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

- c -

• c : FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::BoxElement , IsotopeWaveletTransform< PeakType >::BoxElement
• C : ExtendedIsotopeModel , IsotopeModel , SVMWrapper , LmaIsotopeFitter1D , LmaIsotopeModel
• c0 : PeakWidthEstimator::Result
• c1 : PeakWidthEstimator::Result
• c13MassError_ : DeconvPeak
• c1_ : MapAlignmentAlgorithmSpectrumAlignment , BernNorm
• c2_ : BernNorm
• c_ : mean_and_stddev , TOFCalibration
• C_ELEMENTS : LayerData
• c_mzs_ : IsotopeWaveletTransform< PeakType >
• c_sorted_candidate_ : IsotopeWaveletTransform< PeakType >
• c_spacings_ : IsotopeWaveletTransform< PeakType >
• c_strings_ : StringManager
• C_TERM : ResidueModification
• c_term_mod_ : AASequence
• cache_ : SpectrumAccessOpenMSCached
• CachedmzML() : CachedmzML
• CAD : IonSource
• calc_correct_ : PosteriorErrorProbabilityModel
• calc_incorrect_ : PosteriorErrorProbabilityModel
• calcCentroids() : CentroidData
• calcChargeStateIntensities_() : ProtonDistributionModel
• calcElutionFitScore() : EmgScoring
• calcGridLines() : AxisTickCalculator
• calcLibraryScore() : MRMScoring
• calcLogGridLines() : AxisTickCalculator
• calcRTScore() : MRMScoring
• calcSNScore() : MRMScoring
• calculate_lda_prescore() : OpenSwath_Scores
• calculate_swath_lda_prescore() : OpenSwath_Scores
• calculateAddInfo_() : PeakIntensityPredictor
• calculateAvgWeight_() : ElementDB
• calculateBackwardPart_() : HiddenMarkovModel
• calculateBgEstimation_() : MRMTransitionGroupPicker
• calculateCalibCoeffs_() : TOFCalibration
• calculated_mass_to_charge_ : IdentificationHit
• calculateEmissionProbabilities() : HiddenMarkovModel
• calculateFDRs_() : FalseDiscoveryRate
• calculateForwardPart_() : HiddenMarkovModel
• calculateGaussTable() : SVMWrapper
• calculateGB() : AAIndex
• calculateGridLines_() : Spectrum3DOpenGLCanvas
• calculateMonoWeight_() : ElementDB
• calculateMT_() : RTSimulation
• calculateProteinProbabilities() : PSProteinInference
• calculateProtonDistribution_() : ProtonDistributionModel
• calculateProtonDistributionCharge1_() : ProtonDistributionModel
• calculateProtonDistributionCharge2_() : ProtonDistributionModel
• calculateProtonDistributionGreater2_() : ProtonDistributionModel
• calculateProtonDistributionIonPair_() : ProtonDistributionModel
• calculateSwathScores_() : MRMFeatureFinderScoring
• calculateXICs_() : OfflinePrecursorIonSelection , PSLPFormulation
• calcXcorrCoelutionScore() : MRMScoring
• calcXcorrCoelutionScore_weighted() : MRMScoring
• calcXcorrShape_score() : MRMScoring
• calcXcorrShape_score_weighted() : MRMScoring
• calib_masses_ : TOFCalibration
• calib_peaks_ft_ : TOFCalibration
• calibrate() : TOFCalibration
• calibrateMapGlobally() : InternalCalibration
• calibrateMapList() : InternalCalibration
• calibrateMapSpectrumwise() : InternalCalibration
• CALIBRATION : DataProcessing
• CancelButton_ : ListEditor
• cancelbutton_ : MetaDataBrowser
• canModificationBeApplied_() : SILACLabeler
• CANNOT_WRITE_OUTPUT_FILE : TOPPBase
• canvas() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
• canvas_ : LayerStatisticsDialog , SpectrumWidget
• canvas_3d_ : Spectrum3DOpenGLCanvas
• capacity() : ConstRefVector< ContainerT >
• capacity_ : ConstRefVector< ContainerT >
• CAPTION_3D_SUFFIX_ : TOPPViewBase
• category : ToolDescriptionInternal , ToolExternalDetails
• CE : TransitionTSVReader::TSVTransition
• CEI : IonSource
• cell_dimension : HashGrid< Cluster >
• cell_it_ : HashGrid< Cluster >::Iterator , HashGrid< Cluster >::ConstIterator
• cell_iterator : HashGrid< Cluster >::Iterator , HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >
• cell_type : MzTabSubIdMetaData
• cellClicked_() : SpectraIdentificationViewWidget
• CellContent : HashGrid< Cluster >
• CellIndex : HashGrid< Cluster >
• cellindexAtClustercenter_() : HashGrid< Cluster >
• cells_ : HashGrid< Cluster >
• center : ItraqConstants::ChannelInfo , HierarchicalClustering< PointRef >::TreeNode , DIntervalBase< D >
• center_point_ : QTCluster
• centerOfBin() : Histogram< ValueType, BinSizeType >
• centroid_mz_ : MassTrace
• centroid_position : PeakPickerCWT::PeakArea_
• centroid_rt_ : MassTrace
• centroid_sd_ : MassTrace
• CentroidData() : CentroidData
• centroidDataModus() : SuperHirnParameters
• centroidDataModus_ : CentroidData , SuperHirnParameters
• CentroidPeak() : CentroidPeak
• centroidWindowWidth_ : SuperHirnParameters
• cexp_ : MzMLHandler< MapType > , MzXMLHandler< MapType > , TraMLHandler , MzDataHandler< MapType >
• cf_cf_obj_ : MzQuantMLHandler
• changed_ : QTCluster , TOPPASScene
• changedParameter() : TOPPASScene
• changeElutionTimesByFactor() : FeatureLCProfile
• changeLabel() : TOPPViewBase
• changeLayerFilterState() : SpectrumCanvas
• changeLayerFlag() : TOPPViewBase
• changeLegendVisibility() : SpectrumCanvas , SpectrumWidget
• changeUnassigned() : TOPPViewBase
• changeVisibility() : SpectrumCanvas
• changeVisibleArea_() : Spectrum1DCanvas , SpectrumCanvas
• CHANNEL_COUNT : ItraqConstants
• channel_count : ItraqQuantifier::ItraqQuantifierStats
• channel_description_ : BaseLabeler
• channel_map_ : ItraqChannelExtractor , ItraqQuantifier , ITRAQLabeler
• CHANNELELECTRONMULTIPLIER : IonDetector
• ChannelInfo : ItraqQuantifier , ITRAQLabeler
• ChannelMapType : ItraqChannelExtractor , ItraqConstants , ItraqQuantifier , ITRAQLabeler
• CHANNELS_EIGHTPLEX : ItraqConstants
• CHANNELS_FOURPLEX : ItraqConstants
• CHANNELS_TMT_SIXPLEX : ItraqConstants
• CHANNELTRON : IonDetector
• char_rest_ : MzXMLHandler< MapType >
• characters() : ConsensusXMLFile , CVMappingFile , FeatureXMLFile , MascotXMLHandler , MzDataHandler< MapType > , MzIdentMLHandler , MzMLHandler< MapType > , MzQuantMLHandler , MzXMLHandler< MapType > , PTMXMLHandler , ToolDescriptionHandler , TraMLHandler , UnimodXMLHandler , XMLHandler , XTandemInfileXMLHandler , OMSSAXMLFile , QcMLFile , SemanticValidator , XTandemXMLFile
• CHARGE : DataFilters
• charge : PILISCrossValidation::Peptide , LightTransition , LightPeptide , Peptide , SvmTheoreticalSpectrumGenerator::IonType , IsotopeCluster::ChargedIndexSet , SILACFiltering::BlacklistEntry , SILACPoint , MzTabPeptideSectionRow , MzTabSmallMoleculeSectionRow , Summary , MS1Signal , OptimizePeakDeconvolution::Data , RNPxlReportRow
• charge_ : Peptide , TraMLProduct , EmpiricalFormula , Adduct , FeatureHypothesis , SILACFilter , PepXMLFile , BaseFeature , FeatureHandle , IdentificationHit , PeptideHit , Precursor , ExtendedIsotopeFitter1D , ExtendedIsotopeModel , IsotopeFitter1D , IsotopeModel , LmaIsotopeFitter1D , LmaIsotopeModel , DeconvPeak , OptimizePeakDeconvolution , PrecursorVisualizer
• CHARGE_CALCULATION : DataProcessing
• CHARGE_DECONVOLUTION : DataProcessing
• charge_lower_bound_ : FeatureFindingMetabo
• charge_state : SHFeature
• charge_upper_bound_ : FeatureFindingMetabo
• ChargedIndexSet : FeatureFinderDefs , Fitter1D , IsotopeCluster::ChargedIndexSet
• ChargeDirected : ProtonDistributionModel
• CHARGEMODE : FeatureDeconvolution
• ChargePair() : ChargePair
• ChargeRemote : ProtonDistributionModel
• charges : ProteinIdentification::SearchParameters
• charges_ : MascotInfile , HasPrecursorCharge< SpectrumType > , ProteinIdentificationVisualizer
• chargeTestworthy_() : FeatureDeconvolution
• ChargeType : BaseFeature , FeatureHandle , ModelFitter< PeakType, FeatureType >
• chauvenet() : MRMRTNormalizer
• chauvenet_probability() : MRMRTNormalizer
• check_() : DataFilterDialog
• check_AC() : SHFeature
• check_defaults_ : DefaultParamHandler
• 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_PPMs_ : FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >
• check_raw_spec_name_empty() : LCMS
• check_term_value_types_ : SemanticValidator
• check_units_ : SemanticValidator
• checkBelonging() : BackgroundIntensityBin
• checkCompliance() : BinnedSpectrum
• checkCVTerms() : CVTermList
• checkDBVersion() : DBAdapter
• checkDefaults() : Param
• checkedToDouble_() : EDTAFile
• checkedToInt_() : EDTAFile
• checkFeatureQuality_() : FeatureFinderAlgorithmPicked< PeakType, FeatureType >
• checkFormula_() : Adduct
• checkForRequiredUserParams_() : PrecursorIonSelection
• checkFWHM_() : OptimizePeakDeconvolution
• checkHits_() : IDMapper
• checkIds_() : BaseGroupFinder
• checkIfFeatureExtractionExists() : FTPeakDetectController
• checkIfIniParametersAreApplicable_() : TOPPBase
• checkIfWeAreDone() : TOPPASScene
• checkIsotopeBelongingAndAdjustMass() : MSPeak
• checkMassRanges_() : OfflinePrecursorIonSelection
• checkMassType_() : IDMapper
• checkMaximalRTSpan() : EGHTraceFitter< PeakType > , GaussTraceFitter< PeakType > , TraceFitter< PeakType >
• checkMinimalRTSpan() : EGHTraceFitter< PeakType > , GaussTraceFitter< PeakType > , TraceFitter< PeakType >
• checkName_() : ControlledVocabulary
• checkNeighbour_() : SimpleExtender< PeakType, FeatureType >
• checkParam_() : TOPPBase
• checkParameters_() : MapAlignmentAlgorithmIdentification
• checkPositionForPlausibility_() : IsotopeWaveletTransform< PeakType >
• checkPPMTheoModel_() : IsotopeWaveletTransform< PeakType >
• checkPreferences_() : TOPPViewBase
• checkReferenceIds_() : InternalCalibration
• checkSize() : SaveImageDialog
• checkSolution_() : FeatureDeconvolution
• checksum_ : SourceFile , SourceFileVisualizer
• checksum_type_ : SourceFile , SourceFileVisualizer
• ChecksumType : SourceFile
• checkSwathMap() : OpenSwathHelper
• checkSwathMapAndSelectTransitions() : OpenSwathHelper
• checkValidity_() : TOPPASInputFileDialog , TOPPASIOMappingDialog , TOPPASOutputFilesDialog
• CHEMI : IonSource
• CHEMICAL_DERIVATIVE : ResidueModification
• chemical_formula : MzTabSmallMoleculeSectionRow
• chi_squared_ : LinearRegression
• CHILD : CompNovoIonScoringBase
• children : ControlledVocabulary::CVTerm
• childScan : MSPeak
• chooseElutionProfile_() : RawMSSignalSimulation
• chooseTraceFitter_() : FeatureFinderAlgorithmPicked< PeakType, FeatureType >
• chop() : String
• CHRG : MS2Info , MSPeak
• CHRG_MAP : LCElutionPeak
• chrom_fwhm_ : ElutionPeakDetection , FeatureFindingMetabo
• chrom_index_ : CachedmzML
• chrom_peak_snr_ : ElutionPeakDetection , MassTraceDetection
• Chromatogram() : Chromatogram
• chromatogram_ : SignalToNoiseOpenMS< PeakT > , MzMLHandler< MapType >
• chromatogram_flag_set() : LayerData
• chromatogram_map_ : MRMTransitionGroup< SpectrumType, TransitionType >
• ChromatogramExtractor() : ChromatogramExtractor
• ChromatogramMeta() : ChromatogramMeta
• ChromatogramPeak() : ChromatogramPeak
• ChromatogramPeakType : MzMLHandler< MapType > , MSExperiment< PeakT, ChromatogramPeakT >
• chromatograms : LayerData
• chromatograms_ : MRMTransitionGroup< SpectrumType, TransitionType > , MSExperiment< PeakT, ChromatogramPeakT >
• ChromatogramSettings() : ChromatogramSettings
• ChromatogramTools() : ChromatogramTools
• ChromatogramType : ChromatogramSettings , CachedmzML , MzMLHandler< MapType > , MSExperiment< PeakT, ChromatogramPeakT >
• CHROMATOGRAPHY : IonSource
• CHYMOTRYPSIN : ProteinIdentification
• CI : IonSource
• CID : IonSource , Precursor
• cid_ : MzIdentMLHandler
• CIon : Residue
• CIonMinusOne : Residue
• CIonPlusOne : Residue
• CIonPlusTwo : Residue
• class_models : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• classification_ : ResidueModification
• classifyIsotopes_() : CompNovoIonScoringBase
• clean_all_charge_states_ : ParentPeakMower
• cleanDeconvPeaks() : Deisotoper
• cleanUpTransition() : TransitionTSVReader
• clear() : HiddenMarkovModel , TargetedExperiment , IsotopeDistribution , IMSAlphabet , HashGrid< Cluster > , ConstRefVector< ContainerT > , ConvexHull2D , Date , DateTime , DIntervalBase< D > , DistanceMatrix< Value > , DPosition< D, TCoordinateType > , Matrix< Value > , Param , SparseVector< Value > , DataFilters , StringManager , ConsensusMap , FeatureMap< FeatureT > , MSChromatogram< PeakT > , MSExperiment< PeakT, ChromatogramPeakT > , MSSpectrum< PeakT > , PeakIndex , AveragePosition< D > , BasicStatistics< RealT > , MetaInfo , StopWatch , ParamEditor , TOPPASResources
• clear_() : ElementDB , ResidueDB , DataValue , MetaInfoVisualizer
• clear_feature_list() : LCMS
• clearbutton_ : MetaInfoVisualizer
• clearCache() : LogStreamBuf
• clearChildIds_() : BinnedSpectrum , PersistentObject , MSChromatogram< PeakT > , MSExperiment< PeakT, ChromatogramPeakT > , MSSpectrum< PeakT >
• clearEluents() : Gradient
• clearId() : PersistentObject
• clearInitialTransitionProbabilities() : HiddenMarkovModel
• clearMetaDataArrays() : MSExperiment< PeakT, ChromatogramPeakT >
• clearMetaInfo() : MetaInfoInterface
• clearMSLevels() : PeakFileOptions
• clearPercentages() : Gradient
• clearRanges() : RangeManager< D >
• clearResidues_() : ResidueDB
• clearResult() : ProteinResolver
• clearTags() : Param
• clearTimepoints() : Gradient
• clearTrainingEmissionProbabilities() : HiddenMarkovModel
• clearUniqueId() : UniqueIdInterface
• cleavage_ : MascotInfile
• cleavage_site_ : XTandemInfile
• CleavageModel() : EnzymaticDigestion::CleavageModel
• clicked() : TOPPASVertex
• clipboard_ : TOPPASScene
• clipboard_scene_ : TOPPASBase
• clone() : Digestion , Modification , SampleTreatment , Tagging
• close() : Bzip2Ifstream , GzipIfstream
• closebutton_ : MetaDataBrowser
• closeByTab() : TOPPASBase , TOPPViewBase
• closed_boxes_ : IsotopeWaveletTransform< PeakType >
• closeEvent() : IDEvaluationBase , INIFileEditorWindow , TOPPASBase , TOPPViewBase , SpectrumWidget , TOPPASWidget
• closeFile() : TOPPASBase , TOPPViewBase
• closeListEditor_() : ParamEditorDelegate
• cluster() : ClusterHierarchical , HierarchicalClustering< PointRef > , SILACClustering
• Cluster() : HierarchicalClustering< PointRef >::Cluster
• ClusterAnalyzer() : ClusterAnalyzer
• ClusterCells : HierarchicalClustering< PointRef >
• ClusterCenter : HashGrid< Cluster >
• ClusteredMS2ConsensusSpectrum() : ClusteredMS2ConsensusSpectrum
• ClusterFunctor() : ClusterFunctor
• ClusterHierarchical() : ClusterHierarchical
• clusterIndex_() : HierarchicalClustering< PointRef >
• ClusterPointType : FeatureDeconvolution
• clusterSeeds_() : IsotopeWaveletTransform< PeakType >
• ClusterTrees : HierarchicalClustering< PointRef >
• cm_cf_ids_ : MzQuantMLHandler
• CMD : ProgressLogger
• cmp1_ : LexicographicComparator< Cmp1, Cmp2 >
• cmp2_ : LexicographicComparator< Cmp1, Cmp2 >
• cmp_ : Compomer , PointerComparator< Cmp > , ReverseComparator< Cmp >
• cmpOligos_() : LibSVMEncoder
• cmsq_ : MzQuantMLHandler
• CNG : InstrumentSettings
• CNL : InstrumentSettings
• code_ : LocalLinearMap
• coeff_quad_fit_ : TOFCalibration
• coeffs_ : TransformationModelBSpline , GaussFilter , SavitzkyGolayFilter
• cohesion() : ClusterAnalyzer
• col() : Matrix< Value >
• colIndex() : Matrix< Value >
• collectDecompositionsRecursively_() : IntegerMassDecomposer< ValueType, DecompositionValueType >
• collectSetParameter() : QcMLFile
• COLLISION_QUADRUPOLE : Instrument
• colnames() : IDataFrameWriter , DataMatrix , CSVWriter
• colnames_ : DataMatrix
• color() : MultiGradient
• color_ : Annotation1DPeakItem , ColorSelector , TOPPASEdge
• ColorSelector() : ColorSelector
• cols() : Matrix< Value >
• cols_ : Matrix< Value >
• colTypes : QcMLFile::Attachment
• column_ : HPLC
• combinations_logic_ : CVMappingRule
• CombinationsLogic : CVMappingRule
• command : TOPPASScene::TOPPProcess
• commandline : ToolExternalDetails
• comment_ : SpectrumSettings , ExperimentalSettingsVisualizer , SpectrumSettingsVisualizer , ChromatogramSettings , ExperimentalSettings , HPLC , MetaInfoDescription , Sample , SampleTreatment
• commitAndCloseComboBox_() : ParamEditorDelegate
• commitAndCloseListEditor_() : ParamEditorDelegate
• Compare() : MapAlignmentAlgorithmSpectrumAlignment::Compare
• compare_AC() : MS2Info
• compare_feature_mass() : LCMS
• compareFeatureMassValuesAtPPMLevel() : SHFeature
• compareFiles() : FuzzyStringComparator
• CompareFouriertransform() : CompareFouriertransform
• compareIteratorToPeak() : ProcessData
• compareLines_() : FuzzyStringComparator
• compareMassValuesAtPPMLevel() : SuperHirnUtil
• compareMZFeatureBeloning() : MS1FeatureMerger
• comparepeaks_() : SpectrumCheapDPCorr
• compareSpectra_() : CompNovoIdentificationBase
• compareStreams() : FuzzyStringComparator
• compareStrings() : FuzzyStringComparator
• compatible() : MassDecomposition
• compatibleIDs_() : QTClusterFinder , StablePairFinder
• ComplementFilter() : ComplementFilter
• ComplementMarker() : ComplementMarker
• CompleteLinkage() : CompleteLinkage
• completion_time_ : DataProcessing , DataProcessingVisualizer
• CompNovoIdentification() : CompNovoIdentification
• CompNovoIdentificationBase() : CompNovoIdentificationBase
• CompNovoIdentificationCID() : CompNovoIdentificationCID
• CompNovoIonScoring() : CompNovoIonScoring
• CompNovoIonScoringBase() : CompNovoIonScoringBase
• CompNovoIonScoringCID() : CompNovoIonScoringCID
• Compomer() : Compomer
• compomer_ : ChargePair
• CompomerComponents : Compomer
• CompomerIterator : MassExplainer
• CompomerSide : Compomer
• compomerValid_() : MassExplainer
• composition_ : PTMXMLHandler
• Compound : TargetedExperiment , Compound
• compound_ref_ : ReactionMonitoringTransition , IncludeExcludeTarget
• compounds_ : TargetedExperiment
• compress() : ConvexHull2D
• CompressedInputSource() : CompressedInputSource
• compression : MzMLHandler< MapType >::BinaryData
• compressionType_ : MzXMLHandler< MapType >
• compressSignals_() : RawMSSignalSimulation
• compressTrieDB() : InspectOutfile
• compute() : FeatureDeconvolution , ILPDCWrapper , AScore , MassExplainer
• compute_CHRG() : LCElutionPeak
• compute_delta_area() : LCElutionPeak
• compute_F() : SpectraSTSimilarityScore
• compute_site_determining_ions() : AScore
• computeApexSNR() : ElutionPeakDetection
• computeAveragineSimScore_() : FeatureFindingMetabo
• computeBoundaries_() : EGHModel
• computeClustering_() : QTClusterFinder
• computeConsensus() : ConsensusFeature
• computeConsensusStats_() : LayerStatisticsDialog
• computeCorrelation() : ConsensusMapNormalizerAlgorithmThreshold
• computeCosineSim_() : FeatureFindingMetabo
• computeCoverage() : ProteinIdentification
• computeCumulativeScore() : AScore
• computeDechargeConsensus() : ConsensusFeature
• computeDeltaArea() : MS1FeatureMerger
• computeFeatureStats_() : LayerStatisticsDialog
• computeFit_() : TransformationModelBSpline
• computeFwhmArea() : MassTrace
• computeFwhmAreaRobust() : MassTrace
• computeFwhmAreaSmooth() : MassTrace
• computeFwhmAreaSmoothRobust() : MassTrace
• computeGoodness_() : LinearRegression
• computeHighestPeptides() : AScore
• computeIntensityHist() : BackgroundIntensityBin
• computeIntensityOfMSD_() : ProteinResolver
• computeIsotopeDistributionSize_() : IsotopeWavelet
• computeKernelMatrix() : SVMWrapper
• computeLCElutionPeakParameters() : LCElutionPeak
• computeLinear_() : TransformationModelBSpline
• computeMassTraceNoise() : ElutionPeakDetection
• computeMassTraceSNR() : ElutionPeakDetection
• computeMaxLikelihood() : PosteriorErrorProbabilityModel
• computeMedians_() : MapAlignmentAlgorithmIdentification
• computeMetaAverages_() : LayerStatisticsDialog
• computeMetaDataArrayStats_() : LayerStatisticsDialog
• computeMinSpacing() : IsotopeWaveletTransform< PeakType >
• computeMonoisotopicConsensus() : ConsensusFeature
• computeMS2SpectrumParameters() : MS2ConsensusSpectrum
• computeNewMS1FeatureParameters() : MS1FeatureMerger
• computeNormalizationFactors() : ConsensusMapNormalizerAlgorithmMedian
• computeOLSCoeff_() : FeatureFindingMetabo
• computePeakArea() : MassTrace
• computePeakPriority_() : SimpleExtender< PeakType, FeatureType >
• computePeakStats_() : LayerStatisticsDialog
• computePermutations_() : AScore
• computeProbability() : PosteriorErrorProbabilityModel
• computeQuality_() : QTCluster
• computeRegression() : LinearRegression
• computeRegressionNoIntercept() : LinearRegression
• computeRegressionWeighted() : LinearRegression
• computeSelection() : Spectrum3DOpenGLCanvas
• computeSlice_() : ILPDCWrapper
• computeSliceOld_() : ILPDCWrapper
• computeSmoothedPeakArea() : MassTrace
• computeSTN_() : SignalToNoiseEstimator< Container > , SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• computeTheoretical() : EGHTraceFitter< PeakType > , GaussTraceFitter< PeakType > , TraceFitter< PeakType >
• computeTransformations_() : MapAlignmentAlgorithmIdentification
• computeTupel_() : AScore
• concatenate() : String , StringList
• concentration_ : Sample
• condensIsotopePattern() : ConsensusIsotopePattern
• conditional_prob : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• Configuration : ReactionMonitoringTransition , IncludeExcludeTarget
• configuration_list_ : TraMLProduct
• ConfigurationListType : TraMLHandler
• configurations_ : IncludeExcludeTarget
• configure() : LogConfigHandler
• connect() : DBConnection
• connectEdgeSignals() : TOPPASScene
• connection_ : DBOpenDialog
• connection_name_ : DBConnection
• connectMergerVertexSignals() : TOPPASScene
• connectOutputVertexSignals() : TOPPASScene
• connectToDB_() : TOPPViewBase
• connectToolVertexSignals() : TOPPASScene
• connectVertexSignals() : TOPPASScene
• connectVisualizer_() : MetaDataBrowser
• cons_features_ : MRMTransitionGroup< SpectrumType, TransitionType >
• consensus : LayerData
• Consensus : ProteinResolver::ResolverResult
• consensus_ : BaseLabeler
• consensus_map : ProteinResolver::ResolverResult
• consensus_map_ : ConsensusXMLFile , MSSim
• consensus_maps_ : MSQuantifications
• ConsensusFeature() : ConsensusFeature
• ConsensusID() : ConsensusID
• ConsensusIsotopePattern() : ConsensusIsotopePattern
• ConsensusIterator_ : LayerStatisticsDialog
• ConsensusMap() : ConsensusMap
• ConsensusMapNormalizerAlgorithmMedian() : ConsensusMapNormalizerAlgorithmMedian
• ConsensusMapNormalizerAlgorithmQuantile() : ConsensusMapNormalizerAlgorithmQuantile
• ConsensusMapNormalizerAlgorithmThreshold() : ConsensusMapNormalizerAlgorithmThreshold
• ConsensusMapSharedPtrType : SpectrumCanvas , TOPPViewBase , LayerData , TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• ConsensusMapType : LayerData , TOPPViewBase , SpectrumCanvas , TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• CONSENSUSXML : FileTypes
• ConsensusXMLFile() : ConsensusXMLFile
• consider_H2O_loss_ : ParentPeakMower
• consider_NH3_loss_ : ParentPeakMower
• console_width_ : TOPPBase
• const_abundances_iterator : IMSIsotopeDistribution
• const_bin_iterator : BinnedSpectrum
• const_cell_iterator : HashGrid< Cluster >
• const_grid_iterator : HashGrid< Cluster >
• const_iterator : EmpiricalFormula , IsotopeDistribution , IMSAlphabet , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType > , Matrix< Value > , SparseVector< Value > , MassTrace , HashGrid< Cluster >
• const_mass_iterator : IMSAlphabet
• const_masses_iterator : IMSIsotopeDistribution
• const_modified_residues_ : ResidueDB
• const_name_iterator : IMSAlphabet
• const_peaks_iterator : IMSIsotopeDistribution
• const_pointer : AASequence::ConstIterator , AASequence::Iterator
• const_reference : AASequence::ConstIterator , AASequence::Iterator , ConstRefVector< ContainerT > , SparseVector< Value > , Matrix< Value >
• const_residues_ : ResidueDB
• const_reverse_iterator : ConstRefVector< ContainerT > , Matrix< Value > , SparseVector< Value > , MassTrace
• const_weights_ : SequestOutfile
• CONSTANT : MassAnalyzer
• ConstAreaIterator : MSExperiment< PeakT, ChromatogramPeakT >
• ConstEdgeIterator : TOPPASScene , TOPPASVertex
• ConstEntryIterator : Param::ParamNode
• ConstIterator : EmpiricalFormula , IsotopeDistribution , ConstRefVector< ContainerT > , Map< Key, T > , Matrix< Value > , SparseVector< Value > , String , StringList , ConsensusMap , FeatureMap< FeatureT > , MSExperiment< PeakT, ChromatogramPeakT > , MSSpectrum< PeakT > , Histogram< ValueType, BinSizeType > , AASequence::ConstIterator , HashGrid< Cluster >::ConstIterator , MSChromatogram< PeakT > , AASequence::ConstIterator , Annotations1DContainer , DPosition< D, TCoordinateType >
• ConstNodeIterator : Param::ParamNode
• ConstPeakIterator : PeakPickerCWT
• constraints_type : RealMassDecomposer
• ConstReference : Matrix< Value > , FeatureMap< FeatureT >
• ConstRefVector : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > , ConstRefVector< ContainerT >
• ConstRefVectorConstIterator() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
• ConstRefVectorIterator() : ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
• ConstReverseIterator : Map< Key, T > , Matrix< Value > , SparseVector< Value > , StringList , ConsensusMap , FeatureMap< FeatureT > , MSSpectrum< PeakT > , ConstRefVector< ContainerT > , MSChromatogram< PeakT > , String
• constructClusteredConsenusSpectraFragments() : ClusteredMS2ConsensusSpectrum
• constructConsusPattern() : ConsensusIsotopePattern
• constructMS1FeatureFromMS2Feature() : FTPeakDetectController
• ConstVertexIterator : TOPPASScene
• Contact : TargetedExperiment , Contact
• contact_affiliation : MzTabUnitIdMetaData
• contact_email : MzTabUnitIdMetaData
• contact_info_ : ContactPerson , ContactPersonVisualizer
• contact_name : MzTabUnitIdMetaData
• contact_ref : Configuration , Prediction
• ContactPerson() : ContactPerson
• ContactPersonVisualizer() : ContactPersonVisualizer
• contacts_ : ExperimentalSettings , TargetedExperiment
• container : IMSAlphabet
• container_type : BilinearInterpolation< Key, Value > , Matrix< Value > , LinearInterpolation< Key, Value >
• ContainerType : IsotopeDistribution , BilinearInterpolation< Key, Value > , ConstRefVector< ContainerT > , IMSAlphabetParser< AlphabetElementType, Container, InputSource > , Matrix< Value > , MSSpectrum< PeakT > , EmgModel , LevMarqFitter1D , LmaIsotopeFitter1D::Data , MSChromatogram< PeakT > , LinearInterpolation< Key, Value > , EGHModel
• contains() : StringList , IntList , DoubleList
• containsMS1Scans() : TOPPViewBase
• containsMSLevel() : PeakFileOptions
• containsTag() : MassDecomposition
• contaminants_ : RawMSSignalSimulation
• contaminants_loaded_ : RawMSSignalSimulation
• contaminants_map_ : MSSim
• context_add_ : SpectrumCanvas
• contextMenuEvent() : TOPPASTabBar , EnhancedTabBar , TOPPASEdge , Spectrum3DCanvas , Spectrum2DCanvas , TOPPASScene , MultiGradientSelector , Spectrum1DCanvas , TOPPASLogWindow , TOPPASVertex
• CONTINUOUS : LPWrapper
• CONTINUOUSFLOWFASTATOMBOMBARDMENT : IonSource
• ContinuousWaveletTransform() : ContinuousWaveletTransform
• ContinuousWaveletTransformNumIntegration() : ContinuousWaveletTransformNumIntegration
• ControlledVocabulary() : ControlledVocabulary
• CONVERSION_DTA : DataProcessing
• CONVERSION_MZDATA : DataProcessing
• CONVERSION_MZML : DataProcessing
• CONVERSION_MZXML : DataProcessing
• CONVERSIONDYNODE : IonDetector
• CONVERSIONDYNODEELECTRONMULTIPLIER : IonDetector
• CONVERSIONDYNODEPHOTOMULTIPLIER : IonDetector
• ConversionError() : ConversionError
• convert() : ConsensusMap , StringManager , ConsensusMap , StringManager , TransitionHelper , StringManager , ConsensusMap
• convert_ms_peaks() : ProcessData
• convert_to_LC_elution_peak() : ProcessData
• convertChromatogramsToSpectra() : ChromatogramTools
• convertPeptideIdScores_() : PrecursorIonSelection
• convertPeptideToAASequence() : OpenSwathDataAccessHelper
• convertSeedList() : SeedListGenerator
• convertSpectraToChromatograms() : ChromatogramTools
• convertTargetedExp() : OpenSwathDataAccessHelper
• convertTargetedExperimentToTSV() : TransitionTSVReader
• convertToOpenMSChromatogram() : OpenSwathDataAccessHelper
• convertToOpenMSSpectrum() : OpenSwathDataAccessHelper
• convertToSpectrumPtr() : OpenSwathDataAccessHelper
• convertTSVToTargetedExperiment() : TransitionTSVReader
• convex_hull_ : Feature
• convex_hulls_ : Feature
• convex_hulls_modified_ : Feature
• ConvexHull2D() : ConvexHull2D
• convolve_() : IsotopeDistribution
• convolvePow_() : IsotopeDistribution
• convolveSquare_() : IsotopeDistribution
• cookie_ : MascotRemoteQuery
• coord : HierarchicalClustering< PointRef >::TreeNode
• coordDist_() : HierarchicalClustering< PointRef >
• coordElemDiv_() : HierarchicalClustering< PointRef >
• coordElemGreater_() : HierarchicalClustering< PointRef >
• coordinate_ : DPosition< D, TCoordinateType >
• coordinate_container : BasicStatistics< RealT >
• CoordinateType : Annotations1DContainer , SimpleExtender< PeakType, FeatureType > , BaseModel< D > , DIntervalBase< D > , LmaIsotopeModel , Fitter1D , ChromatogramPeak , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , GaussModel , InterpolationModel , EmgModel , Peak1D , FeaFiModule< PeakType, FeatureType > , AveragePosition< D > , EGHModel , DRange< D > , FeatureDeconvolution , MSSpectrum< PeakT > , Annotation1DItem , LmaIsotopeFitter1D::Data , LmaGaussModel , DBoundingBox< D > , DPosition< D, TCoordinateType > , MSChromatogram< PeakT > , MSExperiment< PeakT, ChromatogramPeakT > , Peak2D , BiGaussModel , ExtendedIsotopeModel , FeatureFinderAlgorithm< PeakType, FeatureType > , IsotopeModel , ModelFitter< PeakType, FeatureType >
• coordScalarDiv_() : HierarchicalClustering< PointRef >
• copy() : Param
• copy_() : TOPPASOutputFileListVertex , HiddenMarkovModel
• copyLayer() : TOPPViewBase
• copySelected() : TOPPASScene
• cord_ : LocalLinearMap
• corner_ : Spectrum3DOpenGLCanvas
• corr_max : Summary
• corr_mean : Summary
• corr_min : Summary
• correctly_assigned_fit_param_ : PosteriorErrorProbabilityModel
• correctMasses() : MRMDecoy
• correlate_() : PeakPickerCWT
• correlationFilter1_() : SILACFilter
• correlationFilter2_() : SILACFilter
• corresponding_protein_accessions_ : PeptideHit
• COTRANSLATIONAL : ResidueModification
• count() : mean_and_stddev , LayerStatisticsDialog::MetaStatsValue_
• count_ : BigString
• count_trans_ : HiddenMarkovModel
• count_trans_all_ : HiddenMarkovModel
• counter : LogStreamBuf::LogCacheStruct
• counter_ : PrecursorIonSelectionPreprocessing
• countFreeIDs() : DocumentIDTagger
• countIntensities_() : SvmTheoreticalSpectrumGeneratorTrainer
• countIonizedResidues_() : IonizationSimulation
• countMissedCleavagesTryptic_() : CompNovoIdentificationBase
• countMS1Zeros() : TOPPViewBase
• countPeptides_() : PeptideAndProteinQuant
• countTargetDecoy() : ProteinResolver
• countTreatments() : Sample
• cov_ : TransformationModelBSpline
• coverage : ProteinResolver::ProteinEntry
• coverage_ : ProteinHit
• cpep_id_ : MzIdentMLHandler
• cpro_id_ : MzIdentMLHandler
• cpu_speed_ : StopWatch
• create() : EmgFitter1D , SteinScottImproveScore , IntList , IsotopeFitter1D , TICFilter , FastaIterator , FastaIteratorIntern , MapAlignmentAlgorithmSpectrumAlignment , MapAlignmentAlgorithmPoseClustering , FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType > , FeatureFinderAlgorithmSimple< PeakType, FeatureType > , SpectrumPrecursorComparator , ProductModel< 2 > , LmaGaussModel , PoseClusteringAffineSuperimposer , FeatureFinderAlgorithmSimplest< PeakType, FeatureType > , GaussModel , LmaIsotopeFitter1D , PoseClusteringShiftSuperimposer , PeakAlignment , StablePairFinder , SimplePairFinder , EdwardsLippertIterator , GaussFitter1D , QTClusterFinder , CompleteLinkage , TrypticIterator , ICPLLabeler , BinnedSumAgreeingIntensities , BinnedSpectralContrastAngle , MapAlignmentEvaluationAlgorithmRecall , LmaGaussFitter1D , IsotopeModel , EGHModel , ZhangSimilarityScore , BiGaussFitter1D , SpectrumCheapDPCorr , ComplementFilter , FeatureFinderAlgorithmSH< PeakType, FeatureType > , VersionInfo::VersionDetails , AverageLinkage , FeatureGroupingAlgorithmLabeled , IntList , LabelFreeLabeler , DoubleList , FeatureFinderAlgorithmMRM< PeakType, FeatureType > , EmgModel , ExtendedIsotopeFitter1D , BiGaussModel , LabeledPairFinder , BinnedSharedPeakCount , StringList , NeutralLossMarker , ComplementMarker , EGHFitter1D , SILACLabeler , IsotopeMarker , IntensityBalanceFilter , NeutralLossDiffFilter , IsotopeDiffFilter , GoodDiffFilter , MapAlignmentEvaluationAlgorithmPrecision , SpectrumAlignmentScore , LmaIsotopeModel , SpectraSTSimilarityScore , DoubleList , CompareFouriertransform , FeatureGroupingAlgorithmQT , O18Labeler , FeatureGroupingAlgorithmIdentification , FeatureGroupingAlgorithmUnlabeled , FeatureFinderAlgorithmPicked< PeakType, FeatureType > , SingleLinkage , EdwardsLippertIteratorTryptic , MapAlignmentAlgorithmIdentification , ExtendedIsotopeModel , Factory< FactoryProduct > , ITRAQLabeler
• create_rows_for_commmon_metavalue_ : SpectraIdentificationViewWidget
• createAdduct_() : MassExplainer
• createAndSolveCombinedLPFeatureBased_() : PSLPFormulation
• createAndSolveCombinedLPForKnownLCMSMapFeatureBased() : PSLPFormulation
• createAndSolveILP_() : PSLPFormulation
• createAndSolveILPForInclusionListCreation() : PSLPFormulation
• createAndSolveILPForKnownLCMSMapFeatureBased() : PSLPFormulation
• createConsensIsotopPattern() : LCElutionPeak
• createContaminants_() : RawMSSignalSimulation
• createDB() : DBAdapter
• createDirs() : TOPPASToolVertex
• createEditor() : ParamEditorDelegate , ListEditorDelegate
• createExperiment() : RTSimulation
• createFeatureElutionProfiles() : SuperHirnParameters
• createFeatureElutionProfiles_ : SuperHirnParameters
• createFeatureMap_() : MSSim
• createHRData() : FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >
• createIfNotExists_() : MetaInfoInterface
• createINI_() : ToolsDialog
• createIntensityDistribution_() : Spectrum1DWidget , SpectrumWidget , Spectrum3DWidget , Spectrum2DWidget
• createMemdumpIndex() : CachedmzML
• createMetaDistribution_() : SpectrumWidget , Spectrum3DWidget , Spectrum1DWidget , Spectrum2DWidget
• createModel() : ModelDescription< D >
• createMRMFeature() : MRMTransitionGroupPicker
• createMZFeatureClusters() : MS1FeatureMerger
• createNewRow() : ListTable
• createOutputDir() : TOPPASOutputFileListVertex
• createPeptide_() : TransitionTSVReader
• createPeptideReferenceMap_() : TargetedExperiment
• createProtein_() : TransitionTSVReader
• createProteinReferenceMap_() : TargetedExperiment
• createProteinSequenceBasedLPInclusionList() : OfflinePrecursorIonSelection
• createProteinToPeptideLinks() : MzTabFile
• createRandomPartitions() : SVMWrapper
• createResources() : TOPPASScene
• createStream_() : StreamHandler
• createTOPPToolsTreeWidget() : TOPPASBase
• createTransition_() : TransitionTSVReader
• creation_date_ : Identification
• CRM : InstrumentSettings
• cropFeature_() : FeatureFinderAlgorithmPicked< PeakType, FeatureType >
• CSV : FileTypes
• CsvFile() : CsvFile
• CSVWriter() : CSVWriter
• CTERM : Modification
• CTerminal : Residue
• curPos() : GzipInputStream , Bzip2InputStream
• curr_region_ : TwoDOptimization
• current_ : SILACFiltering::SpectrumInterpolation , Param::ParamIterator
• current_assay_ : MzQuantMLHandler
• current_cf_id_ : MzQuantMLHandler
• current_chull_ : FeatureXMLFile
• current_col_types_ : MzQuantMLHandler
• current_count_ : MzQuantMLHandler
• current_dm_values_ : MzQuantMLHandler
• current_dp_ : MzQuantMLHandler
• current_feature_ : FeatureXMLFile
• current_files_ : MzQuantMLHandler
• current_id_ : MzQuantMLHandler , MzMLValidator , MzMLHandler< MapType >
• current_id_hit_ : MzIdentMLHandler
• current_layer_ : SpectrumCanvas
• current_mod_location_ : MzIdentMLHandler
• current_modifications_ : PepXMLFile
• current_mz_ : SILACFilter
• current_orderedps_ : MzQuantMLHandler
• current_pas_ : MzQuantMLHandler
• current_path_ : INIFileEditorWindow , TOPPASBase , IDEvaluationBase , TOPPViewBase
• current_peak_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , SimpleSeeder< PeakType, FeatureType >
• current_peptide_ : PepXMLFile
• current_proteins_ : PepXMLFile
• current_row_ : MzQuantMLHandler
• current_scan_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
• current_secs_ : StopWatch
• current_sequence_ : PepXMLFile
• current_spectrum_ : LayerData
• current_spectrum_id_ : MzIdentMLHandler
• current_sws_ : MzQuantMLHandler
• current_system_time_ : StopWatch
• current_usecs_ : StopWatch
• current_user_time_ : StopWatch
• currentChanged_() : EnhancedTabBar , TOPPASTabBar
• currentIdChanged() : TOPPASTabBar , EnhancedTabBar
• currentLayerParametersChanged_() : Spectrum2DCanvas
• currentLayerParamtersChanged_() : Spectrum3DCanvas , Spectrum1DCanvas
• currentPeakData_() : SpectrumCanvas
• curve() : ROCCurve
• custom : MzTabUnitIdMetaData , MzTabSubIdMetaData
• customizations_ : InstrumentVisualizer , Instrument
• cut() : ClusterAnalyzer
• cut_off_ : BaseModel< D >
• cutoffNeg() : ROCCurve
• cutoffPos() : ROCCurve
• cutoffScore_ : MapAlignmentAlgorithmSpectrumAlignment
• CV() : CV , TargetedExperiment
• cv_ : MzQuantMLHandler , SemanticValidator , TraMLHandler , MzIdentMLHandler , MzMLHandler< MapType >
• cv_identifier_ref_ : CVMappingTerm , CVTerm
• CV_label_ : MzTabParameter
• cv_options_ : PILISCrossValidation
• cv_params_ : MSQuantifications::AnalysisSummary
• cv_ref : CVTerm::Unit
• cv_references_ : CVMappingFile , CVMappings
• cv_references_vector_ : CVMappings
• cv_tag_ : SemanticValidator
• cv_terms_ : XMLHandler , CVMappingRule , CVTermList
• cvAcc : QcMLFile::Attachment , QcMLFile::QualityParameter
• CVMappingFile() : CVMappingFile
• CVMappingRule() : CVMappingRule
• CVMappings() : CVMappings
• CVMappingTerm() : CVMappingTerm
• cvp_stack_ : MzQuantMLHandler
• cvParam_() : MzDataHandler< MapType >
• cvRef : QcMLFile::QualityParameter , QcMLFile::Attachment
• CVReference() : CVReference
• cvs_ : TargetedExperiment
• cvStringToEnum_() : XMLHandler
• CVTerm() : CVTerm , ControlledVocabulary::CVTerm , CVTerm , ControlledVocabulary::CVTerm
• CVTermList() : CVTermList
• CYCLOTRON : MassAnalyzer