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

- c -

• c : EmgFitter1D::EgmFitterFunctor
• C : ExtendedIsotopeModel , IsotopeModel
• c_ : CubicSpline2d , QuadraticRegression , SpectrumAccessQuadMZTransforming , mean_and_stddev
• C_ELEMENTS : LayerDataDefs
• c_intensity_ : NucleicAcidSpectrumGenerator , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• C_TERM : OPXLDataStructs , ResidueModification
• c_term_gain_ : DigestionEnzymeProtein
• c_term_mod_ : AASequence
• C_TERM_MODIFICATION_INDEX : ModifiedPeptideGenerator
• C_TERMINAL_AA : PeptideEvidence
• cache_count_ : FASTAContainer< TFI_Vector >
• cacheChunk() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• cached_terms_ : MzMLHandler
• cachedir_ : CachedSwathFileConsumer , MzMLSwathFileConsumer
• CachedmzML() : CachedmzML
• CACHEDMZML : FileTypes
• CachedMzMLHandler() : CachedMzMLHandler
• CachedSwathFileConsumer() : CachedSwathFileConsumer
• CAD : IonSource
• cal_data_ : InternalCalibration
• calc_mass_to_charge : MzTabMSmallMoleculeEvidenceSectionRow , MzTabOSMSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• calc_qfdr_() : XFDRAlgorithm
• calcElutionFitScore() : EmgScoring
• calcFragmentIsotopeDist() : CoarseIsotopePatternGenerator
• calcFragmentIsotopeDist_() : CoarseIsotopePatternGenerator
• calcGridLines() : AxisTickCalculator
• calcLibraryScore() : MRMScoring
• calcLogGridLines() : AxisTickCalculator
• calcMIPrecursorCombinedScore() : MRMScoring
• calcMIPrecursorContrastScore() : MRMScoring
• calcMIPrecursorScore() : MRMScoring
• calcMIScore() : MRMScoring
• calcMIWeightedScore() : MRMScoring
• calcRTScore() : MRMScoring
• calcSeparateMIContrastScore() : MRMScoring
• calcSeparateSNScore() : MRMScoring
• calcSeparateXcorrContrastCoelutionScore() : MRMScoring
• calcSeparateXcorrContrastShapeScore() : MRMScoring
• calcSNScore() : MRMScoring
• calculate_lda_prescore() : OpenSwath_Scores
• calculate_lda_single_transition() : OpenSwath_Scores
• calculate_swath_lda_prescore() : OpenSwath_Scores
• calculateAndAnnotateIndistProteins() : IDBoostGraph
• calculateAndAnnotateIndistProteins_() : IDBoostGraph
• calculateAndFilterFDR_() : NucleicAcidSearchEngine
• calculateAveragine() : FLASHDeconvAlgorithm
• calculateAvgWeight_() : ElementDB
• calculateBias() : AbsoluteQuantitation
• calculateBiasAndR() : AbsoluteQuantitation
• calculateChromatographicIdScores() : OpenSwathScoring
• calculateChromatographicScores() : OpenSwathScoring
• calculateCorrectionFactor() : DBSuitability_friend
• calculateCorrectionFactor_() : DBSuitability
• calculateCoverages() : IdentificationData
• calculated_mass_to_charge_ : IdentificationHit
• calculateDIAIdScores() : OpenSwathScoring
• calculateDIAScores() : OpenSwathScoring
• calculateEstimatedQVal_() : FalseDiscoveryRate
• calculateFDR_() : FeatureFinderIdentificationAlgorithm
• calculateFDRBasic_() : FalseDiscoveryRate
• calculateFDRs_() : FalseDiscoveryRate
• calculateFilterValuesMean() : MRMFeatureFilter
• calculateFilterValuesPercRSD() : MRMFeatureFilter
• calculateFilterValuesVar() : MRMFeatureFilter
• calculateFitQuality_() : ElutionModelFitter
• calculateFME_() : FragmentMassError
• calculateGB() : AAIndex
• calculateGridLines_() : Plot3DOpenGLCanvas
• calculateIntensityRankInMZWindow() : PScore
• calculateIonRatio() : MRMFeatureFilter
• calculateIsotopicPurities() : IsotopeLabelingMDVs
• calculateIsotopicPurity() : IsotopeLabelingMDVs
• calculateLibraryScores() : OpenSwathScoring
• calculateMap() : QCBase::SpectraMap
• calculateMDV() : IsotopeLabelingMDVs
• calculateMDVAccuracies() : IsotopeLabelingMDVs
• calculateMDVAccuracy() : IsotopeLabelingMDVs
• calculateMDVs() : IsotopeLabelingMDVs
• calculateMonoWeight_() : ElementDB
• calculateMZ_() : FeatureFinderAlgorithmMetaboIdent
• calculatePeakLevelSpectra() : PScore
• calculatePeakShapeMetrics() : PeakIntegrator
• calculatePeakShapeMetrics_() : PeakIntegrator
• calculatePermutationPeptideScores_() : AScore
• calculatePrecursorDIAScores() : OpenSwathScoring
• calculatePrecursorMass_() : NucleicAcidSearchEngine
• calculateRankMap() : PScore
• calculateRatio() : AbsoluteQuantitation
• calculateResolution() : MRMFeatureFilter
• calculateRTDifference() : MRMFeatureFilter
• calculateSpectrum_() : TheoreticalSpectrumGenerationDialog
• calculateSuitability_() : DBSuitability
• calculateTheoreticalIsotopesNumber() : EmpiricalFormula
• calculateTIC() : Mobilogram , MSExperiment , MSSpectrum
• calculateVariance_() : FragmentMassError
• calcXcorrCoelutionScore() : MRMScoring
• calcXcorrCoelutionWeightedScore() : MRMScoring
• calcXcorrContrastShapeScore() : MRMScoring
• calcXcorrPrecursorCoelutionScore() : MRMScoring
• calcXcorrPrecursorCombinedCoelutionScore() : MRMScoring
• calcXcorrPrecursorCombinedShapeScore() : MRMScoring
• calcXcorrPrecursorContrastCoelutionScore() : MRMScoring
• calcXcorrPrecursorContrastShapeScore() : MRMScoring
• calcXcorrPrecursorContrastSumFragCoelutionScore() : MRMScoring
• calcXcorrPrecursorContrastSumFragShapeScore() : MRMScoring
• calcXcorrPrecursorShapeScore() : MRMScoring
• calcXcorrShapeScore() : MRMScoring
• calcXcorrShapeWeightedScore() : MRMScoring
• CalDataType : CalibrationData
• CalibrantStats_() : InternalCalibration::CalibrantStats_
• calibrate() : InternalCalibration
• CALIBRATION : DataProcessing
• CalibrationData() : CalibrationData
• callbackStdErr_ : ExternalProcess
• callbackStdOut_ : ExternalProcess
• callUpdateEntries() : DataSelectionTabs
• CancelButton_ : ListEditor
• cancelbutton_ : MetaDataBrowser
• candidateEdges_() : MetaboliteFeatureDeconvolution
• candidates_out_ : FeatureFinderAlgorithmMetaboIdent , FeatureFinderIdentificationAlgorithm
• CANNOT_WRITE_OUTPUT_FILE : TOPPBase
• canRun() : JavaInfo , PythonInfo
• canvas() : Plot1DWidget , Plot2DWidget , Plot3DWidget , PlotWidget
• canvas_ : PlotWidget
• canvas_3d_ : Plot3DOpenGLCanvas
• canvas_coverage_min_ : Plot2DCanvas
• canvasPixelArea() : PlotCanvas
• capacity() : ConstRefVector< ContainerT >
• capacity_ : ConstRefVector< ContainerT >
• CAPTION_3D_SUFFIX_ : TOPPViewBase
• caret_positions_ : Annotation1DCaret< DataPoint >
• CASE : ListUtils
• CaseInsensitiveToCaseSensitiveDecoy : DecoyHelper
• category : ToolDescriptionInternal , ToolExternalDetails
• category_ : ToolInfo
• cbegin() : ExposedVector< VectorElement > , Mobilogram , MSExperiment , NASequence
• cconsensus_map_ : ConsensusXMLHandler
• ccs_ : IDBoostGraph
• cd_ : SwathQC
• cd_spectra_ : SwathQC
• CE : TransitionTSVFile::TSVTransition
• CEI : IonSource
• cell_dimension : HashGrid< Cluster >
• cell_it_ : HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator
• cell_iterator : HashGrid< Cluster > , HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator
• cell_type : MzTabSampleMetaData
• CellContent : HashGrid< Cluster >
• CellIndex : ClusteringGrid , GridBasedClustering< Metric > , HashGrid< Cluster >
• cellindexAtClustercenter_() : HashGrid< Cluster >
• cells_ : ClusteringGrid , HashGrid< Cluster >
• cend() : ExposedVector< VectorElement > , Mobilogram , MSExperiment , NASequence
• center() : DIntervalBase< D > , IsobaricQuantitationMethod::IsobaricChannelInformation , ItraqConstants::ChannelInfo , RangeBase , SwathMap
• center_index_ : ClusterProxyKD
• center_point_ : QTCluster::BulkData
• centerOfBin() : Histogram< ValueType, BinSizeType >
• centre_ : GridBasedCluster
• CENTROID : SpectrumSettings
• centroid_mz_ : MassTrace
• centroid_rt_ : MassTrace
• centroid_sd_ : MassTrace
• centroided_ : FeatureFinderMultiplexAlgorithm
• cexp_ : MzDataHandler , MzMLHandler , MzXMLHandler , TraMLHandler
• changed_ : QTCluster , TOPPASScene
• changedOutputFolder() : TOPPASScene
• changedParameter() : TOPPASScene
• changeLabel() : TOPPViewBase
• changeLayerFilterState() : PlotCanvas
• changeLayerFlag() : TOPPViewBase
• changeLegendVisibility() : PlotCanvas , PlotWidget
• changeUnassigned() : TOPPViewBase
• changeVisibility() : PlotCanvas
• changeVisibleArea1D_() : Plot1DCanvas
• changeVisibleArea_() : Plot1DCanvas , PlotCanvas
• channel_ : MSstatsFile::MSstatsTMTLine_
• channel_count : IsobaricQuantifierStatistics
• CHANNEL_COUNT : ItraqConstants
• channel_names_ : TMTEighteenPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• CHANNELELECTRONMULTIPLIER : IonDetector
• ChannelMapType : ItraqConstants
• channels_ : ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTEighteenPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• CHANNELS_EIGHTPLEX : ItraqConstants
• CHANNELS_FOURPLEX : ItraqConstants
• CHANNELS_TMT_SIXPLEX : ItraqConstants
• CHANNELTRON : IonDetector
• char_rest_ : MzXMLHandler::SpectrumData
• character_buffer_ : MascotXMLHandler
• characters() : CVMappingFile , ConsensusXMLHandler , FeatureXMLHandler , MascotXMLHandler , MzDataHandler , MzIdentMLHandler , MzMLHandler , MzXMLHandler , PTMXMLHandler , SemanticValidator , ToolDescriptionHandler , TraMLHandler , UnimodXMLHandler , XMLHandler , OMSSAXMLFile , QcMLFile , XTandemXMLFile
• charge : NucleicAcidSearchEngine::PrecursorInfo , ConsensusIDAlgorithm::HitInfo
• CHARGE : DataFilters
• charge : ObservationMatch , RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ , InternalCalibration::LockMass , IsotopeCluster::ChargedIndexSet , KDTreeFeatureMaps , MzTabMSmallMoleculeEvidenceSectionRow , MzTabMSmallMoleculeFeatureSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow , PeptideHit::PeakAnnotation , SimpleTSGXLMS::SimplePeak , SiriusMSFile::CompoundInfo , Summary , LightCompound , Peptide
• charge_ : AccurateMassSearchResult , Adduct , AdductInfo , BaseFeature , EmpiricalFormula , ExtendedIsotopeFitter1D , ExtendedIsotopeModel , FeatureHandle , FeatureHypothesis , IdentificationHit , IsotopeFitter1D , IsotopeModel , MultiplexIsotopicPeakPattern , OSWPeptidePrecursor , PeptideHit , PepXMLFile , Precursor , PrecursorVisualizer , PeptideCompound , TraMLProduct
• CHARGE_CALCULATION : DataProcessing
• charge_count : FLASHDeconvHelperStructs::MassFeature
• CHARGE_DECONVOLUTION : DataProcessing
• charge_dummy : PeakGroup
• charge_lower_bound_ : FeatureFindingMetabo
• charge_max_ : FeatureFinderMultiplexAlgorithm
• charge_min_ : FeatureFinderMultiplexAlgorithm
• charge_score_ : PeakGroup
• charge_set_ : PeptideCompound , TraMLProduct
• charge_upper_bound_ : FeatureFindingMetabo
• ChargedIndexSet : FeatureFinderDefs , Fitter1D , IsotopeCluster::ChargedIndexSet
• ChargeDistribution : SwathQC
• ChargeMap : FeatureFinderIdentificationAlgorithm
• CHARGEMODE : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• ChargePair() : ChargePair
• charges : DBSearchParam , ProteinIdentification::SearchParameters
• charges_ : FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound , HasPrecursorCharge< SpectrumType > , XQuestResultXMLHandler , MascotInfile , ProteinIdentificationVisualizer
• chargeTestworthy_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• ChargeToPepHitP : IDFilter
• ChargeType : BaseFeature , FeatureHandle
• chauvenet() : MRMRTNormalizer
• chauvenet_probability() : MRMRTNormalizer
• check_() : DataFilterDialog , TOPPASVertex::TOPPASFilenames
• check_boxes_ : TheoreticalSpectrumGenerationDialog
• check_defaults_ : DefaultParamHandler
• check_term_value_types_ : SemanticValidator
• check_tree() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• check_units_ : SemanticValidator
• check_width_internally_ : PeakPickerIterative
• checkAndGetTermByName() : ControlledVocabulary
• checkAppliedProcessingSteps_() : IdentificationData
• CheckBox() : TheoreticalSpectrumGenerationDialog::CheckBox
• checkCompat_() : BasicProteinInferenceAlgorithm
• checkConditionISO_() : MSstatsFile
• checkConditionLFQ_() : MSstatsFile , TriqlerFile
• checkConvertAndFilterPepHits_ : BayesianProteinInferenceAlgorithm
• checkDatumRange() : TransformationModel
• checkDefaults() : Param
• checked() : Plot1DGoToDialog , Plot2DGoToDialog
• checked_base_name_ : PepXMLFile
• checkedToDouble_() : EDTAFile
• checkedToInt_() : EDTAFile
• checkExtraFeatures() : PercolatorFeatureSetHelper
• checkFDInputReady_() : FLASHDeconvTabWidget
• checkFeatureQuality_() : FeatureFinderAlgorithmPicked
• checkFormula_() : Adduct
• checkForSignificantPeak_() : MultiplexFiltering
• checkHits_() : IDMapper
• checkIds_() : BaseGroupFinder
• checkIfIniParametersAreApplicable_() : TOPPBase
• checkIfWeAreDone() : TOPPASScene
• checkLOD() : AbsoluteQuantitationMethod
• checkLOQ() : AbsoluteQuantitationMethod
• checkMassType_() : IDMapper
• checkMaximalRTSpan() : EGHTraceFitter , GaussTraceFitter , TraceFitter
• checkMetaValue() : MRMFeatureFilter
• checkMinimalRTSpan() : EGHTraceFitter , GaussTraceFitter , TraceFitter
• checkName_() : ControlledVocabulary
• checkNumObservations_() : FeatureFinderIdentificationAlgorithm
• checkOldRunConsistency_() : ConsensusMapMergerAlgorithm , IDMergerAlgorithm
• checkOSWInputReady_() : SwathTabWidget
• checkParam_() : TOPPBase
• checkParameters_() : MapAlignmentAlgorithmIdentification
• checkParentMatches_() : IdentificationData
• checkPreferences_() : TOPPViewBase
• checkPyProphetInput_() : SwathTabWidget
• checkRange() : MRMFeatureFilter
• checkSatellite() : MultiplexFilteredPeak
• checkScoreBetterThanThreshold_() : DBSuitability
• checkScoreTypes_() : IdentificationData
• checkSequenceUniqueness_() : MzTab
• checkSize() : SaveImageDialog
• checkSolution_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• checksum_ : SourceFile , SourceFileVisualizer
• checksum_type_ : SourceFile , SourceFileVisualizer
• ChecksumType : SourceFile
• checkSwathMap() : OpenSwathHelper
• checkSwathMapAndSelectTransitions() : OpenSwathHelper
• checkTDAnnotation_() : IDScoreGetterSetter
• checkTransitions_() : OSWData
• checkUniqueIdentifiers_() : XMLHandler
• checkUnorderedContent_() : MSstatsFile , TriqlerFile
• checkValidity_() : TOPPASInputFileDialog , TOPPASIOMappingDialog , TOPPASOutputFilesDialog
• checkValidWeight() : TransformationModel
• CHEMI : IonSource
• CHEMICAL_DERIVATIVE : ResidueModification
• chemical_formula : MzTabMSmallMoleculeEvidenceSectionRow , MzTabMSmallMoleculeSectionRow , MzTabSmallMoleculeSectionRow
• chemical_name : MzTabMSmallMoleculeEvidenceSectionRow , MzTabMSmallMoleculeSectionRow
• chgLLhoods : MessagePasserFactory< Label >
• chi_squared_ : LinearRegression , QuadraticRegression
• ChildCountType : ACNode
• children : ControlledVocabulary::CVTerm
• chooseBestParameters_() : SimpleSVM
• chooseDecoys_() : ConfidenceScoring
• chooseFilesDialog_() : TOPPViewBase
• chooseTraceFitter_() : FeatureFinderAlgorithmPicked
• chop() : String
• chrom_annotation_ : LayerDataChrom
• chrom_count_total_ : MzMLHandler
• chrom_data_ : FeatureFinderAlgorithmMetaboIdent , FeatureFinderIdentificationAlgorithm
• chrom_fwhm_ : ElutionPeakDetection , FeatureFindingMetabo
• chrom_id_ : MzMLSqliteHandler , MzMLSqliteSwathHandler
• chrom_index_ : CachedmzML , CachedMzMLHandler
• chrom_peak_snr_ : ElutionPeakDetection , MassTraceDetection
• Chromatogram() : Chromatogram
• chromatogram : MzMLHandler::ChromatogramData
• chromatogram_ : MzMLHandler , SignalToNoiseOpenMS< ContainerT >
• chromatogram_count_ : MzMLHandler
• chromatogram_data_ : MzMLHandler
• chromatogram_flag_set() : LayerDataPeak
• chromatogram_ids_ : SpectrumAccessOpenMSInMemory
• chromatogram_map_ : LayerDataChrom , MRMTransitionGroup< ChromatogramType, TransitionType >
• chromatogramIdsMatch() : MRMTransitionGroup< ChromatogramType, TransitionType >
• ChromatogramMeta() : ChromatogramMeta
• ChromatogramNames : ChromatogramSettings
• ChromatogramPeak() : ChromatogramPeak
• ChromatogramPeakT : MSExperiment , OnDiscMSExperiment
• ChromatogramPeakType : MzMLHandler , MSExperiment
• chromatograms_ : MRMTransitionGroup< ChromatogramType, TransitionType > , MSDataSqlConsumer , MSExperiment , SpectrumAccessOpenMSInMemory
• chromatograms_expected_ : MSDataWritingConsumer
• chromatograms_native_ids_ : IndexedMzMLHandler , OnDiscMSExperiment
• chromatograms_offsets_ : IndexedMzMLHandler , MzMLHandler
• chromatograms_written_ : MSDataCachedConsumer , MSDataWritingConsumer
• ChromatogramSettings() : ChromatogramSettings
• ChromatogramTools() : ChromatogramTools
• ChromatogramType : CachedSwathFileConsumer , ChromatogramSettings , FullSwathFileConsumer , IMSDataConsumer , CachedMzMLHandler , MzMLHandler , MSDataCachedConsumer , MSDataSqlConsumer , MSDataWritingConsumer , MSExperiment , MzMLSwathFileConsumer , RegularSwathFileConsumer
• CHROMATOGRAPHY : IonSource
• ChromeleonFile() : ChromeleonFile
• chromsDoubleClicked() : SpectraTreeTab
• chromsSelected() : SpectraTreeTab
• Chunk() : MSSpectrum::Chunk
• chunk_() : FeatureFinderIdentificationAlgorithm
• chunk_offset_ : FASTAContainer< TFI_File >
• chunkAt() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• Chunks() : MSSpectrum::Chunks
• chunks_ : MSSpectrum::Chunks
• chunkSize() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• CI : IonSource
• CID : IonSource , Precursor
• cid_ : MzIdentMLHandler
• CIon : NASequence , Residue
• citations_ : ToolInfo , TOPPBase
• cite_openms_ : TOPPBase
• clampTo() : RangeBase , RangeManager< RangeBases >
• clampToUnsafe() : RangeManager< RangeBases >
• classification_ : ResidueModification
• classifyFeatures_() : FeatureFinderIdentificationAlgorithm
• cleanup() : IdentificationData
• cleanupTransitions_() : TransitionTSVFile
• clear() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , Area< N_DIM > , CalibrationData , ConsensusFeature , ConsensusMap , ConstRefVector< ContainerT > , ConvexHull2D , CsvFile , DataFilters , DataTabBase , Date , DateTime , DBSuitability::SuitabilityData , DeconvolvedSpectrum , DIATreeTab , DistanceMatrix< Value > , DPosition< D, TCoordinateType > , FeatureMap , HashGrid< Cluster > , IdentificationData , IMSAlphabet , DIntervalBase< D > , IsotopeDistribution , KDTreeFeatureMaps , BasicStatistics< RealT > , MetaInfo , Mobilogram , MSChromatogram , MSExperiment , MSSpectrum , NASequence , OSWData , Param , ParamEditor , PeakIndex , QCBase::SpectraMap , RangeBase , RangeManager< RangeBases > , SpectraIDViewTab , SpectraTreeTab , StopWatch , TargetedExperiment , TOPPASResources
• clear_() : DataValue , ElementDB , MetaInfoVisualizer , ParamValue , PeakGroup , SimpleSVM
• clearbutton_ : MetaInfoVisualizer
• clearCache() : LogStreamBuf
• clearCurrentProcessingStep() : IdentificationData
• clearData_ : MSDataCachedConsumer
• clearEluents() : Gradient
• clearMetaDataArrays() : MSExperiment
• clearMetaInfo() : MetaInfoInterface
• clearMSLevels() : PeakFileOptions
• clearPercentages() : Gradient
• clearPrimaryID() : BaseFeature
• clearProteins() : OSWData
• clearRanges() : RangeManager< RangeBases >
• clearTags() : Param
• clearTimepoints() : Gradient
• clearUniqueId() : UniqueIdInterface
• cleavage_ : MascotInfile
• cleavage_regex_ : DigestionEnzyme
• cleavage_site_ : XTandemInfile
• cleavageCorrectionTerm() : PScore
• clicked() : TOPPASVertex
• clipboard_ : TOPPASScene
• clipboard_scene_ : TOPPASBase
• clockTime() : StopWatch::TimeDiff_
• clone() : Annotation1DCaret< DataPoint > , Annotation1DDistanceItem , Annotation1DItem , Annotation1DPeakItem< DataPoint > , Annotation1DTextItem , Annotation1DVerticalLineItem , Digestion , DimBase , DimIM , DimINT , DimMZ , DimRT , Modification , SampleTreatment , Tagging
• cloneWith() : Area< N_DIM >
• close() : Bzip2Ifstream , GzipIfstream , HDF5Connector
• closebutton_ : MetaDataBrowser
• closeByTab() : TOPPASBase , TOPPViewBase
• closeEditor_() : ParamEditorDelegate
• closeEvent() : INIFileEditorWindow , ListFilterDialog , PlotWidget , TOPPASBase , TOPPASWidget , TOPPViewBase
• closeFile() : TOPPASBase
• closeRequested() : EnhancedTabBar
• closeTab() : TOPPViewBase
• cluster() : ClusterHierarchical , GridBasedClustering< Metric > , MultiplexClustering
• cluster_index_ : MinimumDistance
• ClusterAnalyzer() : ClusterAnalyzer
• ClusterCenter : HashGrid< Cluster >
• ClusterFunctor() : ClusterFunctor
• ClusterHierarchical() : ClusterHierarchical
• clusterIndistProteinsAndPeptides() : IDBoostGraph
• clusterIndistProteinsAndPeptidesAndExtendGraph() : IDBoostGraph
• ClusteringGrid() : ClusteringGrid
• ClusterPointType : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• ClusterProxyKD() : ClusterProxyKD
• clusters_ : GridBasedClustering< Metric >
• clusters_final_ : GridBasedClustering< Metric >
• cm_ : LayerStatisticsConsensusMap , LayerStoreDataConsensusMapVisible
• cmap_ : FeatureXMLHandler
• CMD : ProgressLogger
• CMMzTabStream() : MzTab::CMMzTabStream
• cmp : SiriusMSFile::CompoundInfo
• cmp_ : Compomer
• cmp_bs_ : TargetedSpectraExtractor::BinnedSpectrumComparator
• CNG : InstrumentSettings
• CNL : InstrumentSettings
• cnt_decal : InternalCalibration::CalibrantStats_
• cnt_empty : InternalCalibration::CalibrantStats_
• cnt_nomz : InternalCalibration::CalibrantStats_
• cnt_nort : InternalCalibration::CalibrantStats_
• cnt_total : InternalCalibration::CalibrantStats_
• CoarseIsotopePatternGenerator() : CoarseIsotopePatternGenerator
• code_ : Ribonucleotide
• code_map_ : RibonucleotideDB
• coeff_ : MZTrafoModel
• coeffs_ : GaussFilterAlgorithm , SavitzkyGolayFilter
• cohesion() : ClusterAnalyzer
• collapseAll() : TOPPASTreeView
• collapseStringVector() : TVIdentificationViewController
• collect_annotations_ : QTCluster
• collectDecompositionsRecursively_() : IntegerMassDecomposer< ValueType, DecompositionValueType >
• collected_protein_hits_ : IDMergerAlgorithm
• collectFragmentScansInArea_() : Plot2DCanvas
• collectPrecursorCandidates() : OPXLHelper
• collectQCData() : QcMLFile
• collectRatios_() : IsobaricNormalizer
• collectSetParameter() : QcMLFile
• COLLISION_QUADRUPOLE : Instrument
• colnames() : CSVWriter , DataMatrix , IDataFrameWriter
• colnames_ : DataMatrix
• color() : MultiGradient
• color_ : Annotation1DCaret< DataPoint > , Annotation1DPeakItem< DataPoint > , Annotation1DVerticalLineItem , Colorizer , ColorSelector , TOPPASEdge
• color_undo_all_ : Colorizer
• Colorizer() : Colorizer
• colorizer_ : LogStreamBuf
• colors_ : Colorizer
• ColorSelector() : ColorSelector
• colorStream_() : Colorizer
• colTypes : QcMLFile::Attachment
• column_ : HPLC
• column_description_ : ConsensusMap
• columnExists() : SqliteConnector
• ColumnHeader() : ConsensusMap::ColumnHeader
• ColumnHeaders : ConsensusMap
• columnname_to_columnindex_ : ExperimentalDesign::SampleSection
• colunit_peptide : MzTabMetaData
• colunit_protein : MzTabMetaData
• colunit_psm : MzTabMetaData
• colunit_small_molecule : MzTabMetaData , MzTabMMetaData
• colunit_small_molecule_evidence : MzTabMMetaData
• colunit_small_molecule_feature : MzTabMMetaData
• combinations_logic_ : CVMappingRule
• CombinationsLogic : CVMappingRule
• combineMods() : ResidueModification
• combinePrecursorPurities() : PrecursorPurity
• combineTopRanksFromPairs() : OPXLHelper
• combos_ : GridSearch< TupleTypes >
• combos_ready_ : GridSearch< TupleTypes >
• comet_id_ : DigestionEnzymeProtein
• Command() : Command
• command : TOPPASScene::TOPPProcess
• commandline : ToolExternalDetails
• comment_ : ChromatogramSettings , ExperimentalSettings , ExperimentalSettingsVisualizer , HPLC , MetaInfoDescription , Sample , SampleTreatment , SpectrumSettings , SpectrumSettingsVisualizer
• comment_rows_ : MzTab , MzTabM
• commitAndCloseEditor_() : ParamEditorDelegate
• commitAndCloseLineEdit_() : ParamEditorDelegate
• common_name_ : SpectralMatch
• compare_() : Contaminants
• compareChargeStates_() : ConsensusIDAlgorithm
• compareFiles() : FuzzyStringComparator
• compareIDsSmallerScores_() : IDConflictResolverAlgorithm
• compareLines_() : FuzzyStringComparator
• compareMZ_() : AScore
• comparepeaks_() : SpectrumCheapDPCorr
• compareStreams() : FuzzyStringComparator
• compareStrings() : FuzzyStringComparator
• compatible() : MassDecomposition
• compatible_() : PrecursorCorrection
• compatibleIDs_() : StablePairFinder
• CompleteLinkage() : CompleteLinkage
• completion_time_ : DataProcessing , DataProcessingVisualizer
• Compomer() : Compomer
• compomer_ : ChargePair
• CompomerComponents : Compomer
• CompomerIterator : MassExplainer
• CompomerSide : Compomer
• compomerValid_() : MassExplainer
• component_group_name : MRMFeaturePicker::ComponentGroupParams , MRMFeaturePicker::ComponentParams , MRMFeatureQC::ComponentGroupPairQCs , MRMFeatureQC::ComponentGroupQCs
• component_group_pair_qcs : MRMFeatureQC
• component_group_qcs : MRMFeatureQC
• component_name : AbsoluteQuantitationStandards::runConcentration , MRMFeaturePicker::ComponentParams , MRMFeatureQC::ComponentQCs
• component_name_ : AbsoluteQuantitationMethod
• component_qcs : MRMFeatureQC
• composition_ : PTMXMLHandler
• Compound : TargetedExperiment , Compound , LightTargetedExperiment
• compound_adduct : MetaboTargetedAssay
• compound_count : TargetedExperiment::SummaryStatistics
• compound_file : MetaboTargetedAssay
• compound_info : MetaboTargetedAssay::CompoundSpectrumPair , MetaboTargetedAssay::CompoundTargetDecoyPair
• compound_name : MetaboTargetedAssay , LightCompound
• compound_ref_ : IncludeExcludeTarget , ReactionMonitoringTransition
• compound_reference_map_ : TargetedExperiment , LightTargetedExperiment
• compound_reference_map_dirty_ : TargetedExperiment , LightTargetedExperiment
• compound_rt : MetaboTargetedAssay
• CompoundName : TransitionTSVFile::TSVTransition
• CompoundReferenceMapType : TargetedExperiment
• compounds : LightTargetedExperiment
• compounds_ : TargetedExperiment
• CompoundSpectrumPair() : MetaboTargetedAssay::CompoundSpectrumPair
• CompoundTargetDecoyPair() : MetaboTargetedAssay::CompoundTargetDecoyPair
• CompoundTransitionMapType : MRMAssay
• CompoundType : IonMobilityScoring , OpenSwathScoring
• CompoundVectorType : MRMAssay
• compress() : ConvexHull2D
• compressData() : ZlibCompression
• CompressedInputSource() : CompressedInputSource
• compression : MzMLHandlerHelper::BinaryData
• compressionType_ : MzXMLHandler::SpectrumData
• compressString() : ZlibCompression
• compressTrie() : ACTrie
• compressTrieDB() : InspectOutfile
• compute() : AScore , Contaminants , DBSuitability , FeatureDeconvolution , FeatureSummary , FragmentMassError , FWHM , HyperScore , IdentificationSummary , ILPDCWrapper , MassExplainer , MetaboliteFeatureDeconvolution , MissedCleavages , MorpheusScore , Ms2IdentificationRate , Ms2SpectrumStats , MzCalibration , PeptideMass , PSMExplainedIonCurrent , RTAlignment , SpectrumCount , TIC
• compute_additional_points_ : EmgGradientDescent
• compute_F() : SpectraSTSimilarityScore
• compute_peak_quality_ : MRMTransitionGroupPicker
• compute_peak_shape_metrics_ : MRMTransitionGroupPicker
• compute_total_mi_ : MRMTransitionGroupPicker
• compute_z() : EmgGradientDescent , EmgGradientDescent_friend
• computeApexSNR() : ElutionPeakDetection
• computeAveragineSimScore_() : FeatureFindingMetabo
• computeBaseProbability_() : AScore
• computeBestClusterForCenter_() : FeatureGroupingAlgorithmKD
• computeBinnedCoverage() : MRMRTNormalizer
• computeCCs_() : MapAlignmentAlgorithmKD
• computeChiSquare() : LinearRegression
• computeClustering_() : QTClusterFinder
• computeConnectedComponents() : IDBoostGraph
• computeConsensus() : ConsensusFeature
• computeCorrelation() : ConsensusMapNormalizerAlgorithmThreshold
• computeCosineSim_() : AccurateMassSearchEngine , FeatureFindingMetabo
• computeCoverage() : ProteinIdentification
• computeCoverageFromEvidenceMapping_() : ProteinIdentification
• computeCumulativeScore_() : AScore
• computeDataProperties_() : MzMLHandlerHelper
• computeDechargeConsensus() : ConsensusFeature
• computeDeltaScores() : OPXLHelper
• computeFileHash() : FileHandler
• computeFwhmArea() : MassTrace
• computeFwhmAreaSmooth() : MassTrace
• computeGoodness_() : LinearRegression
• computeGrid_() : IonMobilityScoring
• computeHyperScore() : MetaboliteSpectralMatching
• computeHyperScore_() : MetaboliteSpectralMatching
• computeInitialMean() : EmgGradientDescent , EmgGradientDescent_friend
• computeIntensityProfile() : FeatureFinderAlgorithmPickedHelperStructs::MassTraces
• computeIonMobilogram() : IonMobilityScoring
• computeIsotopePatternSimilarity_() : AccurateMassSearchEngine
• computeLabelingStatistics_() : IsobaricQuantifier
• computeLLAndIncorrectPosteriorsFromLogDensities() : PosteriorErrorProbabilityModel
• computeLogLikelihood() : PosteriorErrorProbabilityModel
• computeMassTraceNoise() : ElutionPeakDetection
• computeMassTraceSNR() : ElutionPeakDetection
• computeMedian_() : SignalToNoiseEstimatorMedianRapid
• computeMedianIntensity_() : MassTrace
• computeMedians() : ConsensusMapNormalizerAlgorithmMedian
• computeMedians_() : MapAlignmentAlgorithmIdentification
• computeModifications() : ProteinIdentification
• computeMonoisotopicConsensus() : ConsensusFeature
• computeMuMaxDistance() : EmgGradientDescent , EmgGradientDescent_friend
• computeNoiseInWindows_() : SignalToNoiseEstimatorMedianRapid
• computeNormalizationFactors_() : IsobaricNormalizer
• computePeakArea() : MassTrace
• computePermutations_() : AScore
• computePointY() : LinearRegression
• computePrecursorError() : OPXLHelper
• computePrecursorId() : OpenSwathHelper
• computePrecursorPurities() : PrecursorPurity
• computePrecursorPurity() : PrecursorPurity
• computePrecursorPurity_() : IsobaricChannelExtractor
• computeProbability() : PosteriorErrorProbabilityModel
• computePScore() : PScore
• computeQuality_() : MRMTransitionGroupPicker , QTCluster
• computeRegression() : LinearRegression , QuadraticRegression
• computeRegressionWeighted() : LinearRegression , QuadraticRegression
• computeScore_() : MRMFeatureSelector , MRMFeatureSelector_test
• computeSelection_() : Plot3DOpenGLCanvas
• computeSharedIonCount() : NeighborSeq
• computeSingleScanPrecursorPurity_() : IsobaricChannelExtractor
• computeSiteDeterminingIons_() : AScore
• computeSlice_() : ILPDCWrapper
• computeSliceOld_() : ILPDCWrapper
• computeSmoothedPeakArea() : MassTrace
• computeSonarScores() : SONARScoring
• computeSonarWindows_() : OpenSwathWorkflowSonar
• computeStatistics_() : LayerStatistics , LayerStatisticsConsensusMap , LayerStatisticsFeatureMap , LayerStatisticsIdent , LayerStatisticsPeakMap
• computeStats_() : IsobaricIsotopeCorrector
• computeSTN_() : SignalToNoiseEstimator< Container > , SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• computeTheoretical() : TraceFitter
• computeTrafosByOriginalRT() : MapAlignmentAlgorithmTreeGuided
• computeTransformations_() : MapAlignmentAlgorithmIdentification
• computeTransformedFeatureMaps() : MapAlignmentAlgorithmTreeGuided
• computeTransitionGroupId() : OpenSwathHelper
• computeWeightedChiSquare() : LinearRegression
• computeWithDetail() : HyperScore
• computeXCorr_() : SONARScoring
• concatenate() : ListUtils , String
• concatenateSpectra() : SpectrumAddition
• concatMULTISEPeptideIds() : PercolatorFeatureSetHelper
• concentration_ : Sample
• concentration_units : AbsoluteQuantitationStandards::featureConcentration , AbsoluteQuantitationStandards::runConcentration
• concentration_units_ : AbsoluteQuantitationMethod
• condition_ : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , TriqlerFile::TriqlerLine_
• ConfidenceScoring() : ConfidenceScoring
• config_ : SqMassFile
• Configuration : IncludeExcludeTarget , ReactionMonitoringTransition
• configuration_list_ : TraMLProduct
• ConfigurationListType : TraMLHandler
• configurations_ : IncludeExcludeTarget
• configure() : LogConfigHandler
• conn_ : OSWFile
• connectEdgeSignals() : TOPPASScene
• connection_line_color_ : Annotation1DCaret< DataPoint >
• connectMergerVertexSignals() : TOPPASScene
• connectOutputVertexSignals() : TOPPASScene
• connectToolVertexSignals() : TOPPASScene
• connectVertexSignals() : TOPPASScene
• connectVisualizer_() : MetaDataBrowser
• consensus_feature_filenames : MSstatsFile::AggregatedConsensusInfo , TriqlerFile::AggregatedConsensusInfo
• consensus_feature_intensities : MSstatsFile::AggregatedConsensusInfo , TriqlerFile::AggregatedConsensusInfo
• consensus_feature_labels : MSstatsFile::AggregatedConsensusInfo , TriqlerFile::AggregatedConsensusInfo
• consensus_feature_peptide_hit_user_value_keys_ : MzTab::CMMzTabStream
• consensus_feature_peptide_identification_user_value_keys_ : MzTab::CMMzTabStream
• consensus_feature_retention_times : MSstatsFile::AggregatedConsensusInfo , TriqlerFile::AggregatedConsensusInfo
• consensus_feature_user_value_keys_ : MzTab::CMMzTabStream
• consensus_map_ : FeatureFinderMultiplexAlgorithm , ConsensusXMLHandler , LayerDataConsensus , MzTab::CMMzTabStream
• ConsensusFeature() : ConsensusFeature
• ConsensusIDAlgorithm() : ConsensusIDAlgorithm
• ConsensusIDAlgorithmAverage() : ConsensusIDAlgorithmAverage
• ConsensusIDAlgorithmBest() : ConsensusIDAlgorithmBest
• ConsensusIDAlgorithmIdentity() : ConsensusIDAlgorithmIdentity
• ConsensusIDAlgorithmPEPIons() : ConsensusIDAlgorithmPEPIons
• ConsensusIDAlgorithmPEPMatrix() : ConsensusIDAlgorithmPEPMatrix
• ConsensusIDAlgorithmRanks() : ConsensusIDAlgorithmRanks
• ConsensusIDAlgorithmSimilarity() : ConsensusIDAlgorithmSimilarity
• ConsensusIDAlgorithmWorst() : ConsensusIDAlgorithmWorst
• ConsensusMap() : ConsensusMap
• ConsensusMapMergerAlgorithm() : ConsensusMapMergerAlgorithm
• ConsensusMapNormalizerAlgorithmMedian() : ConsensusMapNormalizerAlgorithmMedian
• ConsensusMapNormalizerAlgorithmQuantile() : ConsensusMapNormalizerAlgorithmQuantile
• ConsensusMapNormalizerAlgorithmThreshold : ConsensusMapNormalizerAlgorithmMedian , ConsensusMapNormalizerAlgorithmThreshold
• ConsensusMapSharedPtrType : LayerDataDefs , PlotCanvas , TOPPViewBase , TVControllerBase
• ConsensusMapType : LayerDataDefs , PlotCanvas , TOPPViewBase , TVControllerBase
• CONSENSUSXML : FileTypes
• ConsensusXMLFile() : ConsensusXMLFile
• ConsensusXMLHandler() : ConsensusXMLHandler
• considered_hits_ : ConsensusIDAlgorithm
• console_width_ : ConsoleUtils
• ConsoleUtils() : ConsoleUtils
• ConsoleWidthTest : ConsoleUtils
• const_abundances_iterator : IMSIsotopeDistribution
• const_cell_iterator : HashGrid< Cluster >
• CONST_CONT_IT : MatchedIterator< CONT_T, TRAIT, CONST_T >
• const_enzymes_ : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• const_grid_iterator : HashGrid< Cluster >
• const_iterator : _Iterator< _Val, _Ref, _Ptr > , KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , CalibrationData , ConsensusFeature , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType > , EmpiricalFormula , ExposedVector< VectorElement > , FeatureFinderAlgorithmPickedHelperStructs::MassTraces , HashGrid< Cluster > , IMSAlphabet , IsotopeDistribution , MassTrace , Mobilogram , MSExperiment , XCorrArrayType
• const_mass_iterator : IMSAlphabet
• const_masses_iterator : IMSIsotopeDistribution
• const_modified_residues_ : ResidueDB
• const_name_iterator : IMSAlphabet
• const_peaks_iterator : IMSIsotopeDistribution
• const_pointer : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , AASequence::ConstIterator , AASequence::Iterator , NASequence::ConstIterator , NASequence::Iterator
• const_reference : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , AASequence::ConstIterator , AASequence::Iterator , ConstRefVector< ContainerT > , ExposedVector< VectorElement > , NASequence::ConstIterator , NASequence::Iterator
• const_residues_ : ResidueDB
• const_reverse_iterator : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , ExposedVector< VectorElement > , IsotopeDistribution , MassTrace , Mobilogram
• const_weights_ : SequestOutfile
• CONSTANT : MassAnalyzer
• ConstAreaIterator : MSExperiment
• ConstEdgeIterator : TOPPASScene , TOPPASVertex
• ConstEntryIterator : Param::ParamNode
• ConstEnzymeIterator : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• ConstExperimentSharedPtrType : LayerDataDefs , PlotCanvas
• ConstIterator() : AASequence::ConstIterator , Annotations1DContainer , ConsensusMap , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType > , EmpiricalFormula , FeatureMap , HashGrid< Cluster >::ConstIterator , IsotopeDistribution , Histogram< ValueType, BinSizeType > , Mobilogram , MSChromatogram , MSExperiment , MSSpectrum , NASequence::ConstIterator , RibonucleotideDB , String , StringListUtils , TextFile
• ConstNodeIterator : Param::ParamNode
• constraints_type : RealMassDecomposer
• ConstRefVector() : ConstRefVector< ContainerT > , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
• ConstRefVectorConstIterator() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
• ConstRefVectorIterator() : ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
• ConstReverseIterator : ConsensusMap , ConstRefVector< ContainerT > , FeatureMap , IsotopeDistribution , Mobilogram , MSChromatogram , MSSpectrum , String , StringListUtils , TextFile
• ConstRibonucleotidePtr : NucleicAcidSearchEngine , ModifiedNASequenceGenerator , NASequence , RibonucleotideDB
• constructFile_() : MSstatsFile , TriqlerFile
• constructHeader_() : IBSpectraFile
• constructTargetDecoyMassMapping() : MetaboTargetedTargetDecoy
• constructTargTransList_() : MRMFeatureSelector , MRMFeatureSelector_test
• constructTransitionsList() : TargetedSpectraExtractor
• constructTransitionsMap_() : MetaboTargetedTargetDecoy
• ConstVertexIterator : TOPPASScene
• consumeChromatogram() : FullSwathFileConsumer , IMSDataConsumer , MSDataAggregatingConsumer , MSDataCachedConsumer , MSDataChainingConsumer , MSDataSqlConsumer , MSDataStoringConsumer , MSDataTransformingConsumer , MSDataWritingConsumer , NoopMSDataConsumer , NoopMSDataWritingConsumer
• consumeCVTerms() : CVTermList , CVTermListInterface
• consumeMS1Spectrum_() : CachedSwathFileConsumer , FullSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• consumer_ : MzMLHandler , MzXMLHandler
• consumers_ : MSDataChainingConsumer
• consumeSpectrum() : FullSwathFileConsumer , IMSDataConsumer , MSDataAggregatingConsumer , MSDataCachedConsumer , MSDataChainingConsumer , MSDataSqlConsumer , MSDataStoringConsumer , MSDataTransformingConsumer , MSDataWritingConsumer , NoopMSDataConsumer , NoopMSDataWritingConsumer
• consumeSwathSpectrum_() : CachedSwathFileConsumer , FullSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• consuming_possible_ : FullSwathFileConsumer
• CONT_IT : MatchedIterator< CONT_T, TRAIT, CONST_T >
• contact : MzTabMetaData , MzTabMMetaData
• Contact : TargetedExperiment , Contact
• contact_info_ : ContactPerson , ContactPersonVisualizer
• contact_ref : Configuration , Prediction
• ContactPerson() : ContactPerson
• ContactPersonVisualizer() : ContactPersonVisualizer
• contacts_ : ExperimentalSettings , TargetedExperiment
• container : IMSAlphabet
• container_type : BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value >
• ContainerType : AcquisitionInfo , ConstRefVector< ContainerT > , EmgModel , IMSAlphabetParser< AlphabetElementType, Container, InputSource > , IsotopeDistribution , LevMarqFitter1D , BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value > , Mobilogram , MSChromatogram , MSSpectrum
• contains() : EmpiricalFormula , FileTypeList , ListUtils , RangeBase
• contains_invalid_references : TargetedExperiment::SummaryStatistics
• containsAll() : RangeManager< RangeBases >
• containsIMData() : MSSpectrum
• containsIntensity() : RangeIntensity
• containsInvalidReferences() : TargetedExperiment
• containsMobility() : RangeMobility
• containsMSLevel() : PeakFileOptions
• containsMZ() : RangeMZ
• containsRT() : RangeRT
• containsScanOfLevel() : MSExperiment
• containsTag() : MassDecomposition
• Contaminants() : Contaminants
• content_ : ExperimentalDesign::SampleSection
• context_add_ : PlotCanvas
• contextMenuEvent() : EnhancedTabBar , LayerListView , LogWindow , MultiGradientSelector , Plot1DCanvas , Plot2DCanvas , Plot3DCanvas , TOPPASEdge , TOPPASScene , TOPPASVertex
• CONTINUOUS : LPWrapper
• CONTINUOUSFLOWFASTATOMBOMBARDMENT : IonSource
• ControlledVocabulary() : ControlledVocabulary
• CONVERSION_DTA : DataProcessing
• CONVERSION_MZDATA : DataProcessing
• CONVERSION_MZML : DataProcessing
• CONVERSION_MZXML : DataProcessing
• CONVERSIONDYNODE : IonDetector
• CONVERSIONDYNODEELECTRONMULTIPLIER : IonDetector
• CONVERSIONDYNODEPHOTOMULTIPLIER : IonDetector
• ConversionError() : ConversionError
• convert() : StringManager , MapConversion , TransitionHelper
• convertChromatogramsToSpectra() : ChromatogramTools
• convertData_() : SimpleSVM
• convertModificationSet_() : XTandemInfile
• convertPeptideToAASequence() : OpenSwathDataAccessHelper
• convertPQPToTargetedExperiment() : TransitionPQPFile
• convertPtr() : StringManager
• convertSeedList() : SeedListGenerator
• convertSpectraToChromatograms() : ChromatogramTools
• convertTargetedCompound() : OpenSwathDataAccessHelper
• convertTargetedExp() : OpenSwathDataAccessHelper
• convertTargetedExperimentToPQP() : TransitionPQPFile
• convertTargetedExperimentToTSV() : TransitionTSVFile
• convertToChromatogramPtr() : OpenSwathDataAccessHelper
• convertToFeatureMap() : FIAMSDataProcessor
• convertToOpenMSChromatogram() : OpenSwathDataAccessHelper
• convertToOpenMSChromatogramFilter() : OpenSwathDataAccessHelper
• convertToOpenMSSpectrum() : OpenSwathDataAccessHelper
• convertToSpectrumPtr() : OpenSwathDataAccessHelper
• convertTransition_() : TransitionTSVFile
• convertTSVToTargetedExperiment() : TransitionTSVFile
• convex_hull_ : Feature
• convex_hulls_ : Feature
• convex_hulls_modified_ : Feature
• ConvexHull2D() : ConvexHull2D
• convolve() : CoarseIsotopePatternGenerator
• convolvePow_() : CoarseIsotopePatternGenerator
• convolveSquare_() : CoarseIsotopePatternGenerator
• cookie_ : MascotRemoteQuery
• Coordinate : MSstatsFile , TriqlerFile
• coordinate_ : DPosition< D, TCoordinateType >
• coordinate_container : BasicStatistics< RealT >
• CoordinateType : Annotations1DContainer , BaseModel , BiGaussModel , ChromatogramPeak , DBoundingBox< D > , DPosition< D, TCoordinateType > , DRange< D > , EmgModel , ExtendedIsotopeModel , FeatureDeconvolution , FeatureFinderAlgorithm , Fitter1D , GaussModel , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , DIntervalBase< D > , InterpolationModel , IsotopeModel , MetaboliteFeatureDeconvolution , MobilityPeak1D , MobilityPeak2D , Mobilogram , MSChromatogram , MSExperiment , MSSpectrum , Peak1D , Peak2D
• copy() : Param
• copy_() : TOPPASOutputFileListVertex
• copyBatchTransitions_() : OpenSwathWorkflow
• copyDirRecursively() : File
• copyLayer() : TOPPViewBase
• copyMetaDataOnly() : ProteinIdentification
• CopyOptions : File
• copySearchParams_() : IDMergerAlgorithm
• copySelected() : TOPPASScene
• copySubset() : Param
• corner_ : Plot3DOpenGLCanvas
• corr_factor : DBSuitability::SuitabilityData
• corr_max : Summary
• corr_mean : Summary
• corr_min : Summary
• correct_window_counter_ : FullSwathFileConsumer
• correctGravityAxisOfVisibleArea_() : Plot1DCanvas
• correctIM() : SwathMapMassCorrection
• correctIsotopicImpurities() : IsobaricIsotopeCorrector
• correctly_assigned_fit_param_ : PosteriorErrorProbabilityModel
• correctMass_() : CoarseIsotopePatternGenerator
• correctMZ() : SwathMapMassCorrection
• correctPeptideIntensities_() : FeatureFinderMultiplexAlgorithm
• correctToHighestIntensityMS1Peak() : PrecursorCorrection
• correctToNearestFeature() : PrecursorCorrection
• correctToNearestMS1Peak() : PrecursorCorrection
• correlation_coefficient_ : AbsoluteQuantitationMethod
• COTRANSLATIONAL : ResidueModification
• count() : squared_difference_counted< _Tp, _Dist > , IdentificationSummary::UniqueID , ROCCurve , SummaryStatistics< T > , mean_and_stddev
• count_ : RangeStats< VALUE_TYPE >
• count_centroided : MzMLFile::SpecInfo
• count_empty_ : ConsensusIDAlgorithm
• count_profile : MzMLFile::SpecInfo
• count_unknown : MzMLFile::SpecInfo
• count_within_range() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• countDecoys() : DecoyHelper
• countEnzymatic_() : PercolatorInfile
• counter : LogStreamBuf::LogCacheStruct , StatsCounter
• countHits() : IDFilter
• countInternalCleavageSites() : EnzymaticDigestion
• countLabelsAndTransitionTypes() : MRMFeatureFilter
• countMissedCleavages_() : EnzymaticDigestion
• countPeptides_() : PeptideAndProteinQuant
• countScansInSwath_() : SwathFile
• countTableRows() : SqliteConnector
• countTreatments() : Sample
• coverage : ParentSequence , MzTabNucleicAcidSectionRow , MzTabProteinSectionRow
• coverage_ : ProteinHit
• COVERAGE_UNKNOWN : ProteinHit
• cpep_id_ : MzIdentMLDOMHandler , MzIdentMLHandler , XQuestResultXMLHandler
• cpro_id_ : MzIdentMLDOMHandler , MzIdentMLHandler , XQuestResultXMLHandler
• cpu_speed_ : StopWatch
• crbegin() : Mobilogram
• create() : ListUtils , ProteinIdentification::Mapping , VersionInfo::VersionDetails
• create_() : DimMapper< N_DIM >
• create_rows_for_commmon_metavalue_ : SpectraIDViewTab
• createAdduct_() : MassExplainer
• createAssayLibrary_() : FeatureFinderIdentificationAlgorithm
• createBFPeptideProbabilisticAdderFactor() : MessagePasserFactory< Label >
• createChargeFactor() : MessagePasserFactory< Label >
• createCompound_() : TransitionTSVFile
• createCompoundReferenceMap_() : TargetedExperiment
• createConsensusFeature_() : QTClusterFinder
• createConsensusMapCache() : MasstraceCorrelator
• createDirs() : TOPPASToolVertex
• createEditor() : ListEditorDelegate , ParamEditorDelegate
• createFlankingAAXMLString_() : IdXMLFile
• createIfNotExists_() : CVTermListInterface , MetaInfoInterface
• createIndices_() : MzMLSqliteHandler
• createINI_() : ToolsDialog
• createMassLookup_() : NeighborSeq
• createMemdumpIndex() : CachedMzMLHandler
• createMMSpawns_() : ACTrie
• createMMSubSpawns_() : ACTrie
• createMRMFeature() : MRMTransitionGroupPicker
• createNewRow() : ListTable
• createOutputDir() : TOPPASOutputFileListVertex
• createPeptide_() : TransitionTSVFile
• createPeptideEvidenceFactor() : MessagePasserFactory< Label >
• createPeptideProbabilisticAdderFactor() : MessagePasserFactory< Label >
• createPeptideReferenceMap_() : TargetedExperiment , LightTargetedExperiment
• createPositionXMLString_() : IdXMLFile
• createProtein_() : TransitionTSVFile
• createProteinFactor() : MessagePasserFactory< Label >
• createProteinReferenceMap_() : TargetedExperiment
• createProteinToPeptideIDMap_() : SpectraIDViewTab
• createProteinToPeptideLinks_() : MzTabFile
• createPseudoSpectra() : MasstraceCorrelator
• createRegularizingSumEvidenceFactor() : MessagePasserFactory< Label >
• createReplicateFactor() : MessagePasserFactory< Label >
• createResidueModificationToResidueMap_() : ModifiedPeptideGenerator
• createResources() : TOPPASScene
• createSpawns_() : ACTrie
• createSpec_() : MSExperiment
• createStream_() : StreamHandler
• createSubSpawns_() : ACTrie
• createSumEvidenceFactor() : MessagePasserFactory< Label >
• createSumFactor() : MessagePasserFactory< Label >
• createTable_() : OMSFileStore
• createTableAppliedProcessingStep_() : OMSFileStore
• createTableBaseFeature_() : OMSFileStore
• createTableCVTerm_() : OMSFileStore
• createTableDataValue_DataType_() : OMSFileStore
• createTableIdentifiedMolecule_() : OMSFileStore
• createTableMetaInfo_() : OMSFileStore
• createTableMoleculeType_() : OMSFileStore
• createTableParentMatches_() : OMSFileStore
• createTables() : MzMLSqliteHandler
• createTheoreticalSpectra_() : AScore
• createToolsList_() : ToolsDialog
• createTOPPToolsTreeWidget() : TOPPASBase
• createTransition_() : TransitionTSVFile
• createUnknownFromMassString() : ResidueModification
• creation_date_ : Identification
• crend() : Mobilogram
• CRITICAL : LogWindow
• CRM : InstrumentSettings
• cropFeature_() : FeatureFinderAlgorithmPicked
• CROSS : OPXLDataStructs
• cross_link : OPXLDataStructs::CrossLinkSpectrumMatch
• cross_link_classes_ : XFDRAlgorithm
• cross_link_mass_ : OpenPepXLLFAlgorithm
• cross_link_mass_iso_shift_ : OpenPepXLAlgorithm
• cross_link_mass_light_ : OpenPepXLAlgorithm
• cross_link_mass_mono_link_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
• cross_link_name_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
• cross_link_position : OPXLDataStructs::ProteinProteinCrossLink
• cross_link_residue1_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
• cross_link_residue2_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
• cross_linker_mass : OPXLDataStructs::ProteinProteinCrossLink
• cross_linker_name : OPXLDataStructs::ProteinProteinCrossLink
• cross_linker_name_ : XQuestResultXMLHandler
• crosslink_class_decoys_ : XFDRAlgorithm
• crosslink_class_fulldecoysinterlinks_ : XFDRAlgorithm
• crosslink_class_fulldecoysintralinks_ : XFDRAlgorithm
• crosslink_class_hybriddecoysinterlinks_ : XFDRAlgorithm
• crosslink_class_hybriddecoysintralinks_ : XFDRAlgorithm
• crosslink_class_interdecoys_ : XFDRAlgorithm
• crosslink_class_interlinks_ : XFDRAlgorithm
• crosslink_class_intradecoys_ : XFDRAlgorithm
• crosslink_class_intralinks_ : XFDRAlgorithm
• crosslink_class_monodecoys_ : XFDRAlgorithm
• crosslink_class_monolinks_ : XFDRAlgorithm
• crosslink_class_targets_ : XFDRAlgorithm
• CrossLinksDB() : CrossLinksDB , ModificationsDB
• CSV : FileTypes
• csv_header : PrecursorCorrection
• CsvFile() : CsvFile
• CSVWriter() : CSVWriter
• ct_regex_ : SpectrumAnnotator
• CTERM : Modification
• CTerminal : Residue
• CubicSpline2d() : CubicSpline2d
• curPos() : Bzip2InputStream , GzipInputStream
• curr_v : IDBoostGraph::dfs_ccsplit_visitor
• current_ : GUIProgressLoggerImpl , Param::ParamIterator
• current_analysis_result_ : IdXMLFile , PepXMLFile
• current_base_name_ : PepXMLFile
• current_charge_ : XTandemXMLFile
• current_chull_ : FeatureXMLHandler
• current_column_pos_ : IndentedStream
• current_considered_hits_ : ConsensusIDAlgorithmRanks
• current_data_ : DIATreeTab
• current_feature_ : FeatureXMLHandler
• current_id_ : MzMLHandler , MzMLValidator , XTandemXMLFile
• current_id_hit_ : MzIdentMLHandler
• current_idx_ : LayerData1DBase
• current_layer_ : LayerStack
• current_logger_ : ProgressLogger
• current_max_charge_ : FLASHDeconvAlgorithm
• current_max_mass_ : FLASHDeconvAlgorithm
• current_min_mass_ : FLASHDeconvAlgorithm
• current_mod_location_ : MzIdentMLHandler
• current_modifications_ : PepXMLFile
• current_number_of_runs_ : ConsensusIDAlgorithmRanks
• current_path_ : FLASHDeconvWizardBase , INIFileEditorWindow , SwathWizardBase , TOPPASBase , TOPPViewBase
• current_peak_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::Param
• current_peptide_ : PepXMLFile
• current_protein_ : XTandemXMLFile
• current_proteins_ : PepXMLFile
• current_psm_idx_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• current_scan_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::Param
• current_sequence_ : PepXMLFile
• current_spectrum_id_ : MzIdentMLHandler
• current_spectrum_search_ : XQuestResultXMLHandler
• current_start_ : XTandemXMLFile
• current_step_ref_ : IdentificationData
• current_stop_ : XTandemXMLFile
• currentCellChanged_() : SpectraIDViewTab
• currentChanged_() : EnhancedTabBar
• currentIdChanged() : EnhancedTabBar
• currentLayerParametersChanged_() : Plot2DCanvas
• currentLayerParamtersChanged_() : Plot1DCanvas , Plot3DCanvas
• currently_locked_ : GUILock
• currently_valid_ : PythonSelector
• currentRowChangedAction_() : LayerListView
• currentSpectraSelectionChanged_() : SpectraIDViewTab
• currentTabChanged() : DataSelectionTabs
• curve() : ROCCurve
• custom : MzTabMAssayMetaData , MzTabMetaData , MzTabMMetaData , MzTabSampleMetaData
• customContextMenuRequested_() : FilterList
• customizations_ : Instrument , InstrumentVisualizer
• cut() : ClusterAnalyzer
• cut_off : DBSuitability::SuitabilityData
• cut_off_ : BaseModel
• cutForTime() : FIAMSDataProcessor
• cutoffNeg() : ROCCurve
• cutoffPos() : ROCCurve
• cuts_after_regex_ : DigestionEnzymeRNA
• cuts_after_regexes_ : RNaseDigestion
• cuts_before_regex_ : DigestionEnzymeRNA
• cuts_before_regexes_ : RNaseDigestion
• cv : MzTabMetaData , MzTabMMetaData
• CV : TargetedExperiment , CV
• cv_ : MzIdentMLDOMHandler , MzIdentMLHandler , MzMLHandler , SemanticValidator , TraMLHandler
• cv_identifier_ref_ : CVMappingTerm , CVTerm
• CV_label_ : MzTabParameter
• cv_ref : CVTerm::Unit
• cv_references_ : CVMappingFile , CVMappings
• cv_references_vector_ : CVMappings
• cv_tag_ : SemanticValidator
• cv_term : ScoreType
• cv_terms_ : CVMappingRule , CVTermList , XMLHandler
• cvAcc : QcMLFile::Attachment , QcMLFile::QualityParameter
• CVMappingFile() : CVMappingFile
• CVMappingRule() : CVMappingRule
• CVMappings() : CVMappings
• CVMappingTerm() : CVMappingTerm
• cvParam_() : MzDataHandler
• cvParamToValue() : XMLHandler
• cvRef : QcMLFile::Attachment , QcMLFile::QualityParameter
• CVReference() : CVReference
• cvs : MzIdentMLDOMHandler::DBSequence
• cvs_ : TargetedExperiment
• cvStringToEnum_() : XMLHandler
• cvt_ptr_ : CVTermListInterface
• CVTerm() : ControlledVocabulary::CVTerm , CVTerm
• CVTermList() : CVTermList
• CVTermListInterface() : CVTermListInterface
• cwd_ : InputFile , InputFileList , TOPPASInputFileListVertex
• Cyan : ColorBrewer::Distinct
• CYCLOTRON : MassAnalyzer