- a -

• A : GaussFitter::GaussFitResult
• a : GumbelDistributionFitter::GumbelDistributionFitResult , GumbelMaxLikelihoodFitter::GumbelDistributionFitResult
• a_ : CubicSpline2d , QuadraticRegression , SpectrumAccessQuadMZTransforming , TOFCalibration
• a_intensity_ : NucleicAcidSpectrumGenerator , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• aa_ : AA
• aa_after_ : PeptideEvidence
• aa_before_ : PeptideEvidence
• aaa_max_ : PeptideIndexing
• aamass_ : GoodDiffFilter
• aB_intensity_ : NucleicAcidSpectrumGenerator
• abort_reasons_ : FeatureFinderAlgorithmPicked
• aborts_ : FeatureFinderAlgorithmPicked
• abs_charge : FLASHDeconvHelperStructs::LogMzPeak
• abs_prec_error : RNPxlReportRow
• absdiff_max_ : FuzzyStringComparator
• absdiff_max_allowed_ : FuzzyStringComparator
• absolute_ : FineIsotopePatternGenerator
• abundance : IMSIsotopeDistribution::Peak
• abundances : PeptideAndProteinQuant::PeptideData , PeptideAndProteinQuant::ProteinData
• ABUNDANCES_SUM_ERROR : IMSIsotopeDistribution
• abundant_mono_mass_difference_ : FLASHDeconvHelperStructs::PrecalculatedAveragine
• ac_mode_ : IonDetectorVisualizer
• acc_ : MassAnalyzerVisualizer
• accdelim_ : MSstatsFile , TriqlerFile
• accession : CVTerm::Unit , ParentSequence , MzIdentMLDOMHandler::DBSequence , SemanticValidator::CVTerm , MzTabNucleicAcidSectionRow , MzTabOligonucleotideSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow
• accession_ : CVMappingTerm , CVTerm , MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , MzTabParameter , OSWProtein , PeptideEvidence , ProteinHit , TriqlerFile::TriqlerLine_
• accession_att_ : SemanticValidator
• accession_resolver_ : IDFilter::DigestionFilter
• accession_to_id_ : ConsensusXMLHandler , FeatureXMLHandler
• accessions : IDFilter::HasMatchingAccession< HitType > , IDFilter::HasMatchingAccessionUnordered< HitType > , PeptideAndProteinQuant::PeptideData , ProteinIdentification::ProteinGroup , RNPxlReportRow
• accessions_ : XQuestResultXMLHandler , PSProteinInference
• accumulated_times_ : StopWatch
• accuracy_ : MassAnalyzer
• acetyl : MQExporterHelper::MQCommonOutputs
• acquisition_info_ : ChromatogramSettings , SpectrumSettings
• acquisition_mode_ : IonDetector
• acquisitioninfo_method_ : AcquisitionInfoVisualizer
• acquisitionnumber_ : AcquisitionVisualizer
• ACSpawn : ACTrieState
• act_cons_element_ : ConsensusXMLHandler
• action_ : TOPPViewMenu::ActionRequirement_
• action_mode_ : PlotCanvas , TOPPASScene
• actions : ProcessingStep
• actions_ : DataProcessingVisualizer
• activate_count_ : FASTAContainer< TFI_Vector >
• activation_energy_ : Precursor , PrecursorVisualizer
• activation_method_ : DeconvolvedSpectrum
• activation_methods_ : Precursor , PrecursorVisualizer
• active : ItraqConstants::ChannelInfo
• actual_aa_sequences_ : PepXMLFileMascot
• actual_compound_ : TraMLHandler
• actual_concentration : AbsoluteQuantitationStandards::featureConcentration , AbsoluteQuantitationStandards::runConcentration
• actual_configuration_ : TraMLHandler
• actual_contact_ : TraMLHandler
• actual_instrument_ : TraMLHandler
• actual_intermediate_products_ : TraMLHandler
• actual_interpretation_ : TraMLHandler
• actual_mod_site_ : OMSSAXMLFile
• actual_mod_type_ : OMSSAXMLFile
• actual_modifications_ : PepXMLFileMascot
• actual_peptide_ : MzIdentMLHandler , TraMLHandler
• actual_peptide_evidence_ : MascotXMLHandler , OMSSAXMLFile
• actual_peptide_evidences_ : OMSSAXMLFile
• actual_peptide_hit_ : MascotXMLHandler , OMSSAXMLFile
• actual_peptide_id_ : OMSSAXMLFile
• actual_prediction_ : TraMLHandler
• actual_product_ : TraMLHandler
• actual_protein_ : MzIdentMLHandler , TraMLHandler
• actual_protein_hit_ : MascotXMLHandler , OMSSAXMLFile
• actual_protein_id_ : OMSSAXMLFile
• actual_publication_ : TraMLHandler
• actual_query_ : MascotXMLHandler
• actual_rt_ : TraMLHandler
• actual_rule_ : CVMappingFile
• actual_sequence_ : PepXMLFileMascot
• actual_software_ : TraMLHandler
• actual_sourcefile_ : TraMLHandler
• actual_target_ : TraMLHandler
• actual_title_ : MascotXMLHandler , PepXMLFileMascot
• actual_transition_ : TraMLHandler
• actual_validation_ : TraMLHandler
• ADC_sampling_frequency_ : IonDetector
• add_2d_context_ : TOPPViewBase
• add_a_ions_ : NucleicAcidSpectrumGenerator , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_aB_ions_ : NucleicAcidSpectrumGenerator
• add_abundant_immonium_ions_ : SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_all_precursor_charges_ : NucleicAcidSpectrumGenerator , TheoreticalSpectrumGenerator
• add_b_ions_ : NucleicAcidSpectrumGenerator , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_c_ions_ : NucleicAcidSpectrumGenerator , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_charges_ : SimpleTSGXLMS , TheoreticalSpectrumGeneratorXLMS
• add_d_ions_ : NucleicAcidSpectrumGenerator
• add_dataprocessing_ : MSDataWritingConsumer
• add_eluent_button_ : GradientVisualizer
• add_first_prefix_ion_ : NucleicAcidSpectrumGenerator , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_isotopes_ : SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_k_linked_ions_ : SimpleTSGXLMS , TheoreticalSpectrumGeneratorXLMS
• add_losses_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_mass_offset_peptides_ : FeatureFinderIdentificationAlgorithm
• add_metainfo_ : NucleicAcidSpectrumGenerator , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_precursor_peaks_ : NucleicAcidSpectrumGenerator , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_timepoint_button_ : GradientVisualizer
• add_up_spectra_ : MRMFeatureFinderScoring , OpenSwathScoring
• add_w_ions_ : NucleicAcidSpectrumGenerator
• add_x_ions_ : NucleicAcidSpectrumGenerator , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_y_ions_ : NucleicAcidSpectrumGenerator , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_z_ions_ : NucleicAcidSpectrumGenerator , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• addbutton_ : MetaInfoVisualizer
• additional_dataprocessing_ : MSDataWritingConsumer
• address_ : ContactPerson , ContactPersonVisualizer
• adduct : NucleicAcidSearchEngine::PrecursorInfo , CsiFingerIdMzTabWriter::CsiAdapterHit , MzTabMSmallMoleculeEvidenceSectionRow , MzTabMSmallMoleculeFeatureSectionRow , SiriusMzTabWriter::SiriusAdapterHit
• adduct_base_ : MassExplainer
• adduct_keys_ : OMSFileStore
• adduct_opt : ObservationMatch
• adduct_refs : IdentificationData::RefTranslator
• adduct_refs_ : OMSFileLoad
• adducts : MzTabMSmallMoleculeSectionRow
• Adducts : TransitionTSVFile::TSVTransition
• adducts_ : IdentificationData
• advanced : ParameterInformation
• advanced_mode_ : ParamEditor
• affected_amino_acids_ : Modification
• affected_channels : IsobaricQuantitationMethod::IsobaricChannelInformation
• affiliation : MzTabContactMetaData
• affixes : DecoyHelper
• align_algorithm_ : MapAlignmentAlgorithmTreeGuided
• aligned_peaks_indices_ : Plot1DCanvas
• aligned_peaks_mz_delta_ : Plot1DCanvas
• alignment_ : AxisWidget , ConsensusIDAlgorithmPEPMatrix
• alignment_layer_1_ : Plot1DCanvas
• alignment_layer_2_ : Plot1DCanvas
• alignment_score_ : Plot1DCanvas
• all_contaminants_ratio : Contaminants::ContaminantsSummary
• all_prefix_occur : DecoyHelper::DecoyStatistics
• ALL_PROTEINS : OSWFile
• all_proteins_count : DecoyHelper::DecoyStatistics
• all_suffix_occur : DecoyHelper::DecoyStatistics
• allow_children_ : CVMappingTerm
• allow_isotope_error_ : XTandemInfile
• allow_missing : IdentificationData::RefTranslator
• allow_nterm_protein_cleavage_ : PeptideIndexing
• allow_output_recycling_ : TOPPASVertex
• allow_short_numbers_ : AxisWidget
• allowed_iso_error_ : FLASHDeconvAlgorithm
• allowed_threads_ : TOPPASScene
• alpha : OPXLDataStructs::ProteinProteinCrossLink
• alpha255_ : Annotation1DVerticalLineItem
• alpha_ : MessagePasserFactory< Label >
• alpha_index : OPXLDataStructs::XLPrecursor
• alpha_seq : OPXLDataStructs::XLPrecursor
• alphabet_ : IntegerMassDecomposer< ValueType, DecompositionValueType > , MassDecompositionAlgorithm
• alphabet_masses_ : Weights
• already_used_ : QTClusterFinder
• always_append_data_ : PeakFileOptions
• ambig_features : PeptideAndProteinQuant::Statistics
• ambiguity_map_ : RibonucleotideDB
• ambiguity_members : MzTabNucleicAcidSectionRow , MzTabProteinSectionRow
• ambiguous_mods_ : NucleicAcidSearchEngine
• aminoacid_ : PepXMLFile::AminoAcidModification
• amount_ : Adduct
• analysis_results_ : PeptideHit
• analysis_summary_ : MSQuantifications , PepXMLFile
• analyzer : MzTabInstrumentMetaData
• anchorPoints_ : MapAlignmentAlgorithmSpectrumAlignment
• annotate_psm_ : SimpleSearchEngineAlgorithm
• annotation : PeptideHit::PeakAnnotation
• Annotation : TransitionTSVFile::TSVTransition
• annotation_ : OSWTransition
• annotations : NucleicAcidSearchEngine::AnnotatedHit
• annotations_ : GridFeature , QTCluster::BulkData
• annotations_1d_ : LayerData1DBase
• apex_index_ : FLASHDeconvHelperStructs::PrecalculatedAveragine
• apex_pos : PeakIntegrator::PeakArea
• apex_rt_ : EGHTraceFitter
• arch_ : OpenMSOSInfo
• area : PeakIntegrator::PeakArea , PeakIntegrator::PeakBackground , PeakShape , TIC::Result
• AreaIterator : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::Param
• arg_binsize_ : XFDRAlgorithm
• arg_maxborder_ : XFDRAlgorithm
• arg_minborder_ : XFDRAlgorithm
• arg_mindeltas_ : XFDRAlgorithm
• arg_minionsmatched_ : XFDRAlgorithm
• arg_minscore_ : XFDRAlgorithm
• arg_no_qvalues_ : XFDRAlgorithm
• arg_param_ : ToolsDialog , TOPPASToolConfigDialog
• arg_uniquex_ : XFDRAlgorithm
• args : Command , TOPPASScene::TOPPProcess
• argument : ParameterInformation
• as_map_ : MzIdentMLDOMHandler
• AScore : ProbablePhosphoSites
• assay : MzTabMetaData , MzTabMMetaData
• assay_refs : MzTabMStudyVariableMetaData , MzTabStudyVariableMetaData
• assays_ : MSQuantifications
• assigned_contaminants_intensity_ratio : Contaminants::ContaminantsSummary
• assigned_contaminants_ratio : Contaminants::ContaminantsSummary
• assigned_scores : ProcessingSoftware
• assignedMS2 : FeatureMapping::FeatureToMs2Indices
• asymmetry_factor : PeakIntegrator::PeakShapeMetrics
• at_ : QcMLFile
• atomic_number_ : Element
• atomic_numbers_ : ElementDB
• ats_ : QcMLFile
• authors : Citation
• auto_max_percentile_ : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• auto_max_stdev_Factor_ : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• AUTO_MODE : PeptideIndexing
• auto_mode_ : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• av_MZ_spacing_ : IsotopeWaveletTransform< PeakType >
• average_correctness : PSMExplainedIonCurrent::Statistics
• average_function : MzTabMStudyVariableMetaData
• average_mass_ : ResidueModification
• average_mono_mass_difference_ : FLASHDeconvHelperStructs::PrecalculatedAveragine
• average_ppm : FragmentMassError::Statistics
• average_weight_ : Element , Residue
• averagine_ : ExtendedIsotopeModel , IsotopeModel , IsotopeWavelet
• averagine_similarity_ : MultiplexFiltering
• averagine_similarity_scaling_ : MultiplexFiltering
• averagine_type_ : MultiplexFiltering
• avg_ : FLASHDeconvAlgorithm
• avg_da_error_ : PeakGroup
• avg_distance_ : ClusterProxyKD
• avg_mass : FLASHDeconvHelperStructs::MassFeature
• avg_mass_ : Ribonucleotide
• avg_mass_delta : Peptide::Modification
• avg_ppm_error_ : PeakGroup
• avge_mass_ : UnimodXMLHandler
• axes_ : Plot3DOpenGLCanvas
• axes_ticks_ : Plot3DOpenGLCanvas