| OpenMS 2.5.0

### - 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
- calculateDecompositionWeightsIsotopicPatterns() : MetaProSIPDecomposition
- calculateDIAIdScores() : OpenSwathScoring
- calculateDIAScores() : OpenSwathScoring
- calculateEmissionProbabilities() : HiddenMarkovModel
- calculateEstimatedQVal_() : FalseDiscoveryRate
- calculateFDR_() : FeatureFinderIdentificationAlgorithm
- calculateFDRBasic_() : FalseDiscoveryRate
- calculateFDRs_() : FalseDiscoveryRate
- calculateFitQuality_() : ElutionModelFitter
- calculateForwardPart_() : HiddenMarkovModel
- calculateGaussTable() : SVMWrapper
- calculateGB() : AAIndex
- calculateGridLines_() : Spectrum3DOpenGLCanvas
- calculateIntensityRankInMZWindow() : PScore
- calculateIonRatio() : MRMFeatureFilter
- calculateIsotopePatternsFor13CRange() : MetaProSIPDecomposition
- calculateIsotopePatternsFor13CRangeOfAveraginePeptide() : MetaProSIPDecomposition
- calculateIsotopePatternsFor15NRange() : MetaProSIPDecomposition
- calculateIsotopePatternsFor15NRangeOfAveraginePeptide() : MetaProSIPDecomposition
- calculateIsotopePatternsFor18ORange() : MetaProSIPDecomposition
- calculateIsotopePatternsFor18ORangeOfAveraginePeptide() : MetaProSIPDecomposition
- calculateIsotopePatternsFor2HRange() : MetaProSIPDecomposition
- calculateIsotopePatternsFor2HRangeOfAveraginePeptide() : MetaProSIPDecomposition
- 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
- calculateSeeds_() : UTILProteomicsLFQ
- 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
- calibrate() : InternalCalibration , TOFCalibration
- CalibrationData() : CalibrationData
- callSiriusQProcess() : SiriusAdapterAlgorithm
- candidateEdges_() : MetaboliteFeatureDeconvolution
- canModificationBeApplied_() : SILACLabeler
- canRun() : JavaInfo
- canvas() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
- capacity() : ConstRefVector< ContainerT >
- cbegin() : NASequence
- cellClicked_() : SpectraIdentificationViewWidget
- cellindexAtClustercenter_() : HashGrid< Cluster >
- cend() : NASequence
- center() : DIntervalBase< D >
- centerOfBin() : Histogram< ValueType, BinSizeType >
- centroidAndCorrectPrecursors_() : UTILProteomicsLFQ
- 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 >
- checkAppliedProcessingSteps_() : IdentificationData
- checkBelonging() : BackgroundIntensityBin
- checkConditionISO_() : MSstatsFile
- checkConditionLFQ_() : MSstatsFile
- checkDatumRange() : TransformationModel
- checkDefaults() : Param
- checked() : Spectrum1DGoToDialog , Spectrum2DGoToDialog
- checkedToDouble_() : EDTAFile
- checkedToInt_() : EDTAFile
- checkExtraFeatures() : PercolatorFeatureSetHelper
- checkExtremePSMScores_() : Epifany
- 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
- checkParam_() : TOPPBase
- checkParameters_() : MapAlignmentAlgorithmIdentification
- checkParentMatches_() : IdentificationData
- checkPositionForPlausibility_() : IsotopeWaveletTransform< PeakType >
- checkPPMTheoModel_() : IsotopeWaveletTransform< PeakType >
- checkPreferences_() : TOPPViewBase
- checkRange() : MRMFeatureFilter
- checkRDependencies() : RIntegration
- checkRunSettings_() : ConsensusMapMergerAlgorithm
- 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_() : FeatureFinderIdentificationAlgorithm
- chunkAt() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
- 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
- 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 >
- clusterSIPPeptides() : MetaProSIPClustering
- 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
- 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 , FeatureDeconvolution , FragmentMassError , HyperScore , ILPDCWrapper , MassExplainer , MetaboliteFeatureDeconvolution , MissedCleavages , MorpheusScore , Ms2IdentificationRate , Ms2SpectrumStats , MzCalibration , 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() : TOPPViewBase
- containsInvalidReferences() : TargetedExperiment
- containsMS1Scans() : TOPPViewBase
- containsMSLevel() : PeakFileOptions
- 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
- convertPSMScores_() : Epifany
- 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
- correlateXICsToMono() : MetaProSIPXICExtraction
- 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 > , 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 >
- createBinnedPeptideRIAData_() : MetaProSIPReporting
- createChargeFactor() : MessagePasserFactory< Label >
- createCompound_() : TransitionTSVFile
- createCompoundReferenceMap_() : TargetedExperiment
- createConsensIsotopPattern() : LCElutionPeak
- createConsensusMapCache() : MasstraceCorrelator
- createContaminants_() : RawMSSignalSimulation
- createCSVReport() : MetaProSIPReporting
- 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
- createPeptideCentricCSVReport() : MetaProSIPReporting
- createPeptideEvidenceFactor() : MessagePasserFactory< Label >
- createPeptideProbabilisticAdderFactor() : MessagePasserFactory< Label >
- createPeptideReferenceMap_() : TargetedExperiment , LightTargetedExperiment
- createPositionXMLString_() : IdXMLFile
- createProtein_() : TransitionTSVFile
- createProteinFactor() : MessagePasserFactory< Label >
- createProteinReferenceMap_() : TargetedExperiment
- createProteinSequenceBasedLPInclusionList() : OfflinePrecursorIonSelection
- createProteinToPeptideLinks_() : MzTabFile
- createPseudoSpectra() : MasstraceCorrelator
- createQualityReport() : MetaProSIPReporting
- 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
- 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
- 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