- c -

cacheChunk() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
CachedmzML() : CachedmzML
CachedMzMLHandler() : CachedMzMLHandler
CachedSwathFileConsumer() : CachedSwathFileConsumer
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
calculateCombos() : GridSearch< TupleTypes >
calculateCorrectionFactor() : DBSuitability_friend
calculateCorrectionFactor_() : DBSuitability
calculateCoverages() : IdentificationData
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
CalibrantStats_() : InternalCalibration::CalibrantStats_
calibrate() : InternalCalibration
CalibrationData() : CalibrationData
callUpdateEntries() : DataSelectionTabs
candidateEdges_() : MetaboliteFeatureDeconvolution
canRun() : JavaInfo , PythonInfo
canvas() : Plot1DWidget , Plot2DWidget , Plot3DWidget , PlotWidget
canvasPixelArea() : PlotCanvas
capacity() : ConstRefVector< ContainerT >
cbegin() : ExposedVector< VectorElement > , Mobilogram , MSExperiment , NASequence
cellindexAtClustercenter_() : HashGrid< Cluster >
cend() : ExposedVector< VectorElement > , Mobilogram , MSExperiment , NASequence
center() : DIntervalBase< D > , RangeBase
centerOfBin() : Histogram< ValueType, BinSizeType >
changedOutputFolder() : TOPPASScene
changedParameter() : TOPPASScene
changeLabel() : TOPPViewBase
changeLayerFilterState() : PlotCanvas
changeLayerFlag() : TOPPViewBase
changeLegendVisibility() : PlotCanvas , PlotWidget
changeUnassigned() : TOPPViewBase
changeVisibility() : PlotCanvas
changeVisibleArea1D_() : Plot1DCanvas
changeVisibleArea_() : Plot1DCanvas , PlotCanvas
characters() : CVMappingFile , ConsensusXMLHandler , FeatureXMLHandler , MascotXMLHandler , MzDataHandler , MzIdentMLHandler , MzMLHandler , 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_tree() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
checkAndGetTermByName() : ControlledVocabulary
checkAppliedProcessingSteps_() : IdentificationData
CheckBox() : TheoreticalSpectrumGenerationDialog::CheckBox
checkCompat_() : BasicProteinInferenceAlgorithm
checkConditionISO_() : MSstatsFile
checkConditionLFQ_() : MSstatsFile , TriqlerFile
checkDatumRange() : TransformationModel
checkDefaults() : Param
checked() : Plot1DGoToDialog , Plot2DGoToDialog
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
checkSwathMap() : OpenSwathHelper
checkSwathMapAndSelectTransitions() : OpenSwathHelper
checkTDAnnotation_() : IDScoreGetterSetter
checkTransitions_() : OSWData
checkUniqueIdentifiers_() : XMLHandler
checkUnorderedContent_() : MSstatsFile , TriqlerFile
checkValidity_() : TOPPASInputFileDialog , TOPPASIOMappingDialog , TOPPASOutputFilesDialog
checkValidWeight() : TransformationModel
chooseDecoys_() : ConfidenceScoring
chooseFilesDialog_() : TOPPViewBase
chooseTraceFitter_() : FeatureFinderAlgorithmPicked
chop() : String
Chromatogram() : Chromatogram
chromatogram_flag_set() : LayerDataPeak
chromatogramIdsMatch() : MRMTransitionGroup< ChromatogramType, TransitionType >
ChromatogramMeta() : ChromatogramMeta
ChromatogramPeak() : ChromatogramPeak
ChromatogramSettings() : ChromatogramSettings
ChromatogramTools() : ChromatogramTools
ChromeleonFile() : ChromeleonFile
chromsDoubleClicked() : SpectraTreeTab
chromsSelected() : SpectraTreeTab
Chunk() : MSSpectrum::Chunk
chunk_() : FeatureFinderIdentificationAlgorithm
chunkAt() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
Chunks() : MSSpectrum::Chunks
chunkSize() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
clampTo() : RangeBase , RangeManager< RangeBases >
clampToUnsafe() : RangeManager< RangeBases >
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
clearCache() : LogStreamBuf
clearCurrentProcessingStep() : IdentificationData
clearEluents() : Gradient
clearMetaDataArrays() : MSExperiment
clearMetaInfo() : MetaInfoInterface
clearMSLevels() : PeakFileOptions
clearPercentages() : Gradient
clearPrimaryID() : BaseFeature
clearProteins() : OSWData
clearRanges() : RangeManager< RangeBases >
clearTags() : Param
clearTimepoints() : Gradient
clearUniqueId() : UniqueIdInterface
cleavageCorrectionTerm() : PScore
clicked() : TOPPASVertex
clockTime() : StopWatch::TimeDiff_
clone() : Annotation1DCaret< DataPoint > , Annotation1DDistanceItem , Annotation1DItem , Annotation1DPeakItem< DataPoint > , Annotation1DTextItem , Annotation1DVerticalLineItem , DimBase , DimIM , DimINT , DimMZ , DimRT , TOPPASInputFileListVertex , TOPPASMergerVertex , TOPPASOutputFileListVertex , TOPPASOutputFolderVertex , TOPPASSplitterVertex , TOPPASToolVertex , TOPPASVertex
cloneWith() : Area< N_DIM >
close() : Bzip2Ifstream , GzipIfstream , HDF5Connector
closeByTab() : TOPPASBase , TOPPViewBase
closeEditor_() : ParamEditorDelegate
closeEvent() : INIFileEditorWindow , ListFilterDialog , PlotWidget , TOPPASBase , TOPPASWidget , TOPPViewBase
closeFile() : TOPPASBase
closeRequested() : EnhancedTabBar
closeTab() : TOPPViewBase
cluster() : ClusterHierarchical , GridBasedClustering< Metric > , MultiplexClustering
ClusterAnalyzer() : ClusterAnalyzer
ClusterFunctor() : ClusterFunctor
ClusterHierarchical() : ClusterHierarchical
clusterIndistProteinsAndPeptides() : IDBoostGraph
clusterIndistProteinsAndPeptidesAndExtendGraph() : IDBoostGraph
ClusteringGrid() : ClusteringGrid
ClusterProxyKD() : ClusterProxyKD
CMMzTabStream() : MzTab::CMMzTabStream
CoarseIsotopePatternGenerator() : CoarseIsotopePatternGenerator
cohesion() : ClusterAnalyzer
collapseAll() : TOPPASTreeView
collapseStringVector() : TVIdentificationViewController
collectDecompositionsRecursively_() : IntegerMassDecomposer< ValueType, DecompositionValueType >
collectFragmentScansInArea_() : Plot2DCanvas
collectPrecursorCandidates() : OPXLHelper
collectQCData() : QcMLFile
collectRatios_() : IsobaricNormalizer
collectSetParameter() : QcMLFile
colnames() : CSVWriter , DataMatrix , IDataFrameWriter
color() : MultiGradient
Colorizer() : Colorizer
ColorSelector() : ColorSelector
colorStream_() : Colorizer
columnExists() : SqliteConnector
ColumnHeader() : ConsensusMap::ColumnHeader
combineMods() : ResidueModification
combinePrecursorPurities() : PrecursorPurity
combineTopRanksFromPairs() : OPXLHelper
Command() : Command
commitAndCloseEditor_() : ParamEditorDelegate
commitAndCloseLineEdit_() : ParamEditorDelegate
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
Compomer() : Compomer
compomerValid_() : MassExplainer
Compound() : Compound
CompoundSpectrumPair() : MetaboTargetedAssay::CompoundSpectrumPair
CompoundTargetDecoyPair() : MetaboTargetedAssay::CompoundTargetDecoyPair
compress() : ConvexHull2D
compressData() : ZlibCompression
CompressedInputSource() : CompressedInputSource
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_F() : SpectraSTSimilarityScore
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
computeIntensitySum() : MassTrace
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
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
concatenate() : ListUtils , String
concatenateSpectra() : SpectrumAddition
concatMULTISEPeptideIds() : PercolatorFeatureSetHelper
ConfidenceScoring() : ConfidenceScoring
configure() : LogConfigHandler
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
ConsensusMap() : ConsensusMap
ConsensusMapMergerAlgorithm() : ConsensusMapMergerAlgorithm
ConsensusMapNormalizerAlgorithmMedian() : ConsensusMapNormalizerAlgorithmMedian
ConsensusMapNormalizerAlgorithmQuantile() : ConsensusMapNormalizerAlgorithmQuantile
ConsensusMapNormalizerAlgorithmThreshold() : ConsensusMapNormalizerAlgorithmThreshold
ConsensusXMLFile() : ConsensusXMLFile
ConsensusXMLHandler() : ConsensusXMLHandler
ConsoleUtils() : ConsoleUtils
ConstIterator() : AASequence::ConstIterator , HashGrid< Cluster >::ConstIterator , NASequence::ConstIterator
ConstRefVector() : ConstRefVector< ContainerT >
ConstRefVectorConstIterator() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
ConstRefVectorIterator() : ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
constructFile_() : MSstatsFile , TriqlerFile
constructHeader_() : IBSpectraFile
constructTargetDecoyMassMapping() : MetaboTargetedTargetDecoy
constructTargTransList_() : MRMFeatureSelector , MRMFeatureSelector_test
constructTransitionsList() : TargetedSpectraExtractor
constructTransitionsMap_() : MetaboTargetedTargetDecoy
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 , FileTypeList , ListUtils , RangeBase
containsAll() : RangeManager< RangeBases >
containsIMData() : MSSpectrum
containsIntensity() : RangeIntensity
containsInvalidReferences() : TargetedExperiment
containsMobility() : RangeMobility
containsMSLevel() : PeakFileOptions
containsMZ() : RangeMZ
containsRT() : RangeRT
containsScanOfLevel() : MSExperiment
containsTag() : MassDecomposition
Contaminants() : Contaminants
contextMenuEvent() : EnhancedTabBar , LayerListView , LogWindow , MultiGradientSelector , Plot1DCanvas , Plot2DCanvas , Plot3DCanvas , TOPPASEdge , TOPPASScene , TOPPASVertex
ControlledVocabulary() : ControlledVocabulary
ConversionError() : ConversionError
convert() : StringManager , MapConversion , TransitionHelper
convertChromatogramsToSpectra() : ChromatogramTools
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
ConvexHull2D() : ConvexHull2D
convolve() : CoarseIsotopePatternGenerator
convolvePow_() : CoarseIsotopePatternGenerator
convolveSquare_() : CoarseIsotopePatternGenerator
copy() : File , Param
copyBatchTransitions_() : OpenSwathWorkflow
copyDirRecursively() : File
copyLayer() : TOPPViewBase
copyMetaDataOnly() : ProteinIdentification
copySearchParams_() : IDMergerAlgorithm
copySelected() : TOPPASScene
copySubset() : Param
correctGravityAxisOfVisibleArea_() : Plot1DCanvas
correctIM() : SwathMapMassCorrection
correctIsotopicImpurities() : IsobaricIsotopeCorrector
correctMass_() : CoarseIsotopePatternGenerator
correctMZ() : SwathMapMassCorrection
correctPeptideIntensities_() : FeatureFinderMultiplexAlgorithm
correctToHighestIntensityMS1Peak() : PrecursorCorrection
correctToNearestFeature() : PrecursorCorrection
correctToNearestMS1Peak() : PrecursorCorrection
count() : squared_difference_counted< _Tp, _Dist > , ROCCurve , mean_and_stddev
count_within_range() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
countDecoys() : DecoyHelper
countEnzymatic_() : PercolatorInfile
countHits() : IDFilter
countInternalCleavageSites() : EnzymaticDigestion
countLabelsAndTransitionTypes() : MRMFeatureFilter
countMissedCleavages_() : EnzymaticDigestion
countPeptides_() : PeptideAndProteinQuant
countScansInSwath_() : SwathFile
countTableRows() : SqliteConnector
crbegin() : Mobilogram
create() : ListUtils , ProteinIdentification::Mapping , VersionInfo::VersionDetails
create_() : DimMapper< N_DIM >
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
crend() : Mobilogram
cropFeature_() : FeatureFinderAlgorithmPicked
CrossLinksDB() : CrossLinksDB
CsvFile() : CsvFile
CSVWriter() : CSVWriter
CubicSpline2d() : CubicSpline2d
curPos() : Bzip2InputStream , GzipInputStream
currentCellChanged_() : SpectraIDViewTab
currentChanged_() : EnhancedTabBar
currentIdChanged() : EnhancedTabBar
currentLayerParametersChanged_() : Plot2DCanvas
currentLayerParamtersChanged_() : Plot1DCanvas , Plot3DCanvas
currentRowChangedAction_() : LayerListView
currentSpectraSelectionChanged_() : SpectraIDViewTab
currentTabChanged() : DataSelectionTabs
curve() : ROCCurve
customContextMenuRequested_() : FilterList
cut() : ClusterAnalyzer
cutForTime() : FIAMSDataProcessor
cutoffNeg() : ROCCurve
cutoffPos() : ROCCurve
CV() : CV
CVMappingFile() : CVMappingFile
CVMappingRule() : CVMappingRule
CVMappings() : CVMappings
CVMappingTerm() : CVMappingTerm
cvParam_() : MzDataHandler
cvParamToValue() : XMLHandler
CVReference() : CVReference
cvStringToEnum_() : XMLHandler
CVTerm() : ControlledVocabulary::CVTerm , CVTerm
CVTermList() : CVTermList
CVTermListInterface() : CVTermListInterface