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
, TOPPASInputFileListVertex
, TOPPASMergerVertex
, TOPPASOutputFileListVertex
, TOPPASOutputFolderVertex
, TOPPASSplitterVertex
, TOPPASToolVertex
, TOPPASVertex
- 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()
: File
, Param
- 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()
: TOPPASOutputVertex
- 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