- a -

A : GaussFitter::GaussFitResult
a : GumbelDistributionFitter::GumbelDistributionFitResult , GumbelMaxLikelihoodFitter::GumbelDistributionFitResult
a_ : CubicSpline2d
A_ : EGHModel , LocalLinearMap
a_ : QuadraticRegression , SpectrumAccessQuadMZTransforming , TOFCalibration
a_intensity_ : NucleicAcidSpectrumGenerator , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
aa_ : AA
aa_after_ : PeptideEvidence
aa_before_ : PeptideEvidence
aa_to_index_ : SvmTheoreticalSpectrumGenerator
aa_to_weight_ : CompNovoIdentificationBase
aaa_max_ : PeptideIndexing
aamass_ : GoodDiffFilter
AAname : EnzymaticDigestionLogModel::BindingSite_
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_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_ : EGHModel , 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