- c -

• cacheChunk() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• CachedmzML() : CachedmzML
• CachedMzMLHandler() : CachedMzMLHandler
• CachedSwathFileConsumer() : CachedSwathFileConsumer
• calc_qfdr_() : XFDRAlgorithm
• calcCentroids() : CentroidData
• calcChargeStateIntensities_() : ProtonDistributionModel
• 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
• calculateAddInfo_() : PeakIntensityPredictor
• calculateAndAnnotateIndistProteins() : IDBoostGraph
• calculateAndAnnotateIndistProteins_() : IDBoostGraph
• calculateAndFilterFDR_() : NucleicAcidSearchEngine
• calculateAvgWeight_() : ElementDB
• calculateBackwardPart_() : HiddenMarkovModel
• calculateBias() : AbsoluteQuantitation
• calculateBiasAndR() : AbsoluteQuantitation
• calculateBoundingBox() : Annotation1DPeakItem
• calculateCalibCoeffs_() : TOFCalibration
• calculateChromatographicIdScores() : OpenSwathScoring
• calculateChromatographicScores() : OpenSwathScoring
• calculateCoverages() : IdentificationData
• calculateDIAIdScores() : OpenSwathScoring
• calculateDIAScores() : OpenSwathScoring
• calculateEmissionProbabilities() : HiddenMarkovModel
• calculateEstimatedQVal_() : FalseDiscoveryRate
• calculateFDR_() : FeatureFinderIdentificationAlgorithm
• calculateFDRBasic_() : FalseDiscoveryRate
• calculateFDRs_() : FalseDiscoveryRate
• calculateFilterValuesMean() : MRMFeatureFilter
• calculateFilterValuesPercRSD() : MRMFeatureFilter
• calculateFilterValuesVar() : MRMFeatureFilter
• calculateFitQuality_() : ElutionModelFitter
• calculateForwardPart_() : HiddenMarkovModel
• calculateGaussTable() : SVMWrapper
• calculateGB() : AAIndex
• calculateGridLines_() : Spectrum3DOpenGLCanvas
• calculateIntensityRankInMZWindow() : PScore
• calculateIonRatio() : MRMFeatureFilter
• calculateLibraryScores() : OpenSwathScoring
• calculateMap() : QCBase::SpectraMap
• calculateMonoWeight_() : ElementDB
• calculateMT_() : RTSimulation
• calculatePeakLevelSpectra() : PScore
• calculatePeakShapeMetrics() : PeakIntegrator
• calculatePeakShapeMetrics_() : PeakIntegrator
• calculatePermutationPeptideScores_() : AScore
• calculatePrecursorDIAScores() : OpenSwathScoring
• calculatePrecursorMass_() : NucleicAcidSearchEngine
• calculateProteinProbabilities() : PSProteinInference
• calculateProtonDistribution_() : ProtonDistributionModel
• calculateProtonDistributionCharge1_() : ProtonDistributionModel
• calculateProtonDistributionCharge2_() : ProtonDistributionModel
• calculateProtonDistributionGreater2_() : ProtonDistributionModel
• calculateProtonDistributionIonPair_() : ProtonDistributionModel
• calculateRankMap() : PScore
• calculateRatio() : AbsoluteQuantitation
• calculateResolution() : MRMFeatureFilter
• calculateRTDifference() : MRMFeatureFilter
• calculateTheoreticalIsotopesNumber() : EmpiricalFormula
• calculateXICs_() : OfflinePrecursorIonSelection , PSLPFormulation
• calcXcorrCoelutionScore() : MRMScoring
• calcXcorrCoelutionWeightedScore() : MRMScoring
• calcXcorrContrastCoelutionScore() : MRMScoring
• calcXcorrContrastShapeScore() : MRMScoring
• calcXcorrPrecursorCoelutionScore() : MRMScoring
• calcXcorrPrecursorCombinedCoelutionScore() : MRMScoring
• calcXcorrPrecursorCombinedShapeScore() : MRMScoring
• calcXcorrPrecursorContrastCoelutionScore() : MRMScoring
• calcXcorrPrecursorContrastShapeScore() : MRMScoring
• calcXcorrPrecursorShapeScore() : MRMScoring
• calcXcorrShapeScore() : MRMScoring
• calcXcorrShapeWeightedScore() : MRMScoring
• CalibrantStats_() : InternalCalibration::CalibrantStats_
• calibrate() : InternalCalibration , TOFCalibration
• CalibrationData() : CalibrationData
• callSiriusQProcess() : SiriusAdapterAlgorithm
• candidateEdges_() : MetaboliteFeatureDeconvolution
• canModificationBeApplied_() : SILACLabeler
• canRun() : JavaInfo , PythonInfo
• canvas() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
• capacity() : ConstRefVector< ContainerT >
• cbegin() : NASequence
• cellClicked_() : SpectraIdentificationViewWidget
• cellindexAtClustercenter_() : HashGrid< Cluster >
• cend() : NASequence
• center() : DIntervalBase< D >
• centerOfBin() : Histogram< ValueType, BinSizeType >
• CentroidData() : CentroidData
• centroidDataModus() : SuperHirnParameters
• CentroidPeak() : CentroidPeak
• changedOutputFolder() : TOPPASScene
• changedParameter() : TOPPASScene
• changeElutionTimesByFactor() : FeatureLCProfile
• changeLabel() : TOPPViewBase
• changeLayerFilterState() : SpectrumCanvas
• changeLayerFlag() : TOPPViewBase
• changeLegendVisibility() : SpectrumCanvas , SpectrumWidget
• changeUnassigned() : TOPPViewBase
• changeVisibility() : SpectrumCanvas
• changeVisibleArea_() : Spectrum1DCanvas , SpectrumCanvas
• characters() : ConsensusXMLFile , CVMappingFile , FeatureXMLFile , MascotXMLHandler , MzDataHandler , MzIdentMLHandler , MzMLHandler , MzQuantMLHandler , MzXMLHandler , PTMXMLHandler , SemanticValidator , ToolDescriptionHandler , TraMLHandler , UnimodXMLHandler , XMLHandler , OMSSAXMLFile , QcMLFile , XTandemXMLFile
• charge() : KDTreeFeatureMaps
• ChargedIndexSet() : IsotopeCluster::ChargedIndexSet
• ChargePair() : ChargePair
• chargeTestworthy_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• chauvenet() : MRMRTNormalizer
• chauvenet_probability() : MRMRTNormalizer
• check_() : DataFilterDialog , TOPPASVertex::TOPPASFilenames
• check_AC() : SHFeature
• check_elution_peak() : ProcessData
• check_elution_peak_belong() : ProcessData
• check_feature_list_empty() : LCMS
• check_LCMS_name() : LCMS
• check_match_by_id() : SHFeature
• check_MODIFICATION() : MS2Info
• check_MS2_empty() : SHFeature
• check_MZ_occurence() : ProcessData
• check_raw_spec_name_empty() : LCMS
• check_tree() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• checkAndGetTermByName() : ControlledVocabulary
• checkAppliedProcessingSteps_() : IdentificationData
• checkBelonging() : BackgroundIntensityBin
• checkConditionISO_() : MSstatsFile
• checkConditionLFQ_() : MSstatsFile
• checkDatumRange() : TransformationModel
• checkDefaults() : Param
• checked() : Spectrum1DGoToDialog , Spectrum2DGoToDialog
• checkedToDouble_() : EDTAFile
• checkedToInt_() : EDTAFile
• checkExtraFeatures() : PercolatorFeatureSetHelper
• checkFeatureQuality_() : FeatureFinderAlgorithmPicked
• checkFeatureSpectraNumber() : SiriusAdapterAlgorithm
• checkFormula_() : Adduct
• checkForRequiredUserParams_() : PrecursorIonSelection
• checkForSignificantPeak_() : MultiplexFiltering
• checkHits_() : IDMapper
• checkIds_() : BaseGroupFinder
• checkIfFeatureExtractionExists() : FTPeakDetectController
• checkIfIniParametersAreApplicable_() : TOPPBase
• checkIfWeAreDone() : TOPPASScene
• checkIsotopeBelongingAndAdjustMass() : MSPeak
• checkLOD() : AbsoluteQuantitationMethod
• checkLOQ() : AbsoluteQuantitationMethod
• checkMassRanges_() : OfflinePrecursorIonSelection
• 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
• checkPositionForPlausibility_() : IsotopeWaveletTransform< PeakType >
• checkPPMTheoModel_() : IsotopeWaveletTransform< PeakType >
• checkPreferences_() : TOPPViewBase
• checkPyProphetInput_() : SwathTabWidget
• checkRange() : MRMFeatureFilter
• checkSatellite() : MultiplexFilteredPeak
• checkScoreTypes_() : IdentificationData
• checkSequenceUniqueness_() : MzTab
• checkSize() : SaveImageDialog
• checkSolution_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• checkSwathMap() : OpenSwathHelper
• checkSwathMapAndSelectTransitions() : OpenSwathHelper
• checkTDAnnotation_() : IDScoreGetterSetter
• checkUniqueIdentifiers_() : XMLHandler
• checkUnorderedContent_() : MSstatsFile
• checkValidity_() : TOPPASInputFileDialog , TOPPASIOMappingDialog , TOPPASOutputFilesDialog
• checkValidWeight() : TransformationModel
• chooseBestParameters_() : SimpleSVM
• chooseDecoys_() : ConfidenceScoring
• chooseElutionProfile_() : RawMSSignalSimulation
• chooseTraceFitter_() : FeatureFinderAlgorithmPicked
• chop() : String , StringUtils
• Chromatogram() : Chromatogram
• chromatogram_flag_set() : LayerData
• chromatogramIdsMatch() : MRMTransitionGroup< ChromatogramType, TransitionType >
• ChromatogramMeta() : ChromatogramMeta
• ChromatogramPeak() : ChromatogramPeak
• ChromatogramSettings() : ChromatogramSettings
• ChromatogramTools() : ChromatogramTools
• ChromeleonFile() : ChromeleonFile
• Chunk() : MSSpectrum::Chunk
• chunk_() : FeatureFinderIdentificationAlgorithm
• chunkAt() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• Chunks() : MSSpectrum::Chunks
• chunkSize() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• classifyFeatures_() : FeatureFinderIdentificationAlgorithm
• classifyIsotopes_() : CompNovoIonScoringBase
• cleanDeconvPeaks() : Deisotoper
• cleanup() : IdentificationData
• cleanupTransitions_() : TransitionTSVFile
• clear() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , CalibrationData , ConsensusFeature , ConsensusMap , ConstRefVector< ContainerT > , ConvexHull2D , CsvFile , DataFilters , Date , DateTime , DistanceMatrix< Value > , DPosition< D, TCoordinateType > , FeatureMap , HashGrid< Cluster > , HiddenMarkovModel , IMSAlphabet , DIntervalBase< D > , IsotopeDistribution , KDTreeFeatureMaps , AveragePosition< D > , BasicStatistics< RealT > , Matrix< Value > , MetaInfo , MSChromatogram , MSExperiment , MSSpectrum , NASequence , Param , ParamEditor , PeakIndex , QCBase::SpectraMap , StopWatch , TargetedExperiment , TIC , TOPPASResources
• clear_() : DataValue , ElementDB , MetaInfoVisualizer , ResidueDB
• clear_feature_list() : LCMS
• clearCache() : LogStreamBuf
• clearCurrentProcessingStep() : IdentificationData
• clearEluents() : Gradient
• clearInitialTransitionProbabilities() : HiddenMarkovModel
• clearMetaDataArrays() : MSExperiment
• clearMetaInfo() : MetaInfoInterface
• clearMSLevels() : PeakFileOptions
• clearPercentages() : Gradient
• clearRanges() : RangeManager< D >
• clearResidueModifications_() : ResidueDB
• clearResidues_() : ResidueDB
• clearResult() : ProteinResolver
• clearTags() : Param
• clearTimepoints() : Gradient
• clearTrainingEmissionProbabilities() : HiddenMarkovModel
• clearUniqueId() : UniqueIdInterface
• cleavageCorrectionTerm() : PScore
• CleavageModel_() : EnzymaticDigestionLogModel::CleavageModel_
• clicked() : TOPPASVertex
• clockTime() : StopWatch::TimeDiff_
• clone() : Digestion , Modification , SampleTreatment , Tagging
• close() : Bzip2Ifstream , GzipIfstream , HDF5Connector
• closeByTab() : TOPPASBase , TOPPViewBase
• closeEvent() : INIFileEditorWindow , SpectrumWidget , TOPPASBase , TOPPASWidget , TOPPViewBase
• closeFile() : TOPPASBase , TOPPViewBase
• closeListEditor_() : ParamEditorDelegate
• cluster() : ClusterHierarchical , GridBasedClustering< Metric > , MultiplexClustering
• ClusterAnalyzer() : ClusterAnalyzer
• ClusteredMS2ConsensusSpectrum() : ClusteredMS2ConsensusSpectrum
• ClusterFunctor() : ClusterFunctor
• ClusterHierarchical() : ClusterHierarchical
• clusterIndistProteinsAndPeptides() : IDBoostGraph
• clusterIndistProteinsAndPeptidesAndExtendGraph() : IDBoostGraph
• ClusteringGrid() : ClusteringGrid
• ClusterProxyKD() : ClusterProxyKD
• clusterSeeds_() : IsotopeWaveletTransform< PeakType >
• CMMzTabStream() : MzTab::CMMzTabStream
• cmpOligos_() : LibSVMEncoder
• CoarseIsotopePatternGenerator() : CoarseIsotopePatternGenerator
• cohesion() : ClusterAnalyzer
• col() : Matrix< Value >
• colIndex() : Matrix< Value >
• collapseStringVector() : TOPPViewIdentificationViewBehavior
• collectDecompositionsRecursively_() : IntegerMassDecomposer< ValueType, DecompositionValueType >
• collectFragmentScansInArea() : Spectrum2DCanvas
• collectPrecursorCandidates() : OPXLHelper
• collectRatios_() : IsobaricNormalizer
• collectSetParameter() : QcMLFile
• colnames() : CSVWriter , DataMatrix , IDataFrameWriter
• color() : MultiGradient
• ColorSelector() : ColorSelector
• cols() : Matrix< Value >
• columnExists() : SqliteConnector
• ColumnHeader() : ConsensusMap::ColumnHeader
• combineMods() : ResidueModification
• combinePrecursorPurities() : PrecursorPurity
• combineTopRanksFromPairs() : OPXLHelper
• commitAndCloseComboBox_() : ParamEditorDelegate
• commitAndCloseLineEdit_() : ParamEditorDelegate
• commitAndCloseListEditor_() : ParamEditorDelegate
• Compare() : MapAlignmentAlgorithmSpectrumAlignment::Compare
• compare_() : Contaminants
• compare_AC() : MS2Info
• compare_feature_mass() : LCMS
• compareByFirst() : SpectraMerger
• compareChargeStates_() : ConsensusIDAlgorithm
• compareFeatureMassValuesAtPPMLevel() : SHFeature
• compareFiles() : FuzzyStringComparator
• compareIDsSmallerScores_() : IDConflictResolverAlgorithm
• compareIteratorToPeak() : ProcessData
• compareLines_() : FuzzyStringComparator
• compareMassValuesAtPPMLevel() : SuperHirnUtil
• compareMZ_() : AScore
• compareMZFeatureBeloning() : MS1FeatureMerger
• comparepeaks_() : SpectrumCheapDPCorr
• compareSpectra_() : CompNovoIdentificationBase
• compareStreams() : FuzzyStringComparator
• compareStrings() : FuzzyStringComparator
• compatible() : MassDecomposition
• compatible_() : PrecursorCorrection
• compatibleIDs_() : StablePairFinder
• ComplementFilter() : ComplementFilter
• ComplementMarker() : ComplementMarker
• CompleteLinkage() : CompleteLinkage
• CompNovoIdentification() : CompNovoIdentification
• CompNovoIdentificationBase() : CompNovoIdentificationBase
• CompNovoIdentificationCID() : CompNovoIdentificationCID
• CompNovoIonScoring() : CompNovoIonScoring
• CompNovoIonScoringBase() : CompNovoIonScoringBase
• CompNovoIonScoringCID() : CompNovoIonScoringCID
• Compomer() : Compomer
• compomerValid_() : MassExplainer
• Compound() : Compound
• compress() : ConvexHull2D
• CompressedInputSource() : CompressedInputSource
• compressSignals_() : RawMSSignalSimulation
• compressString() : ZlibCompression
• compressTrieDB() : InspectOutfile
• compute() : AScore , Contaminants , DBSuitability , FeatureDeconvolution , FragmentMassError , FWHM , HyperScore , ILPDCWrapper , MassExplainer , MetaboliteFeatureDeconvolution , MissedCleavages , MorpheusScore , Ms2IdentificationRate , Ms2SpectrumStats , MzCalibration , PeptideMass , RTAlignment , TIC
• compute_CHRG() : LCElutionPeak
• compute_delta_area() : LCElutionPeak
• compute_F() : SpectraSTSimilarityScore
• compute_z() : EmgGradientDescent , EmgGradientDescent_friend
• computeApexSNR() : ElutionPeakDetection
• computeAveragineSimScore_() : FeatureFindingMetabo
• computeBaseProbability_() : AScore
• computeBestClusterForCenter_() : FeatureGroupingAlgorithmKD
• computeBinnedCoverage() : MRMRTNormalizer
• computeBoundaries_() : EGHModel
• computeCCs_() : MapAlignmentAlgorithmKD
• computeChiSquare() : LinearRegression
• computeClustering_() : QTClusterFinder
• computeConnectedComponents() : IDBoostGraph
• computeConsensus() : ConsensusFeature
• computeConsensusStats_() : LayerStatisticsDialog
• computeCorrelation() : ConsensusMapNormalizerAlgorithmThreshold
• computeCosineSim_() : AccurateMassSearchEngine , FeatureFindingMetabo
• computeCoverage() : ProteinIdentification
• computeCumulativeScore_() : AScore
• computeDataProperties_() : MzMLHandlerHelper
• computeDechargeConsensus() : ConsensusFeature
• computeDeltaArea() : MS1FeatureMerger
• computeDeltaScores() : OPXLHelper
• computeFeatureStats_() : LayerStatisticsDialog
• computeFileHash() : FileHandler
• computeFwhmArea() : MassTrace
• computeFwhmAreaSmooth() : MassTrace
• computeGoodness_() : LinearRegression
• computeHyperScore() : MetaboliteSpectralMatching
• computeHyperScore_() : MetaboliteSpectralMatching
• computeInitialMean() : EmgGradientDescent , EmgGradientDescent_friend
• computeIntensityHist() : BackgroundIntensityBin
• computeIntensityOfMSD_() : ProteinResolver
• computeIntensityProfile() : FeatureFinderAlgorithmPickedHelperStructs::MassTraces
• computeIsotopeDistributionSize_() : IsotopeWavelet
• computeIsotopePatternSimilarity_() : AccurateMassSearchEngine
• computeKernelMatrix() : SVMWrapper
• computeLabelingStatistics_() : IsobaricQuantifier
• computeLCElutionPeakParameters() : LCElutionPeak
• computeLLAndIncorrectPosteriorsFromLogDensities() : PosteriorErrorProbabilityModel
• computeLogLikelihood() : PosteriorErrorProbabilityModel
• computeMassTraceNoise() : ElutionPeakDetection
• computeMassTraceSNR() : ElutionPeakDetection
• computeMedian_() : SignalToNoiseEstimatorMedianRapid
• computeMedianIntensity_() : MassTrace
• computeMedians() : ConsensusMapNormalizerAlgorithmMedian
• computeMedians_() : MapAlignmentAlgorithmIdentification
• computeMetaAverages_() : LayerStatisticsDialog
• computeMetaDataArrayStats_() : LayerStatisticsDialog
• computeMinSpacing() : IsotopeWaveletTransform< PeakType >
• computeModifications() : ProteinIdentification
• computeMonoisotopicConsensus() : ConsensusFeature
• computeMS2SpectrumParameters() : MS2ConsensusSpectrum
• computeMuMaxDistance() : EmgGradientDescent , EmgGradientDescent_friend
• computeNewMS1FeatureParameters() : MS1FeatureMerger
• computeNoiseInWindows_() : SignalToNoiseEstimatorMedianRapid
• computeNormalizationFactors_() : IsobaricNormalizer
• computePeakArea() : MassTrace
• computePeakStats_() : LayerStatisticsDialog
• computePermutations_() : AScore
• 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_() : Spectrum3DOpenGLCanvas
• computeSingleScanPrecursorPurity_() : IsobaricChannelExtractor
• computeSiteDeterminingIons_() : AScore
• computeSlice_() : ILPDCWrapper
• computeSliceOld_() : ILPDCWrapper
• computeSmoothedPeakArea() : MassTrace
• computeSonarScores() : SONARScoring
• computeSonarWindows_() : OpenSwathWorkflowSonar
• computeStats_() : IsobaricIsotopeCorrector
• computeSTN_() : SignalToNoiseEstimator< Container > , SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• computeTheoretical() : TraceFitter
• computeTrafosByOriginalRT() : MapAlignmentAlgorithmTreeGuided
• computeTransformations_() : MapAlignmentAlgorithmIdentification
• computeTransformedFeatureMaps() : MapAlignmentAlgorithmTreeGuided
• computeTransitionGroupId() : OpenSwathHelper
• computeWeightedChiSquare() : LinearRegression
• computeXCorr_() : SONARScoring
• concatenate() : ListUtils , String
• concatMULTISEPeptideIds() : PercolatorFeatureSetHelper
• condensIsotopePattern() : ConsensusIsotopePattern
• ConfidenceScoring() : ConfidenceScoring
• configure() : LogConfigHandler
• ConnectedComponent() : ConnectedComponent
• connectEdgeSignals() : TOPPASScene
• connectMergerVertexSignals() : TOPPASScene
• connectOutputVertexSignals() : TOPPASScene
• connectToolVertexSignals() : TOPPASScene
• connectVertexSignals() : TOPPASScene
• connectVisualizer_() : MetaDataBrowser
• ConsensusFeature() : ConsensusFeature
• ConsensusIDAlgorithm() : ConsensusIDAlgorithm
• ConsensusIDAlgorithmAverage() : ConsensusIDAlgorithmAverage
• ConsensusIDAlgorithmBest() : ConsensusIDAlgorithmBest
• ConsensusIDAlgorithmIdentity() : ConsensusIDAlgorithmIdentity
• ConsensusIDAlgorithmPEPIons() : ConsensusIDAlgorithmPEPIons
• ConsensusIDAlgorithmPEPMatrix() : ConsensusIDAlgorithmPEPMatrix
• ConsensusIDAlgorithmRanks() : ConsensusIDAlgorithmRanks
• ConsensusIDAlgorithmSimilarity() : ConsensusIDAlgorithmSimilarity
• ConsensusIDAlgorithmWorst() : ConsensusIDAlgorithmWorst
• ConsensusIsotopePattern() : ConsensusIsotopePattern
• ConsensusMap() : ConsensusMap
• ConsensusMapMergerAlgorithm() : ConsensusMapMergerAlgorithm
• ConsensusMapNormalizerAlgorithmMedian() : ConsensusMapNormalizerAlgorithmMedian
• ConsensusMapNormalizerAlgorithmQuantile() : ConsensusMapNormalizerAlgorithmQuantile
• ConsensusMapNormalizerAlgorithmThreshold() : ConsensusMapNormalizerAlgorithmThreshold
• ConsensusXMLFile() : ConsensusXMLFile
• ConsoleUtils() : ConsoleUtils
• ConstIterator() : AASequence::ConstIterator , HashGrid< Cluster >::ConstIterator , NASequence::ConstIterator
• ConstRefVector() : ConstRefVector< ContainerT >
• ConstRefVectorConstIterator() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
• ConstRefVectorIterator() : ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
• constructClusteredConsenusSpectraFragments() : ClusteredMS2ConsensusSpectrum
• constructConsusPattern() : ConsensusIsotopePattern
• constructFile_() : MSstatsFile
• constructHeader_() : IBSpectraFile
• constructMS1FeatureFromMS2Feature() : FTPeakDetectController
• constructTargTransList_() : MRMFeatureSelector , MRMFeatureSelector_test
• consumeChromatogram() : FullSwathFileConsumer , IMSDataConsumer , MSDataAggregatingConsumer , MSDataCachedConsumer , MSDataChainingConsumer , MSDataSqlConsumer , MSDataStoringConsumer , MSDataTransformingConsumer , MSDataWritingConsumer , NoopMSDataConsumer , NoopMSDataWritingConsumer
• consumeCVTerms() : CVTermList , CVTermListInterface
• consumeMS1Spectrum_() : CachedSwathFileConsumer , FullSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• consumeSpectrum() : FullSwathFileConsumer , IMSDataConsumer , MSDataAggregatingConsumer , MSDataCachedConsumer , MSDataChainingConsumer , MSDataSqlConsumer , MSDataStoringConsumer , MSDataTransformingConsumer , MSDataWritingConsumer , NoopMSDataConsumer , NoopMSDataWritingConsumer
• consumeSwathSpectrum_() : CachedSwathFileConsumer , FullSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• Contact() : Contact
• ContactPerson() : ContactPerson
• ContactPersonVisualizer() : ContactPersonVisualizer
• contains() : EmpiricalFormula , ListUtils
• containsIMData() : MSSpectrum
• containsInvalidReferences() : TargetedExperiment
• containsMSLevel() : PeakFileOptions
• containsScanOfLevel() : MSExperiment
• containsTag() : MassDecomposition
• Contaminants() : Contaminants
• contextMenuEvent() : EnhancedTabBar , MultiGradientSelector , Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , TOPPASEdge , TOPPASLogWindow , TOPPASScene , TOPPASTabBar , TOPPASVertex
• ContinuousWaveletTransform() : ContinuousWaveletTransform
• ContinuousWaveletTransformNumIntegration() : ContinuousWaveletTransformNumIntegration
• ControlledVocabulary() : ControlledVocabulary
• ConversionError() : ConversionError
• convert() : StringManager , MapConversion , TransitionHelper
• convert_ms_peaks() : ProcessData
• convert_to_LC_elution_peak() : ProcessData
• convertChromatogramsToSpectra() : ChromatogramTools
• convertData_() : SimpleSVM
• convertModificationSet_() : XTandemInfile
• convertPeptideIdScores_() : PrecursorIonSelection
• convertPeptideToAASequence() : OpenSwathDataAccessHelper
• convertPQPToTargetedExperiment() : TransitionPQPFile
• 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
• ConvexHull2D() : ConvexHull2D
• convolve_() : CoarseIsotopePatternGenerator
• convolvePow_() : CoarseIsotopePatternGenerator
• convolveSquare_() : CoarseIsotopePatternGenerator
• copy() : Param
• copy_() : HiddenMarkovModel , TOPPASOutputFileListVertex
• copyBatchTransitions_() : OpenSwathWorkflow
• copyDirRecursively() : File
• copyLayer() : TOPPViewBase
• copySearchParams_() : IDMergerAlgorithm
• copySelected() : TOPPASScene
• copySubset() : Param
• correctAreaToObeyMinMaxRanges_() : SpectrumWidget
• correctIM() : SwathMapMassCorrection
• correctIsotopicImpurities() : IsobaricIsotopeCorrector
• correctMass_() : CoarseIsotopePatternGenerator
• correctMZ() : SwathMapMassCorrection
• correctPeptideIntensities_() : FeatureFinderMultiplexAlgorithm
• correctToHighestIntensityMS1Peak() : PrecursorCorrection
• correctToNearestFeature() : PrecursorCorrection
• correctToNearestMS1Peak() : PrecursorCorrection
• correlate_() : PeakPickerCWT
• count() : squared_difference_counted< _Tp, _Dist > , ROCCurve , mean_and_stddev
• count_within_range() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• countFreeIDs() : DocumentIDTagger
• countHits() : IDFilter
• countIntensities_() : SvmTheoreticalSpectrumGeneratorTrainer
• countIonizedResidues_() : IonizationSimulation
• countLabelsAndTransitionTypes() : MRMFeatureFilter
• countMissedCleavages_() : EnzymaticDigestion
• countMissedCleavagesTryptic_() : CompNovoIdentificationBase
• countPeptides_() : PeptideAndProteinQuant
• countScansInSwath_() : SwathFile
• countTargetDecoy() : ProteinResolver
• countTreatments() : Sample
• create() : AverageLinkage , BiGaussFitter1D , BiGaussModel , BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSumAgreeingIntensities , ComplementFilter , ComplementMarker , CompleteLinkage , EGHFitter1D , EGHModel , EmgFitter1D , EmgModel , ExtendedIsotopeFitter1D , ExtendedIsotopeModel , Factory< FactoryProduct > , FeatureFinderAlgorithmIsotopeWavelet , FeatureFinderAlgorithmMRM , FeatureFinderAlgorithmPicked , FeatureFinderAlgorithmSH , FeatureGroupingAlgorithmKD , FeatureGroupingAlgorithmLabeled , FeatureGroupingAlgorithmQT , FeatureGroupingAlgorithmUnlabeled , GaussFitter1D , GaussModel , GoodDiffFilter , GUIProgressLoggerImpl , ICPLLabeler , IntensityBalanceFilter , IsotopeDiffFilter , IsotopeFitter1D , IsotopeMarker , IsotopeModel , ITRAQLabeler , LabeledPairFinder , LabelFreeLabeler , ListUtils , MapAlignmentEvaluationAlgorithmPrecision , MapAlignmentEvaluationAlgorithmRecall , NeutralLossDiffFilter , NeutralLossMarker , O18Labeler , PeakAlignment , PoseClusteringAffineSuperimposer , PoseClusteringShiftSuperimposer , ProductModel< 2 > , ProteinIdentification::Mapping , QTClusterFinder , SILACLabeler , SimplePairFinder , SingleLinkage , SpectraSTSimilarityScore , SpectrumAlignmentScore , SpectrumCheapDPCorr , SpectrumPrecursorComparator , StablePairFinder , SteinScottImproveScore , TICFilter , VersionInfo::VersionDetails , ZhangSimilarityScore
• createAdduct_() : MassExplainer
• createAndSolveCombinedLPFeatureBased_() : PSLPFormulation
• createAndSolveCombinedLPForKnownLCMSMapFeatureBased() : PSLPFormulation
• createAndSolveILP_() : PSLPFormulation
• createAndSolveILPForInclusionListCreation() : PSLPFormulation
• createAndSolveILPForKnownLCMSMapFeatureBased() : PSLPFormulation
• createAssayLibrary_() : FeatureFinderIdentificationAlgorithm
• createBFPeptideProbabilisticAdderFactor() : MessagePasserFactory< Label >
• createChargeFactor() : MessagePasserFactory< Label >
• createCompound_() : TransitionTSVFile
• createCompoundReferenceMap_() : TargetedExperiment
• createConsensIsotopPattern() : LCElutionPeak
• createConsensusFeature_() : QTClusterFinder
• createConsensusMapCache() : MasstraceCorrelator
• createContaminants_() : RawMSSignalSimulation
• createDirs() : TOPPASToolVertex
• createEditor() : ListEditorDelegate , ParamEditorDelegate
• createExperiment() : RTSimulation
• createFeatureElutionProfiles() : SuperHirnParameters
• createFeatureMap_() : MSSim
• createFlankingAAXMLString_() : IdXMLFile
• createHRData() : FeatureFinderAlgorithmIsotopeWavelet
• createIfNotExists_() : CVTermListInterface , MetaInfoInterface
• createIndices_() : MzMLSqliteHandler
• createINI_() : ToolsDialog
• createIntensityDistribution_() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
• createMemdumpIndex() : CachedMzMLHandler
• createMetaDistribution_() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
• createModel() : ModelDescription< D >
• createMRMFeature() : MRMTransitionGroupPicker
• createMZFeatureClusters() : MS1FeatureMerger
• createNewRow() : ListTable
• createOutputDir() : TOPPASOutputFileListVertex
• createPeptide_() : TransitionTSVFile
• createPeptideEvidenceFactor() : MessagePasserFactory< Label >
• createPeptideProbabilisticAdderFactor() : MessagePasserFactory< Label >
• createPeptideReferenceMap_() : TargetedExperiment , LightTargetedExperiment
• createPositionXMLString_() : IdXMLFile
• createProtein_() : TransitionTSVFile
• createProteinFactor() : MessagePasserFactory< Label >
• createProteinReferenceMap_() : TargetedExperiment
• createProteinSequenceBasedLPInclusionList() : OfflinePrecursorIonSelection
• createProteinToPeptideLinks_() : MzTabFile
• createPseudoSpectra() : MasstraceCorrelator
• createRandomPartitions() : SVMWrapper
• createRegularizingSumEvidenceFactor() : MessagePasserFactory< Label >
• createReplicateFactor() : MessagePasserFactory< Label >
• createResidueModificationToResidueMap_() : ModifiedPeptideGenerator
• createResources() : TOPPASScene
• createSpec_() : MSExperiment
• createStream_() : StreamHandler
• createSumEvidenceFactor() : MessagePasserFactory< Label >
• createSumFactor() : MessagePasserFactory< Label >
• createTables() : MzMLSqliteHandler
• createTheoreticalSpectra_() : AScore
• createTOPPToolsTreeWidget() : TOPPASBase
• createTransition_() : TransitionTSVFile
• createUnknownFromMassString() : ResidueModification
• cropFeature_() : FeatureFinderAlgorithmPicked
• CrossLinksDB() : CrossLinksDB
• CsvFile() : CsvFile
• CSVWriter() : CSVWriter
• CubicSpline2d() : CubicSpline2d
• curPos() : Bzip2InputStream , GzipInputStream
• currentChanged_() : EnhancedTabBar , TOPPASTabBar
• currentIdChanged() : EnhancedTabBar , TOPPASTabBar
• currentLayerParametersChanged_() : Spectrum2DCanvas
• currentLayerParamtersChanged_() : Spectrum1DCanvas , Spectrum3DCanvas
• curve() : ROCCurve
• customContextMenuRequested_() : FilterList
• cut() : ClusterAnalyzer
• cutForTime() : FIAMSDataProcessor
• cutoffNeg() : ROCCurve
• cutoffPos() : ROCCurve
• CV() : CV
• CVMappingFile() : CVMappingFile
• CVMappingRule() : CVMappingRule
• CVMappings() : CVMappings
• CVMappingTerm() : CVMappingTerm
• cvParam_() : MzDataHandler
• CVReference() : CVReference
• cvStringToEnum_() : XMLHandler
• CVTerm() : ControlledVocabulary::CVTerm , CVTerm
• CVTermList() : CVTermList
• CVTermListInterface() : CVTermListInterface