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

- a -

• A : GaussFitter::GaussFitResult
• a : GumbelDistributionFitter::GumbelDistributionFitResult , GumbelMaxLikelihoodFitter::GumbelDistributionFitResult
• a_ : CubicSpline2d
• A_ : EGHModel , LocalLinearMap
• a_ : QuadraticRegression , SpectrumAccessQuadMZTransforming , TOFCalibration
• a_intensity_ : NucleicAcidSpectrumGenerator , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• AA : Modification , MS2Info
• aa_after_ : PeptideEvidence
• AA_AT_CTERM : Modification
• AA_AT_NTERM : Modification
• aa_before_ : PeptideEvidence
• AA_SUBSTITUTION : ResidueModification
• aa_to_index_ : SvmTheoreticalSpectrumGenerator
• aa_to_weight_ : CompNovoIdentificationBase
• aaa_max_ : PeptideIndexing
• AAAfter : PeptideIndexing::PeptideProteinMatchInformation
• AABefore : PeptideIndexing::PeptideProteinMatchInformation
• AAIndex() : AAIndex
• aamass_ : GoodDiffFilter
• AAname : EnzymaticDigestionLogModel::BindingSite_
• AASequence() : AASequence
• AASequence::ConstIterator : AASequence::Iterator
• AASequenceIdentity() : MRMDecoy
• aB_intensity_ : NucleicAcidSpectrumGenerator
• abort_() : FeatureFinderAlgorithmPicked
• abort_reasons_ : FeatureFinderAlgorithmPicked
• abortPipeline() : TOPPASBase , TOPPASScene
• aborts_ : FeatureFinderAlgorithmPicked
• abortTOPPTool() : TOPPViewBase
• aboutToBeDestroyed() : SpectrumWidget , TOPPASWidget
• aboutToCloseId() : EnhancedTabBar , TOPPASTabBar
• abs_prec_error : RNPxlReportRow
• absdiff_max_ : FuzzyStringComparator
• absdiff_max_allowed_ : FuzzyStringComparator
• absolute_ : FineIsotopePatternGenerator
• absolutePath() : File
• AbsoluteQuantitation() : AbsoluteQuantitation
• AbsoluteQuantitationMethodFile() : AbsoluteQuantitationMethodFile
• AbsoluteQuantitationStandards() : AbsoluteQuantitationStandards
• AbsoluteQuantitationStandardsFile() : AbsoluteQuantitationStandardsFile
• ABSORPTION : InstrumentSettings
• ABSORPTION_CHROMATOGRAM : ChromatogramSettings
• abundance : IMSIsotopeDistribution::Peak
• abundance_type : IMSIsotopeDistribution
• abundances : PeptideAndProteinQuant::PeptideData , PeptideAndProteinQuant::ProteinData
• abundances_container : IMSIsotopeDistribution
• abundances_iterator : IMSIsotopeDistribution
• ABUNDANCES_SUM_ERROR : IMSIsotopeDistribution
• AC : MS2Info
• ac_mode_ : IonDetectorVisualizer
• acc_ : MassAnalyzerVisualizer
• accdelim_ : MSstatsFile
• accession : CVTerm::Unit , ParentMolecule , MzIdentMLDOMHandler::DBSequence , SemanticValidator::CVTerm , MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , 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
• accessionEqual_() : ConsensusMapMergerAlgorithm , IDMergerAlgorithm
• accessionHash_() : ConsensusMapMergerAlgorithm , IDMergerAlgorithm
• accessions : IDFilter::HasMatchingAccession< HitType > , IDFilter::HasMatchingAccessionUnordered< HitType > , PeptideAndProteinQuant::PeptideData , ProteinIdentification::ProteinGroup , RNPxlReportRow
• accessions_ : XQuestResultXMLHandler , PSProteinInference
• accumulated_times_ : StopWatch
• accumulateFilterValues() : MRMFeatureFilter
• accuracy_ : MassAnalyzer
• AccurateMassSearchEngine() : AccurateMassSearchEngine
• AccurateMassSearchResult() : AccurateMassSearchResult
• acidic() : AAIndex
• ACQMODENULL : IonDetector
• Acquisition() : Acquisition
• acquisition_info_ : ChromatogramSettings , SpectrumSettings
• acquisition_mode_ : IonDetector
• AcquisitionInfo() : AcquisitionInfo
• acquisitioninfo_method_ : AcquisitionInfoVisualizer
• AcquisitionInfoVisualizer() : AcquisitionInfoVisualizer
• AcquisitionMode : IonDetector
• acquisitionnumber_ : AcquisitionVisualizer
• AcquisitionVisualizer() : AcquisitionVisualizer
• AcqusHandler() : AcqusHandler
• act_cons_element_ : ConsensusXMLFile
• action_mode_ : SpectrumCanvas , TOPPASScene
• ActionMode : XMLHandler , TOPPASScene
• actionModeChange() : Spectrum3DOpenGLCanvas , SpectrumCanvas
• ActionModes : SpectrumCanvas
• actions : DataProcessingStep
• actions_ : DataProcessingVisualizer
• activate1DSpectrum() : TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• activate_count_ : FASTAContainer< TFI_Vector >
• activateAsPrecursorPeak() : MSPeak
• activateBehavior() : TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• activateCache() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• activateLayer() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas
• activatePrecalculationMode() : MultiGradient
• activateSpectrum() : Spectrum1DCanvas
• activation_energy_ : Precursor , PrecursorVisualizer
• activation_methods_ : Precursor , PrecursorVisualizer
• ActivationMethod : Precursor
• active : ItraqConstants::ChannelInfo
• activeLayerIndex() : SpectrumCanvas
• activeSubWindow_() : TOPPASBase
• 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
• AD : IonSource
• adaptPenScaling_() : Spectrum2DCanvas
• ADC : IonDetector
• ADC_sampling_frequency_ : IonDetector
• add() : Compomer , DataFilters , AveragePosition< D > , MetaDataBrowser , MSSpectrum::Chunks , QTCluster , TOPPASResources
• add1DSignal_() : RawMSSignalSimulation
• add2Buttons_() : BaseVisualizerGUI
• add2DSignal_() : RawMSSignalSimulation
• add_() : MetaInfoVisualizer
• 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_alignment_error() : LCMS
• 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_feature() : LCMS
• add_first_prefix_ion_ : NucleicAcidSpectrumGenerator , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_isotopes_ : SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_k_linked_ions_ : SimpleTSGXLMS , TheoreticalSpectrumGeneratorXLMS
• add_LC_elution_peak() : LCMSCData
• add_losses_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_matched_feature() : SHFeature
• add_metainfo_ : NucleicAcidSpectrumGenerator , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_modification() : MS2Info
• add_MS2_info() : SHFeature
• add_precursor_peaks_ : NucleicAcidSpectrumGenerator , SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• add_raw_peak_to_LC_MS_run() : FTPeakDetectController
• add_raw_spec_name() : LCMS
• add_raw_spec_name_map() : LCMS
• add_scan_raw_data() : ProcessData
• 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
• addAbundantImmoniumIons_() : TheoreticalSpectrumGenerator
• addAMinusBPeaks_() : NucleicAcidSpectrumGenerator
• addAnalysisResults() : PeptideHit
• addBaseLine_() : RawMSSignalSimulation
• addBetaAccessions() : OPXLHelper
• addBooleanComboBox_() : BaseVisualizerGUI
• addButton_() : BaseVisualizerGUI
• addbutton_ : MetaInfoVisualizer
• addChargedSpectrum_() : NucleicAcidSpectrumGenerator
• addCheckboxItemToBottomRow_() : SpectraIdentificationViewWidget
• addChromatogram() : MRMTransitionGroup< ChromatogramType, TransitionType > , MSExperiment
• addChromatograms() : OpenSwathCalibrationWorkflow , OpenSwathWorkflowSonar
• addCluster() : ClusteringGrid
• addClusterElements_() : QTClusterFinder
• addColumn() : LPWrapper
• addComboBox_() : BaseVisualizerGUI
• addCOMETFeatures() : PercolatorFeatureSetHelper
• addCompound() : TargetedExperiment
• addCONCATSEFeatures() : PercolatorFeatureSetHelper
• addConfiguration() : IncludeExcludeTarget , TraMLProduct
• addConsensusFeature_() : FeatureGroupingAlgorithmKD
• addConsensusMap() : MSQuantifications
• addConstraint_() : MRMFeatureSelector
• addContact() : TargetedExperiment
• addCV() : TargetedExperiment
• addCVReference() : CVMappings
• addCVTerm() : CVMappingRule , CVTermList , CVTermListInterface
• addData() : LinearRegressionWithoutIntercept , TOPPViewBase
• addData_() : MSExperiment::ContainerAdd_< ContainerValueType, addMassTraces > , MSExperiment::ContainerAdd_< ContainerValueType, false > , MSExperiment::ContainerAdd_< ContainerValueType, true >
• addDataFile() : TOPPViewBase
• addDataProcessing() : MSDataWritingConsumer
• addDataProcessing_() : SpectrumCanvas , TOPPBase
• addDetectorNoise_() : RawMSSignalSimulation
• addDoubleItemToBottomRow_() : SpectraIdentificationViewWidget
• addDoubleLineEdit_() : BaseVisualizerGUI
• addEdge() : TOPPASScene
• addEluent() : Gradient
• addEluent_() : GradientVisualizer
• addEmptyLine_() : TOPPBase
• addEntry_() : SpectrumLookup
• addEnzyme_() : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• addEnzymeInfo() : SequestInfile
• addExcludeTarget() : TargetedExperiment
• addExternalType() : ToolDescription
• addFakeMSMSToFeature() : FTPeakDetectController
• addFeature() : KDTreeFeatureMaps , MRMFeature , MRMTransitionGroup< ChromatogramType, TransitionType >
• addFile() : FileWatcher
• addFiles_() : InputFileList
• addFragmentPeaks_() : NucleicAcidSpectrumGenerator
• addHit() : PeptideIndexing::FoundProteinFunctor , SpectrumIdentification
• addHits_() : PeptideIndexing
• addHoveringEdge() : TOPPASScene
• addIncludeTarget() : TargetedExperiment
• addInEdge() : TOPPASVertex
• addInstrument() : TargetedExperiment
• addIntensity() : BackgroundIntensityBin
• addIntermediateProduct() : ReactionMonitoringTransition
• addInterpretation() : IncludeExcludeTarget , TraMLProduct
• addIntItemToBottomRow_() : SpectraIdentificationViewWidget
• addIntLineEdit_() : BaseVisualizerGUI
• addIonMatchStatistics() : SpectrumAnnotator
• addIsotopeCluster_() : TheoreticalSpectrumGenerator
• addIsotopeTrace() : ConsensusIsotopePattern
• additional_dataprocessing_ : MSDataWritingConsumer
• addKLinkedIonPeaks_() : SimpleTSGXLMS , TheoreticalSpectrumGeneratorXLMS
• addLabel_() : BaseVisualizerGUI
• addLabelAnnotation_() : Spectrum1DCanvas
• addLabelToProteinHits_() : ICPLLabeler
• addLayer() : SpectrumCanvas
• addLCelutionProfile() : FTPeakDetectController
• addLine() : TextFile
• addLinearIonLosses_() : TheoreticalSpectrumGeneratorXLMS
• addLinearPeaks_() : SimpleTSGXLMS , TheoreticalSpectrumGeneratorXLMS
• addLineEdit_() : BaseVisualizerGUI
• addLineEditButton_() : BaseVisualizerGUI
• addListView_() : BaseVisualizerGUI
• addLosses_() : SimpleTSGXLMS , TheoreticalSpectrumGenerator
• addLossesFaster_() : TheoreticalSpectrumGenerator
• addLossFormula() : Residue
• addLossName() : Residue
• addMappingRule() : CVMappings
• addMaps() : KDTreeFeatureMaps
• addMASCOTFeatures() : PercolatorFeatureSetHelper
• addMassTrace() : FeatureHypothesis
• addMatches_() : ModificationDefinitionsSet
• addMaxInclusionListSizeConstraints_() : PSLPFormulation
• addMetaDataMetricsToMzTab() : Ms2IdentificationRate , TIC
• addMetaInfoToOptionalColumns() : MzTab
• addMetaValues() : MetaInfoInterface
• addMetaValues_() : XQuestResultXMLHandler
• addMissingRTsToPeptideIDs() : SpectrumMetaDataLookup
• addMissingSpectrumReferences() : SpectrumMetaDataLookup
• addModification() : ModificationDefinitionsSet , ModificationsDB
• addModification_() : TransitionTSVFile
• addModificationsSequences_() : MRMAssay
• addModificationToPeptideHit_() : ICPLLabeler , ITRAQLabeler , O18Labeler , SILACLabeler
• addMS1elutionSignal() : FeatureLCProfile
• addMS1Map_() : CachedSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• addMS2ConsensusSpectrum() : ClusteredMS2ConsensusSpectrum
• addMS2Feature() : SHFeature
• addMS2FeatureToMS1Feature() : FTPeakDetectController
• addMS2Fragment() : MS2ConsensusSpectrum
• addMSGFFeatures() : PercolatorFeatureSetHelper
• addMSLevel() : PeakFileOptions
• addMSPeak() : BackgroundIntensityBin
• addMSRunMetaData_() : MzTab
• addMULTISEFeatures() : PercolatorFeatureSetHelper
• addMzMetaValues_() : MzCalibration
• addMzTabMoleculeParentContext_() : IdentificationDataConverter
• addMzTabSEScores_() : IdentificationDataConverter
• addNewState() : HiddenMarkovModel
• addNewSwathMap_() : CachedSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• addNTermLossFormula() : Residue
• addNTermLossName() : Residue
• addOptionalColumnsToSectionRow_() : MzTabFile
• addOutEdge() : TOPPASVertex
• addOutsideMS1elutionSignal() : FeatureLCProfile
• addPeak() : MultiplexFilteredMSExperiment
• addPeak_() : PeakPickerCWT , TheoreticalSpectrumGeneratorXLMS
• addPeakAnnotation() : Spectrum1DCanvas
• addPeakAnnotations_() : TOPPViewIdentificationViewBehavior
• addPeakAnnotationsFromID_() : TOPPViewIdentificationViewBehavior
• addPeakMSScan() : BackgroundControl
• addPeaks_() : TheoreticalSpectrumGenerator
• addPepEvidenceToRows() : MzTab
• addPeptide() : TargetedExperiment
• addPeptideAndAssociatedProteinsWithRunInfo_() : IDBoostGraph
• addPeptideEvidence() : PeptideHit
• addPeptideIDWithAssociatedProteins_() : IDBoostGraph
• addPeptideRT_() : FeatureFinderIdentificationAlgorithm
• addPeptideSequences_() : MapAlignmentAlgorithmTreeGuided
• addPeptideToMap_() : FeatureFinderIdentificationAlgorithm
• addPercolatorFeatureList() : OPXLHelper
• addPoint() : ConvexHull2D
• addPoints() : ConvexHull2D
• addPrecursorAcquisitionNumberConstraint_() : PSLPFormulation
• addPrecursorChromatogram() : MRMTransitionGroup< ChromatogramType, TransitionType >
• addPrecursorCVTerm() : IncludeExcludeTarget , ReactionMonitoringTransition
• addPrecursorFeature() : MRMFeature
• addPrecursorLabels1D_() : TOPPViewIdentificationViewBehavior
• addPrecursorPeaks_() : SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• addPredecessorState() : HMMState
• addPredictionTerm() : IncludeExcludeTarget , ReactionMonitoringTransition
• addPrimaryMSRunPath() : ProteinIdentification
• addProcessingStep() : ScoredProcessingResult
• addProductCVTerm() : IncludeExcludeTarget , ReactionMonitoringTransition
• addProtein() : TargetedExperiment
• addProteinCoverageConstraint_() : PSLPFormulation
• addProteinGroups_() : ConsensusXMLFile , IdXMLFile
• addProteinPositionMetaValues() : OPXLHelper
• addProteinToILP_() : PSLPFormulation
• addPublication() : TargetedExperiment
• addRatio() : ConsensusFeature
• addRecentFile_() : TOPPViewBase
• addReferenceFormat() : SpectrumLookup
• addResidue_() : ResidueDB
• addResidueSet() : Residue
• address_ : ContactPerson , ContactPersonVisualizer
• AddressLookup : IdentificationData
• addRow() : CsvFile , LPWrapper
• addRTBinCapacityConstraint_() : PSLPFormulation
• addRTFitData() : MapAlignmentAlgorithmKD
• addRunAttachment() : QcMLFile
• addRunQualityParameter() : QcMLFile
• addSample() : ExperimentalDesign::SampleSection
• addSatellite() : MultiplexFilteredPeak
• addSatelliteProfile() : MultiplexFilteredPeak
• addScore() : IdentificationData , ScoredProcessingResult , MRMFeature
• addSearchMetaData_() : MzTab
• addSection() : Param
• addSeparator_() : BaseVisualizerGUI
• addSetAttachment() : QcMLFile
• addSetQualityParameter() : QcMLFile
• addShiftedPeakFragmentAnnotation_() : RNPxlFragmentAnnotationHelper
• addShotNoise_() : RawMSSignalSimulation
• addSingleChargedIons_() : CompNovoIonScoringBase
• addSoftware() : TargetedExperiment
• addSourceFile() : TargetedExperiment
• addSpectrum() : MSExperiment
• addSpectrumIdentification() : Identification
• addSpectrumMetaData_() : MzMLHandler
• addSpectrumToLibrary() : MSPGenericFile , MSPGenericFile_friend
• addStepSizeConstraint_() : PSLPFormulation
• addSuccessorState() : HMMState
• addSynonym() : DigestionEnzyme , Residue , ResidueModification
• addSynonymTransition() : HiddenMarkovModel
• addTab() : EnhancedTabBar , TOPPASTabBar
• addTag() : Param
• addTags() : Param
• addTargetCVTerm() : TargetedExperiment
• addText_() : TOPPBase
• addTextEdit_() : BaseVisualizerGUI
• addTextItemToBottomRow_() : SpectraIdentificationViewWidget
• addTheoreticalSpectrumLayer_() : TOPPViewIdentificationViewBehavior
• addTimepoint() : Gradient
• addTimepoint_() : GradientVisualizer
• addToCache_() : LogStreamBuf
• addToGroup() : FeatureGroupingAlgorithmUnlabeled
• addTOPPASFile() : TOPPASBase
• addTransition() : MRMTransitionGroup< ChromatogramType, TransitionType > , TargetedExperiment
• addTreatment() : Sample
• adduct : NucleicAcidSearchEngine::PrecursorInfo
• Adduct() : Adduct
• adduct : SiriusMzTabWriter::SiriusAdapterHit
• adduct_base_ : MassExplainer
• AdductInfo() : AdductInfo
• Adducts : TransitionTSVFile::TSVTransition
• AdductsType : Adduct , MassExplainer
• addUpSpectra() : SpectrumAddition
• addUserLabelAnnotation_() : Spectrum1DCanvas
• addUserPeakAnnotation_() : Spectrum1DCanvas
• addValue() : BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value >
• addVariable_() : MRMFeatureSelector
• addVertex() : TOPPASScene
• addVertexWithLookup_() : IDBoostGraph
• addVSpacer_() : BaseVisualizerGUI
• addWhiteNoise_() : RawMSSignalSimulation
• addXLinkIonLosses_() : TheoreticalSpectrumGeneratorXLMS
• addXLinkIonPeaks_() : SimpleTSGXLMS , TheoreticalSpectrumGeneratorXLMS
• addXLTargetDecoyMV() : OPXLHelper
• addXTANDEMFeatures() : PercolatorFeatureSetHelper
• adjustBuffer_() : SpectrumCanvas
• adjustCorrectToMS1Precursor() : ProcessData
• advanced : ParameterInformation
• ADVANCED_ITEM : ParamEditor
• advanced_mode_ : ParamEditor
• advanceFollowUp() : IsobaricChannelExtractor::PuritySate_
• advanceTarget_() : MatchedIterator< CONT_T, TRAIT, CONST_T >
• affected_amino_acids_ : Modification
• affiliation : MzTabContactMetaData
• affineGapalign_() : MapAlignmentAlgorithmSpectrumAlignment
• after() : SysInfo::MemUsage
• aggregateInfo_() : MSstatsFile
• AggregationMethod : BasicProteinInferenceAlgorithm
• AhoCorasickAmbiguous() : AhoCorasickAmbiguous
• AI : IonSource
• AIon : NASequence , Residue
• align() : MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering , MapAlignmentAlgorithmSpectrumAlignment
• align_algorithm_ : MapAlignmentAlgorithmTreeGuided
• aligned_peaks_indices_ : Spectrum1DCanvas
• aligned_peaks_mz_delta_ : Spectrum1DCanvas
• Alignment : AxisPainter
• ALIGNMENT : DataProcessing
• 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
• aliphatic() : AAIndex
• all_contaminants_ratio : Contaminants::ContaminantsSummary
• allInputsReady() : TOPPASVertex
• allocator_type : _Alloc_base< _Tp, _Alloc > , KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , Matrix< Value >
• AllocatorType : Matrix< Value >
• allow_children_ : CVMappingTerm
• allow_isotope_error_ : XTandemInfile
• allow_output_recycling_ : TOPPASVertex
• allow_short_numbers_ : AxisWidget
• allowed_threads_ : TOPPASScene
• allowedTol() : DaTrait , PpmTrait , ValueTrait
• allParentsAreDecoys() : IdentifiedSequence< SeqType >
• allSameMolecule() : QueryMatchGroup
• allSameQuery() : QueryMatchGroup
• alpha : OPXLDataStructs::ProteinProteinCrossLink
• alpha_ : MessagePasserFactory< Label >
• alpha_index : OPXLDataStructs::XLPrecursor
• alpha_seq : OPXLDataStructs::XLPrecursor
• alphabet_ : IntegerMassDecomposer< ValueType, DecompositionValueType > , MassDecompositionAlgorithm
• alphabet_mass_type : Weights
• alphabet_masses_ : Weights
• alphabet_masses_type : Weights
• already_used_ : QTClusterFinder
• always_append_data_ : PeakFileOptions
• AM_MEASURE : SpectrumCanvas
• AM_MOVE : TOPPASScene
• AM_NEW_EDGE : TOPPASScene
• AM_TRANSLATE : SpectrumCanvas
• AM_ZOOM : SpectrumCanvas
• ambAA_seen : Spawn< TNeedle >
• ambig_features : PeptideAndProteinQuant::Statistics
• ambiguity_map_ : RibonucleotideDB
• ambiguity_members : MzTabNucleicAcidSectionRow , MzTabProteinSectionRow
• ambiguous_mods_ : NucleicAcidSearchEngine
• aminoacid_ : PepXMLFile::AminoAcidModification
• AminoAcidModification() : PepXMLFile::AminoAcidModification
• AminusB : NASequence
• amount_ : Adduct
• analysis_results_ : PeptideHit
• analysis_summary_ : MSQuantifications , PepXMLFile
• AnalysisSummary() : MSQuantifications::AnalysisSummary
• ANALYSISXML : FileTypes
• analyzeHeader_() : QuantitativeExperimentalDesign
• analyzeLCElutionPeak() : LCElutionPeak
• analyzer : MzTabInstrumentMetaData
• ANALYZERNULL : MassAnalyzer
• AnalyzerType : MassAnalyzer
• anchorPoints_ : MapAlignmentAlgorithmSpectrumAlignment
• AND : CVMappingRule
• annotate() : IDMapper , RNPxlReport
• annotate_() : AccurateMassSearchEngine
• annotate_feature_() : MetaboliteFeatureDeconvolution
• annotate_psm_ : SimpleSearchEngineAlgorithm
• annotateBestPerPeptide() : IDFilter
• annotateBestPerPeptidePerRun() : IDFilter
• annotateBestPerPeptidePerRunWithData() : IDFilter
• annotateBestPerPeptideWithData() : IDFilter
• annotateFeatures_() : FeatureFinderIdentificationAlgorithm
• annotateFeaturesFinalizeAssay_() : FeatureFinderIdentificationAlgorithm
• annotateIndistProteins() : IDBoostGraph
• annotateIndistProteins_() : IDBoostGraph
• annotateIon() : MRMIonSeries
• annotateMatches() : SpectrumAnnotator
• annotateMS1FromMassFingerprinting_() : TOPPViewBase
• annotateQuantificationsToProteins() : PeptideAndProteinQuant
• annotateSpectra() : TargetedSpectraExtractor
• annotateSwathMapsFromFile() : SwathWindowLoader
• annotateTransition() : MRMIonSeries
• annotateTransitionCV() : MRMIonSeries
• annotateWithID() : TOPPViewBase
• annotation : PeptideHit::PeakAnnotation
• Annotation : TransitionTSVFile::TSVTransition
• Annotation1DCaret() : Annotation1DCaret
• Annotation1DDistanceItem() : Annotation1DDistanceItem
• Annotation1DItem() : Annotation1DItem
• Annotation1DPeakItem() : Annotation1DPeakItem
• Annotation1DTextItem() : Annotation1DTextItem
• annotations : NucleicAcidSearchEngine::AnnotatedHit
• Annotations1DContainer() : Annotations1DContainer
• annotations_ : GridFeature , QTCluster::BulkData
• annotations_1d : LayerData
• AnnotationState : BaseFeature
• AnnotationStatistics() : AnnotationStatistics
• annotationToCV_() : MRMIonSeries
• annotationToCVTermList_() : MRMIonSeries
• ANYWHERE : ResidueModification , Ribonucleotide
• AP_MALDI : IonSource
• APCI : IonSource
• APEX : LCElutionPeak
• apex_peak_intensity : SHFeature
• apex_pos : PeakIntegrator::PeakArea
• apex_rt_ : EGHModel , EGHTraceFitter
• apexMS1Signal : FeatureLCProfile
• apexScan : MS2ConsensusSpectrum
• API : IonSource
• append() : ToolDescription , TOPPASVertex::TOPPASFilenames
• appendASCII() : StringManager
• appendChromatogram() : IChromatogramsWriter
• appendColumns() : ConsensusMap
• appendConsumer() : MSDataChainingConsumer
• appendRows() : ConsensusMap
• appendSpectrum() : ISpectraWriter
• APPI : IonSource
• AppliedProcessingStep : IdentificationData , AppliedProcessingStep
• AppliedProcessingSteps : IdentificationData
• apply() : ComplementFilter , ComplementMarker , ConsensusIDAlgorithm , DeNovoPostScoring , FalseDiscoveryRate , FilterFunctor , GoodDiffFilter , IDDecoyProbability , IntensityBalanceFilter , IsotopeDiffFilter , IsotopeMarker , NeutralLossDiffFilter , NeutralLossMarker , PeakMarker , TICFilter , TransformationDescription
• apply_() : ConsensusIDAlgorithm , ConsensusIDAlgorithmIdentity , ConsensusIDAlgorithmSimilarity , IDDecoyProbability
• applyAtMostOneVariableModification_() : ModifiedNASequenceGenerator , ModifiedPeptideGenerator
• applyBasic() : FalseDiscoveryRate
• applyCalibration() : AbsoluteQuantitation
• applyDesign2Resolver() : QuantitativeExperimentalDesign
• applyDilation_() : MorphologicalFilter
• applyDilationSimple_() : MorphologicalFilter
• applyErosion_() : MorphologicalFilter
• applyErosionSimple_() : MorphologicalFilter
• applyEstimated() : FalseDiscoveryRate
• applyEstimatedParameters() : EmgGradientDescent , EmgGradientDescent_friend
• applyEvaluateProteinIDs() : FalseDiscoveryRate
• applyFixedModifications() : ModifiedNASequenceGenerator , ModifiedPeptideGenerator
• applyFunctionOnPeptideHits() : MapUtilities< MapType >
• applyFunctionOnPeptideHits_() : MapUtilities< MapType >
• applyFunctionOnPeptideIDs() : MapUtilities< MapType >
• applyFunctionOnPeptideIDs_() : MapUtilities< MapType >
• applyFunctorOnCCs() : IDBoostGraph
• applyFunctorOnCCsST() : IDBoostGraph
• applyLabelToProteinHit_() : SILACLabeler
• applyLogTransformation() : Histogram< ValueType, BinSizeType >
• applyMemberFunction() : ConsensusMap , Feature , FeatureMap
• applyToBaseFeature_() : MapAlignmentTransformer
• applyToConsensusFeature_() : MapAlignmentTransformer
• applyTOFConversion_() : TOFCalibration
• applyToFeature_() : MapAlignmentTransformer
• applyToQueryMatches() : FalseDiscoveryRate
• applyTransformation() : InternalCalibration
• applyTransformation_() : InternalCalibration
• applyTransformations() : KDTreeFeatureMaps
• applyVariableModifications() : ModifiedNASequenceGenerator , ModifiedPeptideGenerator
• arch_ : OpenMSOSInfo
• area : PeakIntegrator::PeakArea , PeakIntegrator::PeakBackground , PeakShape
• areaBegin() : MSExperiment
• areaBeginConst() : MSExperiment
• areaEnd() : MSExperiment
• areaEndConst() : MSExperiment
• AreaIterator() : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , MSExperiment
• AreaType : MSExperiment , SpectrumCanvas
• 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
• argument_type : IDFilter::DigestionFilter , IDFilter::GetMatchingItems< HitType, Entry > , IDFilter::HasDecoyAnnotation< HitType > , IDFilter::HasGoodScore< HitType > , IDFilter::HasMatchingAccession< HitType > , IDFilter::HasMatchingAccessionUnordered< HitType > , IDFilter::HasMaxMetaValue< HitType > , IDFilter::HasMaxRank< HitType > , IDFilter::HasMetaValue< HitType > , IDFilter::HasNoHits< IdentificationType > , IDFilter::PeptideDigestionFilter , mean_and_stddev
• ARRAYDETECTOR : IonDetector
• ARTIFACT : ResidueModification
• as_map_ : MzIdentMLDOMHandler
• asBool_() : XMLHandler
• AScore() : AScore , ProbablePhosphoSites
• asDateTime_() : XMLHandler
• asDouble_() : XMLHandler
• asFloat_() : XMLHandler
• ASI : IonSource
• asInt_() : XMLHandler
• askForOutputDir() : TOPPASScene
• asMass() : AccurateMassSearchEngine::CompareEntryAndMass_
• asMutable() : FeatureHandle
• Assay() : MSQuantifications::Assay
• assay : MzTabMetaData
• assay_refs : MzTabStudyVariableMetaData
• assays_ : MSQuantifications
• assembleInclusionListForProteinBasedLP_() : PSLPFormulation
• assembleRunMap_() : MSstatsFile
• assign() : ConstRefVector< ContainerT > , DIntervalBase< D >
• assignDeltaScore_() : PercolatorFeatureSetHelper
• assigned_contaminants_intensity_ratio : Contaminants::ContaminantsSummary
• assigned_contaminants_ratio : Contaminants::ContaminantsSummary
• assigned_scores : DataProcessingSoftware
• assignedMS2 : FeatureMapping::FeatureToMs2Indices
• assignMS2IndexToFeature() : FeatureMapping
• assignRanks() : PeptideIdentification , ProteinIdentification
• assignTypes_() : XFDRAlgorithm
• assignUIDs() : MSQuantifications
• associateMS2FeatureToMS1Feature() : FTPeakDetectController
• asUInt_() : XMLHandler
• asVector() : Matrix< Value >
• AsymmetricStatistics() : AsymmetricStatistics< RealT >
• asymmetry_factor : PeakIntegrator::PeakShapeMetrics
• at() : QCBase::SpectraMap
• at_ : QcMLFile
• atEnd() : FASTAFile
• atomic_number_ : Element
• atomic_numbers_ : ElementDB
• ats_ : QcMLFile
• Attachment() : QcMLFile::Attachment
• attributeAsDouble_() : XMLHandler
• attributeAsDoubleList_() : XMLHandler
• attributeAsInt_() : XMLHandler
• attributeAsIntList_() : XMLHandler
• attributeAsString_() : XMLHandler
• attributeAsStringList_() : XMLHandler
• AUC() : ROCCurve
• AUI : IonSource
• authors : Citation
• auto_charge_ : SiriusAdapterAlgorithm
• auto_max_percentile_ : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• auto_max_stdev_Factor_ : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• AUTO_MODE : PeptideIndexing
• auto_mode_ : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• AUTOMAXBYPERCENT : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• AUTOMAXBYSTDEV : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• autoUpdateProjections() : Spectrum2DWidget
• av_MZ_spacing_ : IsotopeWaveletTransform< PeakType >
• AVERAGE : ProteinIdentification
• average() : SpectraMerger
• AVERAGE : WeightWrapper , XTandemInfile
• average_mass_ : ResidueModification
• average_ppm : FragmentMassError::FMEStatistics
• average_weight_ : Element , Residue
• AverageBlocks : SpectraMerger
• averageCentroidSpectra_() : SpectraMerger
• averageCoefficients_() : TOFCalibration
• averageErrors_() : TOFCalibration
• AverageLinkage() : AverageLinkage
• averageMass() : IsotopeDistribution
• averagePopulationAberration() : ClusterAnalyzer
• AveragePosition() : AveragePosition< D >
• averageProfileSpectra_() : SpectraMerger
• averageSilhouetteWidth() : ClusterAnalyzer
• averagine_ : ExtendedIsotopeModel , IsotopeModel , IsotopeWavelet
• AVERAGINE_NUM : ExtendedIsotopeModel , IsotopeModel
• averagine_similarity_ : MultiplexFiltering
• averagine_similarity_scaling_ : MultiplexFiltering
• averagine_type_ : MultiplexFiltering
• Averagines : ExtendedIsotopeModel , IsotopeModel
• 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
• AXIALEJECTIONLINEARIONTRAP : MassAnalyzer
• AxisPainter() : AxisPainter
• AxisTickCalculator() : AxisTickCalculator
• AxisTickVector : Spectrum3DOpenGLCanvas
• AxisWidget() : AxisWidget