
interpolation_ : InterpolationModel
interpolation_mode_ : MultiGradient
interpolation_step_ : Fitter1D , InterpolationModel
interpretation_list_ : IncludeExcludeTarget , TraMLProduct
ints_32 : MzMLHandlerHelper::BinaryData
ints_64 : MzMLHandlerHelper::BinaryData
intsum_alpha : OPXLDataStructs::CrossLinkSpectrumMatch
intsum_beta : OPXLDataStructs::CrossLinkSpectrumMatch
inv_table_steps_ : IsotopeWavelet
inventory_ : Factory< FactoryProduct > , SingletonRegistry
IOG : IsoSpecOrderedGeneratorWrapper
ion_cutoff_percentage_ : SequestInfile
ion_detectors_ : Instrument
ion_ladder_visible_ : Plot1DCanvas
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_types : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
ionization : SiriusMSFile::CompoundInfo
ionization_method_ : IonSource , IonSourceVisualizer
ionization_type_ : IonizationSimulation
iontype : Interpretation
is_absdiff_small_ : FuzzyStringComparator
is_active_ : ChargePair , DataFilters
IS_actual_concentration : AbsoluteQuantitationStandards::featureConcentration , AbsoluteQuantitationStandards::runConcentration
IS_component_name : AbsoluteQuantitationStandards::runConcentration
is_decoy : ParentSequence , IDFilter::HasDecoyAnnotation< HitType >
is_decoy_ : OSWTransition
is_end_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::Param , MatchedIterator< CONT_T, TRAIT, CONST_T >
IS_feature : AbsoluteQuantitationStandards::featureConcentration
is_first_time_loading_ : SpectraIDViewTab
is_initialized_ : AccurateMassSearchEngine
is_instantiated_ : ModificationsDB
is_internal : ToolDescriptionInternal
is_inverse_orientation_ : AxisWidget
is_isotope_1_mono : CompNovoIonScoringBase::IonScore
is_log_ : AxisWidget
IS_name_ : AbsoluteQuantitationMethod
is_number : FuzzyStringComparator::StreamElement_
is_openpepxl_ : XQuestResultXMLHandler
is_positive : FLASHDeconvHelperStructs::LogMzPeak
is_positive_ : FLASHDeconvAlgorithm , PeakGroup
is_prefix : DecoyHelper::Result , FalseDiscoveryRate::DecoyStringHelper::Result
is_protein_note_ : XTandemXMLFile
is_protein_terminus_ : PepXMLFile::AminoAcidModification
is_ready_ : PythonModuleRequirement
is_repeatable_ : CVMappingTerm
is_running_ : StopWatch
is_sorted : MSSpectrum::Chunk
is_space : FuzzyStringComparator::StreamElement_
is_spectrum_note_ : XTandemXMLFile
is_status_success_ : FuzzyStringComparator
is_targeted_ : PeakGroup
is_variable_ : PepXMLFile::AminoAcidModification
isd_group : ProteinResolver::MSDGroup , ProteinResolver::PeptideEntry , ProteinResolver::ProteinEntry
isds : ProteinResolver::ResolverResult
iso_ : MassAnalyzerVisualizer
iso_da_distance_ : FLASHDeconvAlgorithm , PeakGroup
iso_distrib_ : FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound
iso_gen_ : FeatureFinderAlgorithmMetaboIdent
iso_map_ : TwoDOptimization
iso_map_iter : TwoDOptimization::Data
iso_number_ms2_negative : IsobaricQuantifierStatistics
iso_number_reporter_different : IsobaricQuantifierStatistics
iso_number_reporter_negative : IsobaricQuantifierStatistics
iso_offset : FLASHDeconvHelperStructs::MassFeature
iso_pattern_ : FeatureHypothesis
iso_score : SiriusMzTabWriter::SiriusAdapterHit
iso_similarity_ : AccurateMassSearchEngine
iso_solution_different_intensity : IsobaricQuantifierStatistics
iso_total_intensity_negative : IsobaricQuantifierStatistics
isolation_width_ : MassAnalyzer
isolation_window_size_ : FLASHDeconvAlgorithm
isotope : NucleicAcidSearchEngine::PrecursorInfo
isotope_correction_enabled_ : IsobaricQuantifier
isotope_corrections_ : ITRAQLabeler
isotope_correlation : OpenSwath_Scores
isotope_cosine_score_ : PeakGroup
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_pmin_ : FeatureFinderAlgorithmMetaboIdent , FeatureFinderIdentificationAlgorithm
isotope_probs_ : FeatureFinderAlgorithmMetaboIdent , FeatureFinderIdentificationAlgorithm
isotope_score : FLASHDeconvHelperStructs::MassFeature
isotope_stdev_ : ExtendedIsotopeFitter1D , ExtendedIsotopeModel , IsotopeFitter1D , IsotopeModel
ISOTOPECORRECTIONS_EIGHTPLEX : ItraqConstants
ISOTOPECORRECTIONS_FOURPLEX : ItraqConstants
ISOTOPECORRECTIONS_TMT_SIXPLEX : ItraqConstants
isotopeIndex : FLASHDeconvHelperStructs::LogMzPeak
isotopes_ : Element , FLASHDeconvHelperStructs::PrecalculatedAveragine , IMSElement
isotopes_per_peptide_max_ : FeatureFinderMultiplexAlgorithm , MultiplexFiltering
isotopes_per_peptide_min_ : FeatureFinderMultiplexAlgorithm , MultiplexFiltering
isotopes_sim_score_ : AccurateMassSearchResult
isotopomer : MzTabMSmallMoleculeFeatureSectionRow
it_ : ConsensusXMLHandler
it_q_ : ACTrieState
it_query : ACSpawn
it_ref_ : MatchedIterator< CONT_T, TRAIT, CONST_T >
it_tgt_ : MatchedIterator< CONT_T, TRAIT, CONST_T >
item_ : shared_xerces_ptr< T > , unique_xerces_ptr< T >
itemenclosed_ : CsvFile
items : FileTypeList::FilterElements_ , IDFilter::GetMatchingItems< HitType, Entry >
items_ : FilterableList
items_wo_bl_ : FilterableList
itemseperator_ : CsvFile
ITG : IsoSpecThresholdGeneratorWrapper , IsoSpecThresholdWrapper
itraq_type_ : ITRAQLabeler