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

- i -

i : Base64::Reinterpreter32_, Base64::Reinterpreter64_
i_ : Index
IA_CHARGE_INDEX : NuXLConstants
IA_DENOVO_TAG_INDEX : NuXLConstants
IA_RANK_INDEX : NuXLConstants
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, IDMergerAlgorithm, IdXMLFile, Identification, IdentificationHit, MzIdentMLHandler, SpectrumIdentification, OSWProtein, OSWTransition, PeptideIdentification, ProteinIdentification, QTCluster::BulkData, ResidueModification
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
ida_log_file_ : FLASHDeconvAlgorithm
idec : MzIdentMLDOMHandler::PeptideEvidence
ident_run_idx : IDRipper::RipFileIdentifier
identification_date_ : ProteinIdentificationVisualizer
identification_method : MzTabMSmallMoleculeEvidenceSectionRow
identification_rate : Ms2IdentificationRate::IdentificationRateData
identification_threshold_ : PeptideIdentificationVisualizer, ProteinIdentificationVisualizer
identified : IDMapper::PeptideIdentificationListState
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
identifier_ : Acquisition, CVMappingRule, CVReference, DocumentIdentifierVisualizer, MascotXMLHandler, PeptideIdentificationVisualizer, ProteinIdentificationVisualizer
identifier_id_ : ConsensusXMLHandler, FeatureXMLHandler
identifier_to_msrunpath : ProteinIdentification::Mapping
identifying : TransitionFlags
identifying_transition : TransitionTSVFile::TSVTransition
idrunid_2_idrunindex_ : MzTab::CMMzTabStream, MzTab::IDMzTabStream
ids : FeatureFinderIdentificationAlgorithm::RTRegion
ids_ : LayerStatisticsIdent, LayerStoreDataIdentVisible, SpectrumLookup
idview_controller_ : DataSelectionTabs
idx : MassTraceDetection::PeakCandidate
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_iso_calib_ : Biosaur2Algorithm
ignore_missed_cleavages_ : IDFilter::DigestionFilter
ignore_update : SpectraIDViewTab
IL_equivalent_ : PeptideIndexing
ILG : IsoSpecTotalProbGeneratorWrapper, IsoSpecTotalProbWrapper
im : MassTraceDetection::PeakCandidate
im_correction_function_ : SwathMapMassCorrection
im_delta : OpenSwath_Scores
im_delta_score : OpenSwath_Scores
im_drift : OpenSwath_Scores
im_drift_extra_pcnt_ : OpenSwathScoring
im_drift_left : OpenSwath_Scores
im_drift_right : OpenSwath_Scores
im_drift_weighted : OpenSwath_Scores
im_estimation_padding_factor_ : SwathMapMassCorrection
im_extra_drift_ : MRMFeatureFinderScoring
im_extraction_window : ChromExtractParams
im_extraction_window_ : SwathMapMassCorrection
im_fwhm_idx_ : MassTraceDetection
im_ind_contrast_coelution : OpenSwath_Scores
im_ind_contrast_shape : OpenSwath_Scores
im_ind_sum_contrast_coelution : OpenSwath_Scores
im_ind_sum_contrast_shape : OpenSwath_Scores
im_log_intensity : OpenSwath_Scores
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_stats_ : FeatureFinderIdentificationAlgorithm
im_tolerance_cluster_ : PeakPickerIM
im_type_ : SpectrumSettings
im_window_ : FeatureFinderAlgorithmMetaboIdent
im_xcorr_coelution_score : OpenSwath_Scores
im_xcorr_shape_score : OpenSwath_Scores
imLower : SwathMap
immonium_score : NuXLAnnotatedHit
imUpper : SwathMap
in_description_ : FeatureXMLHandler
in_edges_ : TOPPASVertex
in_ini_section_ : ToolDescriptionHandler
in_spectrum_list_ : MzMLHandler
inchi : IdentifiedCompound, MzTabMSmallMoleculeEvidenceSectionRow, MzTabMSmallMoleculeSectionRow
inchi_key : MzTabSmallMoleculeSectionRow
inchi_string_ : SpectralMatch
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_apex_position : OpenSwath_Ind_Scores
ind_area_intensity : OpenSwath_Ind_Scores
ind_asymmetry_factor : OpenSwath_Ind_Scores
ind_baseline_delta_2_height : OpenSwath_Ind_Scores
ind_end_position_at_10 : OpenSwath_Ind_Scores
ind_end_position_at_5 : OpenSwath_Ind_Scores
ind_end_position_at_50 : OpenSwath_Ind_Scores
ind_fwhm : OpenSwath_Ind_Scores
ind_im_contrast_coelution : OpenSwath_Ind_Scores
ind_im_contrast_shape : OpenSwath_Ind_Scores
ind_im_delta : OpenSwath_Ind_Scores
ind_im_delta_score : OpenSwath_Ind_Scores
ind_im_drift : OpenSwath_Ind_Scores
ind_im_drift_left : OpenSwath_Ind_Scores
ind_im_drift_right : OpenSwath_Ind_Scores
ind_im_log_intensity : OpenSwath_Ind_Scores
ind_im_sum_contrast_coelution : OpenSwath_Ind_Scores
ind_im_sum_contrast_shape : 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_points_across_baseline : OpenSwath_Ind_Scores
ind_points_across_half_height : OpenSwath_Ind_Scores
ind_slope_of_baseline : OpenSwath_Ind_Scores
ind_start_position_at_10 : OpenSwath_Ind_Scores
ind_start_position_at_5 : OpenSwath_Ind_Scores
ind_start_position_at_50 : OpenSwath_Ind_Scores
ind_tailing_factor : OpenSwath_Ind_Scores
ind_total_area_intensity : OpenSwath_Ind_Scores
ind_total_mi : OpenSwath_Ind_Scores
ind_total_width : 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 : FLASHHelperClasses::MassFeature, ChromatogramMeta, SpectrumMeta, PeakCandidate, 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
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_size_ : DistanceMatrix< Value >
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, XTandemInfile
input_files_ : IdentificationData
input_line_1_ : FuzzyStringComparator
input_line_2_ : FuzzyStringComparator
insert_pos : Args
inside_ : LinearInterpolation< Key, Value >
inside_0_ : BilinearInterpolation< Key, Value >
inside_1_ : BilinearInterpolation< Key, Value >
instance_ : LogConfigHandler, UniqueIdGenerator
instance_number_ : TOPPBase
institution_ : ContactPerson, ContactPersonVisualizer
instrument : MzTabMetaData, MzTabMMetaData
instrument_ : ExperimentalSettings, HPLC, InspectInfile
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_scale_ : Plot3DOpenGLCanvas
int_sum : OPXLDataStructs::CrossLinkSpectrumMatch
integer_data_arrays_ : Mobilogram, MSChromatogram, MSSpectrum, ProteinIdentification::ProteinGroup
integrated_intensities_ : PeakPickerChromatogram, PeakPickerMobilogram
integrated_intensity : PeakCandidate
integration_type_ : PeakIntegrator
INTEGRATION_TYPE_INTENSITYSUM : PeakIntegrator
INTEGRATION_TYPE_SIMPSON : PeakIntegrator
INTEGRATION_TYPE_TRAPEZOID : PeakIntegrator
intensities : Biosaur2Algorithm::Hill, TIC::Result
intensity : FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern, FeatureFinderAlgorithmPickedHelperStructs::Seed, FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern, FLASHHelperClasses::LogMzPeak, MassTraceDetection::Apex, MassTraceDetection::PeakCandidate, NuXLFragmentAnnotationHelper::FragmentAnnotationDetail_, OpenSwath_Scores, PeptideHit::PeakAnnotation
intensity_ : ChromatogramPeak, MobilityPeak1D, MobilityPeak2D, MultiplexSatelliteProfile, Peak1D, Peak2D, PeakGroup, TriqlerFile::TriqlerLine_
intensity_apex : Biosaur2Algorithm::Hill, Biosaur2Algorithm::PeptideFeature
INTENSITY_AXIS_TITLE : PlotWidget
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_sum : Biosaur2Algorithm::Hill, Biosaur2Algorithm::PeptideFeature
intensity_thresholds_ : FeatureFinderAlgorithmPicked
intensity_u : MRMFeatureQC::ComponentGroupQCs, MRMFeatureQC::ComponentQCs
intercept : ConfidenceScoring::GLM_
intercept_ : LinearRegression, TransformationModelLinear
interfering_peak_count : PrecursorPurity::PurityScores
interfering_peaks : PrecursorPurity::PurityScores
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
internal_to_zp1_monoweight_ : Residue
internal_to_zp2_monoweight_ : Residue
interp_ : TransformationModelInterpolated
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
IOG : IsoSpecOrderedGeneratorWrapper
ion_cutoff_percentage_ : SequestInfile
ion_detectors_ : Instrument
ion_ladder_visible_ : Plot1DCanvas
ion_mobilities : Biosaur2Algorithm::Hill
ion_mobilities_ : FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound
ion_mobility : Biosaur2Algorithm::PeptideFeature, ChromatogramExtractorAlgorithm::ExtractionCoordinates
ion_mobility_idx_ : MassTraceDetection
ion_mobility_median : Biosaur2Algorithm::Hill
ion_mobility_tolerance_ : MassTraceDetection
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
ionization : SiriusMSFile::CompoundInfo
ionization_method_ : IonSource, IonSourceVisualizer
iontype : Interpretation
is_absdiff_small_ : FuzzyStringComparator
is_active_ : ChargePair, DataFilters
IS_actual_concentration : AbsoluteQuantitationStandards::featureConcentration, AbsoluteQuantitationStandards::runConcentration
is_build_ : FragmentIndex
IS_component_name : AbsoluteQuantitationStandards::runConcentration
is_decoy : FLASHHelperClasses::MassFeature, 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_log_ : AxisWidget
is_main_score_type : IDScoreSwitcherAlgorithm::ScoreSearchResult
IS_name_ : AbsoluteQuantitationMethod
is_number : FuzzyStringComparator::StreamElement_
is_openpepxl_ : XQuestResultXMLHandler
is_positive : FLASHHelperClasses::LogMzPeak
is_positive_ : PeakGroup, SpectralDeconvolution
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
iso_ : MassAnalyzerVisualizer
iso_count_for_DL_scoring_ : PeakGroupScoring
iso_da_distance_ : PeakGroup, SpectralDeconvolution
iso_distrib_ : FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound
iso_gen_ : FeatureFinderAlgorithmMetaboIdent
iso_number_ms2_negative : IsobaricQuantifierStatistics
iso_number_reporter_different : IsobaricQuantifierStatistics
iso_number_reporter_negative : IsobaricQuantifierStatistics
iso_offset : FLASHHelperClasses::MassFeature
iso_pattern_ : FeatureHypothesis
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_correlation : OpenSwath_Scores
isotope_cosine_score_ : PeakGroup
isotope_distance_ : ExtendedIsotopeModel, IsotopeModel
isotope_distribution_ : IsotopeModel
isotope_distributions_ : FeatureFinderAlgorithmPicked
isotope_error : NuXLAnnotatedHit, PeptideSearchEngineFIAlgorithm::AnnotatedHit_, SimpleSearchEngineAlgorithm::AnnotatedHit_
isotope_error_ : FragmentIndex::SpectrumMatch
isotope_filt_svm_ : FeatureFindingMetabo
isotope_filtering_model_ : FeatureFindingMetabo
isotope_label_type_ : MSstatsFile::MSstatsLine_
isotope_lorentz_fwhm_ : IsotopeModel
isotope_model_ : TheoreticalSpectrumGenerator
isotope_number : Biosaur2Algorithm::IsotopeCandidate
isotope_overlap : OpenSwath_Scores
isotope_pmin_ : FeatureFinderAlgorithmMetaboIdent, FeatureFinderIdentificationAlgorithm
isotope_probs_ : FeatureFinderAlgorithmMetaboIdent, FeatureFinderIdentificationAlgorithm
isotope_score : FLASHHelperClasses::MassFeature
isotope_stdev_ : ExtendedIsotopeFitter1D, ExtendedIsotopeModel, IsotopeFitter1D, IsotopeModel
ISOTOPECORRECTIONS_EIGHTPLEX : ItraqConstants
ISOTOPECORRECTIONS_FOURPLEX : ItraqConstants
ISOTOPECORRECTIONS_TMT_SIXPLEX : ItraqConstants
isotopeIndex : FLASHHelperClasses::LogMzPeak
isotopes : Biosaur2Algorithm::PatternCandidate, Biosaur2Algorithm::PeptideFeature
isotopes_ : Element, FLASHHelperClasses::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 : ACScout
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
itol_ : Biosaur2Algorithm
iuse_ : Biosaur2Algorithm
ivf_ : Biosaur2Algorithm