| OpenMS 2.5.0

### - a -

- A : GaussFitter::GaussFitResult
- a : GumbelDistributionFitter::GumbelDistributionFitResult , GumbelMaxLikelihoodFitter::GumbelDistributionFitResult
- a_ : CubicSpline2d
- A_ : EGHModel , LocalLinearMap
- a_ : QuadraticRegression , SpectrumAccessQuadMZTransforming , TOFCalibration
- a_intensity_ : NucleicAcidSpectrumGenerator , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
- AA : MS2Info
- aa_after_ : PeptideEvidence
- aa_before_ : PeptideEvidence
- aa_to_index_ : SvmTheoreticalSpectrumGenerator
- aa_to_weight_ : CompNovoIdentificationBase
- aaa_max_ : PeptideIndexing
- AAAfter : PeptideIndexing::PeptideProteinMatchInformation
- AABefore : PeptideIndexing::PeptideProteinMatchInformation
- aamass_ : GoodDiffFilter
- AAname : EnzymaticDigestionLogModel::BindingSite_
- aB_intensity_ : NucleicAcidSpectrumGenerator
- abort_reasons_ : FeatureFinderAlgorithmPicked
- aborts_ : FeatureFinderAlgorithmPicked
- abs_prec_error : RNPxlReportRow
- absdiff_max_ : FuzzyStringComparator
- absdiff_max_allowed_ : FuzzyStringComparator
- absolute_ : FineIsotopePatternGenerator
- abundance : IMSIsotopeDistribution::Peak , SIPIncorporation
- abundances : PeptideAndProteinQuant::PeptideData , PeptideAndProteinQuant::ProteinData
- ABUNDANCES_SUM_ERROR : IMSIsotopeDistribution
- AC : MS2Info
- ac_mode_ : IonDetectorVisualizer
- acc_ : MassAnalyzerVisualizer
- accdelim_ : MSstatsFile
- accession : CVTerm::Unit , ParentMolecule , MzIdentMLDOMHandler::DBSequence , SemanticValidator::CVTerm , MzTabNucleicAcidSectionRow , MzTabOligonucleotideSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow
- accession_ : CVMappingTerm , CVTerm , MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , MzTabParameter , PeptideEvidence , ProteinHit
- accession_att_ : SemanticValidator
- accession_resolver_ : IDFilter::DigestionFilter
- accession_to_id_ : ConsensusXMLFile , FeatureXMLFile
- accessions : IDFilter::HasMatchingAccession< HitType > , IDFilter::HasMatchingAccessionUnordered< HitType > , PeptideAndProteinQuant::PeptideData , ProteinIdentification::ProteinGroup , RNPxlReportRow , SIPPeptide
- accessions_ : XQuestResultXMLHandler , PSProteinInference
- accumulated : SIPPeptide
- accuracy_ : MassAnalyzer
- acquisition_info_ : ChromatogramSettings , SpectrumSettings
- acquisition_mode_ : IonDetector
- acquisitioninfo_method_ : AcquisitionInfoVisualizer
- acquisitionnumber_ : AcquisitionVisualizer
- act_cons_element_ : ConsensusXMLFile
- action_mode_ : SpectrumCanvas , TOPPASScene
- actions : DataProcessingStep
- actions_ : DataProcessingVisualizer
- activate_count_ : FASTAContainer< TFI_Vector >
- activation_energy_ : Precursor , PrecursorVisualizer
- 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 , SiriusMzTabWriter::SiriusAdapterHit
- adduct_base_ : MassExplainer
- Adducts : TransitionTSVFile::TSVTransition
- advanced : ParameterInformation
- advanced_mode_ : ParamEditor
- affected_amino_acids_ : Modification
- affiliation : MzTabContactMetaData
- align_algorithm_ : MapAlignmentAlgorithmTreeGuided
- aligned_peaks_indices_ : Spectrum1DCanvas
- aligned_peaks_mz_delta_ : Spectrum1DCanvas
- alignment_ : AxisWidget , ConsensusIDAlgorithmPEPMatrix
- ALIGNMENT_ERROR : LCMS
- alignment_error_down : SHFeature
- alignment_error_up : SHFeature
- alignment_layer_1_ : Spectrum1DCanvas
- alignment_layer_2_ : Spectrum1DCanvas
- alignment_score_ : Spectrum1DCanvas
- all_contaminants_ratio : Contaminants::ContaminantsSummary
- allow_children_ : CVMappingTerm
- allow_isotope_error_ : XTandemInfile
- allow_output_recycling_ : TOPPASVertex
- allow_short_numbers_ : AxisWidget
- allow_unmatched_ : PeptideIndexing
- allowed_threads_ : TOPPASScene
- alpha : OPXLDataStructs::ProteinProteinCrossLink
- 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
- ambAA_seen : Spawn< TNeedle >
- 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
- annotation : PeptideHit::PeakAnnotation
- Annotation : TransitionTSVFile::TSVTransition
- annotations : NucleicAcidSearchEngine::AnnotatedHit
- annotations_ : GridFeature , QTCluster
- annotations_1d : LayerData
- APEX : LCElutionPeak
- apex_peak_intensity : SHFeature
- apex_pos : PeakIntegrator::PeakArea
- apex_rt_ : EGHModel , EGHTraceFitter
- apexMS1Signal : FeatureLCProfile
- apexScan : MS2ConsensusSpectrum
- arch : OpenMSOSInfo
- area : PeakIntegrator::PeakArea , PeakIntegrator::PeakBackground , PeakShape
- arg_binsize_ : XFDRAlgorithm
- arg_map_ : ToolsDialog
- 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 : TOPPASScene::TOPPProcess
- argument : ParameterInformation
- as_map_ : MzIdentMLDOMHandler
- AScore : ProbablePhosphoSites
- assay : MzTabMetaData
- assay_refs : MzTabStudyVariableMetaData
- assays_ : MSQuantifications
- assigned_contaminants_intensity_ratio : Contaminants::ContaminantsSummary
- assigned_contaminants_ratio : Contaminants::ContaminantsSummary
- assigned_scores : DataProcessingSoftware
- assignedMS2 : FeatureMapping::FeatureToMs2Indices
- asymmetry_factor : PeakIntegrator::PeakShapeMetrics
- at_ : QcMLFile
- atomic_number_ : Element
- atomic_numbers_ : ElementDB
- ats_ : QcMLFile
- attachment_ : MRMFeatureFilter
- authors : Citation
- auto_charge_ : SiriusAdapterAlgorithm
- auto_max_percentile_ : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
- auto_max_stdev_Factor_ : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
- auto_mode_ : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
- av_MZ_spacing_ : IsotopeWaveletTransform< PeakType >
- average_mass_ : ResidueModification
- average_ppm : FragmentMassError::FMEStatistics
- average_weight_ : Element , Residue
- averagine_ : ExtendedIsotopeModel , IsotopeModel , IsotopeWavelet
- averagine_similarity_ : MultiplexFiltering
- averagine_similarity_scaling_ : MultiplexFiltering
- averagine_type_ : MultiplexFiltering
- avg : LayerStatisticsDialog::MetaStatsValue_
- avg_charge_ : LayerStatisticsDialog
- avg_distance_ : ClusterProxyKD
- avg_elements_ : LayerStatisticsDialog
- avg_intensity_ : LayerStatisticsDialog
- avg_mass_ : Ribonucleotide
- avg_mass_delta : Peptide::Modification
- avg_quality_ : LayerStatisticsDialog
- avge_mass_ : UnimodXMLHandler
- axes_ : Spectrum3DOpenGLCanvas
- axes_ticks_ : Spectrum3DOpenGLCanvas