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

- c -

• C : ExtendedIsotopeModel
• c : FeatureFinderAlgorithmIsotopeWavelet::BoxElement
• C : IsotopeModel
• c : IsotopeWaveletTransform< PeakType >::BoxElement
• C : SVMWrapper
• c13MassError_ : DeconvPeak
• c1_ : BernNorm , MapAlignmentAlgorithmSpectrumAlignment
• c2_ : BernNorm
• c_ : CubicSpline2d , QuadraticRegression , SpectrumAccessQuadMZTransforming , TOFCalibration , mean_and_stddev
• C_ELEMENTS : LayerData
• c_intensity_ : NucleicAcidSpectrumGenerator , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• c_mzs_ : IsotopeWaveletTransform< PeakType >
• c_spacings_ : IsotopeWaveletTransform< PeakType >
• C_TERM : OPXLDataStructs , ResidueModification
• c_term_gain_ : DigestionEnzymeProtein
• c_term_mod_ : AASequence
• C_TERMINAL_AA : PeptideEvidence
• cache_count_ : FASTAContainer< TFI_Vector >
• cacheChunk() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• cached_spectrum_ : LayerData
• cached_terms_ : MzMLHandler
• cachedir_ : CachedSwathFileConsumer , MzMLSwathFileConsumer
• CachedmzML() : CachedmzML
• CACHEDMZML : FileTypes
• CachedMzMLHandler() : CachedMzMLHandler
• CachedSwathFileConsumer() : CachedSwathFileConsumer
• CAD : IonSource
• cal_data_ : InternalCalibration
• calc_mass_to_charge : MzTabOSMSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• 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
• calculated_mass_to_charge_ : IdentificationHit
• calculateDIAIdScores() : OpenSwathScoring
• calculateDIAScores() : OpenSwathScoring
• calculateEmissionProbabilities() : HiddenMarkovModel
• calculateEstimatedQVal_() : FalseDiscoveryRate
• calculateFDR_() : FeatureFinderIdentificationAlgorithm
• calculateFDRBasic_() : FalseDiscoveryRate
• calculateFDRs_() : FalseDiscoveryRate
• calculateFilterValuesMean() : MRMFeatureFilter
• calculateFilterValuesPercRSD() : MRMFeatureFilter
• calculateFilterValuesVar() : MRMFeatureFilter
• calculateFitQuality_() : ElutionModelFitter
• calculateForwardPart_() : HiddenMarkovModel
• calculateGaussTable() : SVMWrapper
• calculateGB() : AAIndex
• calculateGridLines_() : Spectrum3DOpenGLCanvas
• calculateIntensityRankInMZWindow() : PScore
• calculateIonRatio() : MRMFeatureFilter
• calculateLibraryScores() : OpenSwathScoring
• calculateMap() : QCBase::SpectraMap
• calculateMonoWeight_() : ElementDB
• calculateMT_() : RTSimulation
• calculatePeakLevelSpectra() : PScore
• calculatePeakShapeMetrics() : PeakIntegrator
• calculatePeakShapeMetrics_() : PeakIntegrator
• calculatePermutationPeptideScores_() : AScore
• calculatePrecursorDIAScores() : OpenSwathScoring
• calculatePrecursorMass_() : NucleicAcidSearchEngine
• calculateProteinProbabilities() : PSProteinInference
• calculateProtonDistribution_() : ProtonDistributionModel
• calculateProtonDistributionCharge1_() : ProtonDistributionModel
• calculateProtonDistributionCharge2_() : ProtonDistributionModel
• calculateProtonDistributionGreater2_() : ProtonDistributionModel
• calculateProtonDistributionIonPair_() : ProtonDistributionModel
• calculateRankMap() : PScore
• calculateRatio() : AbsoluteQuantitation
• calculateResolution() : MRMFeatureFilter
• calculateRTDifference() : MRMFeatureFilter
• calculateTheoreticalIsotopesNumber() : EmpiricalFormula
• calculateXICs_() : OfflinePrecursorIonSelection , PSLPFormulation
• calcXcorrCoelutionScore() : MRMScoring
• calcXcorrCoelutionWeightedScore() : MRMScoring
• calcXcorrContrastCoelutionScore() : MRMScoring
• calcXcorrContrastShapeScore() : MRMScoring
• calcXcorrPrecursorCoelutionScore() : MRMScoring
• calcXcorrPrecursorCombinedCoelutionScore() : MRMScoring
• calcXcorrPrecursorCombinedShapeScore() : MRMScoring
• calcXcorrPrecursorContrastCoelutionScore() : MRMScoring
• calcXcorrPrecursorContrastShapeScore() : MRMScoring
• calcXcorrPrecursorShapeScore() : MRMScoring
• calcXcorrShapeScore() : MRMScoring
• calcXcorrShapeWeightedScore() : MRMScoring
• CalDataType : CalibrationData
• calib_masses_ : TOFCalibration
• calib_peaks_ft_ : TOFCalibration
• CalibrantStats_() : InternalCalibration::CalibrantStats_
• calibrate() : InternalCalibration , TOFCalibration
• CALIBRATION : DataProcessing
• CalibrationData() : CalibrationData
• callbackStdErr_ : ExternalProcess
• callbackStdOut_ : ExternalProcess
• callSiriusQProcess() : SiriusAdapterAlgorithm
• CancelButton_ : ListEditor
• cancelbutton_ : MetaDataBrowser
• candidateEdges_() : MetaboliteFeatureDeconvolution
• candidates_ : SiriusAdapterAlgorithm
• candidates_out_ : FeatureFinderIdentificationAlgorithm
• canModificationBeApplied_() : SILACLabeler
• CANNOT_WRITE_OUTPUT_FILE : TOPPBase
• canRun() : JavaInfo , PythonInfo
• canvas() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
• canvas_ : LayerStatisticsDialog , SpectrumWidget
• canvas_3d_ : Spectrum3DOpenGLCanvas
• canvas_coverage_min_ : Spectrum2DCanvas
• capacity() : ConstRefVector< ContainerT >
• capacity_ : ConstRefVector< ContainerT >
• CAPTION_3D_SUFFIX_ : TOPPViewBase
• caret_positions_ : Annotation1DCaret
• CASE : ListUtils
• CaseInsensitiveToCaseSensitiveDecoy : DecoyHelper
• category : ToolDescriptionInternal , ToolExternalDetails
• cbegin() : NASequence
• ccs_ : IDBoostGraph
• cd_ : SwathQC
• cd_spectra_ : SwathQC
• CE : TransitionTSVFile::TSVTransition
• CEI : IonSource
• cell_dimension : HashGrid< Cluster >
• cell_it_ : HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator
• cell_iterator : HashGrid< Cluster > , HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator
• cell_type : MzTabSampleMetaData
• cellClicked_() : SpectraIdentificationViewWidget
• CellContent : HashGrid< Cluster >
• CellIndex : ClusteringGrid , GridBasedClustering< Metric > , HashGrid< Cluster >
• cellindexAtClustercenter_() : HashGrid< Cluster >
• cells_ : ClusteringGrid , HashGrid< Cluster >
• cend() : NASequence
• center() : DIntervalBase< D > , IsobaricQuantitationMethod::IsobaricChannelInformation , ItraqConstants::ChannelInfo , SwathMap
• center_index_ : ClusterProxyKD
• center_point_ : QTCluster::BulkData
• centerOfBin() : Histogram< ValueType, BinSizeType >
• centre_ : GridBasedCluster
• CENTROID : SpectrumSettings
• centroid_mz_ : MassTrace
• centroid_position : PeakPickerCWT::PeakArea_
• centroid_rt_ : MassTrace
• centroid_sd_ : MassTrace
• CentroidData() : CentroidData
• centroidDataModus() : SuperHirnParameters
• centroidDataModus_ : CentroidData , SuperHirnParameters
• centroided_ : FeatureFinderMultiplexAlgorithm
• CentroidPeak() : CentroidPeak
• centroidWindowWidth_ : SuperHirnParameters
• cexp_ : MzDataHandler , MzMLHandler , MzXMLHandler , TraMLHandler
• cf_cf_obj_ : MzQuantMLHandler
• changed_ : QTCluster , TOPPASScene
• changedOutputFolder() : TOPPASScene
• changedParameter() : TOPPASScene
• changeElutionTimesByFactor() : FeatureLCProfile
• changeLabel() : TOPPViewBase
• changeLayerFilterState() : SpectrumCanvas
• changeLayerFlag() : TOPPViewBase
• changeLegendVisibility() : SpectrumCanvas , SpectrumWidget
• changeUnassigned() : TOPPViewBase
• changeVisibility() : SpectrumCanvas
• changeVisibleArea_() : Spectrum1DCanvas , SpectrumCanvas
• channel_ : MSstatsFile::MSstatsTMTLine_
• channel_count : IsobaricQuantifierStatistics
• CHANNEL_COUNT : ItraqConstants
• channel_description_ : BaseLabeler
• channel_id_minus_1 : IsobaricQuantitationMethod::IsobaricChannelInformation
• channel_id_minus_2 : IsobaricQuantitationMethod::IsobaricChannelInformation
• channel_id_plus_1 : IsobaricQuantitationMethod::IsobaricChannelInformation
• channel_id_plus_2 : IsobaricQuantitationMethod::IsobaricChannelInformation
• channel_map_ : ITRAQLabeler
• channel_names_ : TMTElevenPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• CHANNELELECTRONMULTIPLIER : IonDetector
• ChannelInfo : ITRAQLabeler
• ChannelMapType : ItraqConstants , ITRAQLabeler
• channels_ : ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• CHANNELS_EIGHTPLEX : ItraqConstants
• CHANNELS_FOURPLEX : ItraqConstants
• CHANNELS_TMT_SIXPLEX : ItraqConstants
• CHANNELTRON : IonDetector
• char_rest_ : MzXMLHandler::SpectrumData
• character_buffer_ : MascotXMLHandler
• characters() : ConsensusXMLFile , CVMappingFile , FeatureXMLFile , MascotXMLHandler , MzDataHandler , MzIdentMLHandler , MzMLHandler , MzQuantMLHandler , MzXMLHandler , PTMXMLHandler , SemanticValidator , ToolDescriptionHandler , TraMLHandler , UnimodXMLHandler , XMLHandler , OMSSAXMLFile , QcMLFile , XTandemXMLFile
• charge : NucleicAcidSearchEngine::PrecursorInfo , ConsensusIDAlgorithm::HitInfo
• CHARGE : DataFilters
• charge : MoleculeQueryMatch , RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ , InternalCalibration::LockMass , IsotopeCluster::ChargedIndexSet , KDTreeFeatureMaps , MS1Signal , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow , OptimizePeakDeconvolution::Data , PeptideHit::PeakAnnotation , RNPxlReportRow , SimpleTSGXLMS::SimplePeak , SiriusMSFile::CompoundInfo , Summary , SvmTheoreticalSpectrumGenerator::IonType , LightCompound , Peptide
• charge_ : AccurateMassSearchResult , Adduct , AdductInfo , BaseFeature , DeconvPeak , EmpiricalFormula , ExtendedIsotopeFitter1D , ExtendedIsotopeModel , FeatureHandle , FeatureHypothesis , IdentificationHit , IsotopeFitter1D , IsotopeModel , MultiplexIsotopicPeakPattern , OptimizePeakDeconvolution , PeptideHit , PepXMLFile , Precursor , PrecursorVisualizer , PeptideCompound , TraMLProduct
• CHARGE_CALCULATION : DataProcessing
• CHARGE_DECONVOLUTION : DataProcessing
• charge_lower_bound_ : FeatureFindingMetabo
• charge_max_ : FeatureFinderMultiplexAlgorithm
• charge_min_ : FeatureFinderMultiplexAlgorithm
• charge_set_ : PeptideCompound , TraMLProduct
• charge_state : SHFeature
• charge_upper_bound_ : FeatureFindingMetabo
• ChargedIndexSet : FeatureFinderDefs , Fitter1D , IsotopeCluster::ChargedIndexSet
• ChargeDirected : ProtonDistributionModel
• ChargeDistribution : SwathQC
• ChargeMap : FeatureFinderIdentificationAlgorithm
• CHARGEMODE : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• ChargePair() : ChargePair
• ChargeRemote : ProtonDistributionModel
• charges : DBSearchParam , ProteinIdentification::SearchParameters
• charges_ : HasPrecursorCharge< SpectrumType > , XQuestResultXMLHandler , MascotInfile , ProteinIdentificationVisualizer
• chargeTestworthy_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• ChargeToPepHitP : IDFilter
• ChargeType : BaseFeature , FeatureHandle
• chauvenet() : MRMRTNormalizer
• chauvenet_probability() : MRMRTNormalizer
• check_() : DataFilterDialog , TOPPASVertex::TOPPASFilenames
• 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
• check_raw_spec_name_empty() : LCMS
• check_term_value_types_ : SemanticValidator
• check_tree() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• check_units_ : SemanticValidator
• check_width_internally_ : PeakPickerIterative
• checkAndGetTermByName() : ControlledVocabulary
• checkAppliedProcessingSteps_() : IdentificationData
• checkBelonging() : BackgroundIntensityBin
• checkConditionISO_() : MSstatsFile
• checkConditionLFQ_() : MSstatsFile
• checkConvertAndFilterPepHits_ : BayesianProteinInferenceAlgorithm
• checkDatumRange() : TransformationModel
• checkDefaults() : Param
• checked() : Spectrum1DGoToDialog , Spectrum2DGoToDialog
• checked_base_name_ : PepXMLFile
• checkedToDouble_() : EDTAFile
• checkedToInt_() : EDTAFile
• checkExtraFeatures() : PercolatorFeatureSetHelper
• checkFeatureQuality_() : FeatureFinderAlgorithmPicked
• checkFeatureSpectraNumber() : SiriusAdapterAlgorithm
• checkFormula_() : Adduct
• checkForRequiredUserParams_() : PrecursorIonSelection
• checkForSignificantPeak_() : MultiplexFiltering
• checkHits_() : IDMapper
• checkIds_() : BaseGroupFinder
• checkIfFeatureExtractionExists() : FTPeakDetectController
• checkIfIniParametersAreApplicable_() : TOPPBase
• checkIfWeAreDone() : TOPPASScene
• checkIsotopeBelongingAndAdjustMass() : MSPeak
• checkLOD() : AbsoluteQuantitationMethod
• checkLOQ() : AbsoluteQuantitationMethod
• checkMassRanges_() : OfflinePrecursorIonSelection
• checkMassType_() : IDMapper
• checkMaximalRTSpan() : EGHTraceFitter , GaussTraceFitter , TraceFitter
• checkMetaValue() : MRMFeatureFilter
• checkMinimalRTSpan() : EGHTraceFitter , GaussTraceFitter , TraceFitter
• checkName_() : ControlledVocabulary
• checkNumObservations_() : FeatureFinderIdentificationAlgorithm
• checkOldRunConsistency_() : ConsensusMapMergerAlgorithm , IDMergerAlgorithm
• checkOSWInputReady_() : SwathTabWidget
• checkParam_() : TOPPBase
• checkParameters_() : MapAlignmentAlgorithmIdentification
• checkParentMatches_() : IdentificationData
• checkPositionForPlausibility_() : IsotopeWaveletTransform< PeakType >
• checkPPMTheoModel_() : IsotopeWaveletTransform< PeakType >
• checkPreferences_() : TOPPViewBase
• checkPyProphetInput_() : SwathTabWidget
• checkRange() : MRMFeatureFilter
• checkSatellite() : MultiplexFilteredPeak
• checkScoreTypes_() : IdentificationData
• checkSequenceUniqueness_() : MzTab
• checkSize() : SaveImageDialog
• checkSolution_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• checksum_ : SourceFile , SourceFileVisualizer
• checksum_type_ : SourceFile , SourceFileVisualizer
• ChecksumType : SourceFile
• checkSwathMap() : OpenSwathHelper
• checkSwathMapAndSelectTransitions() : OpenSwathHelper
• checkTDAnnotation_() : IDScoreGetterSetter
• checkUniqueIdentifiers_() : XMLHandler
• checkUnorderedContent_() : MSstatsFile
• checkValidity_() : TOPPASInputFileDialog , TOPPASIOMappingDialog , TOPPASOutputFilesDialog
• checkValidWeight() : TransformationModel
• CHEMI : IonSource
• CHEMICAL_DERIVATIVE : ResidueModification
• chemical_formula : MzTabSmallMoleculeSectionRow
• chgLLhoods : MessagePasserFactory< Label >
• chi_squared_ : LinearRegression , QuadraticRegression
• CHILD : CompNovoIonScoringBase
• children : ControlledVocabulary::CVTerm
• childScan : MSPeak
• chooseBestParameters_() : SimpleSVM
• chooseDecoys_() : ConfidenceScoring
• chooseElutionProfile_() : RawMSSignalSimulation
• chooseTraceFitter_() : FeatureFinderAlgorithmPicked
• chop() : String , StringUtils
• CHRG : MS2Info , MSPeak
• CHRG_MAP : LCElutionPeak
• chrom_count_total_ : MzMLHandler
• chrom_data_ : FeatureFinderIdentificationAlgorithm
• chrom_fwhm_ : ElutionPeakDetection , FeatureFindingMetabo
• chrom_id_ : MzMLSqliteHandler , MzMLSqliteSwathHandler
• chrom_index_ : CachedmzML , CachedMzMLHandler
• chrom_peak_snr_ : ElutionPeakDetection , MassTraceDetection
• Chromatogram() : Chromatogram
• chromatogram : MzMLHandler::ChromatogramData
• chromatogram_ : MzMLHandler , SignalToNoiseOpenMS< ContainerT >
• chromatogram_count_ : MzMLHandler
• chromatogram_data_ : MzMLHandler
• chromatogram_flag_set() : LayerData
• chromatogram_ids_ : SpectrumAccessOpenMSInMemory
• chromatogram_map_ : MRMTransitionGroup< ChromatogramType, TransitionType >
• chromatogramIdsMatch() : MRMTransitionGroup< ChromatogramType, TransitionType >
• ChromatogramMeta() : ChromatogramMeta
• ChromatogramNames : ChromatogramSettings
• ChromatogramPeak() : ChromatogramPeak
• ChromatogramPeakT : MSExperiment , OnDiscMSExperiment
• ChromatogramPeakType : MzMLHandler , MSExperiment
• chromatograms : LayerData
• chromatograms_ : MRMTransitionGroup< ChromatogramType, TransitionType > , MSDataSqlConsumer , MSExperiment , SpectrumAccessOpenMSInMemory
• chromatograms_expected_ : MSDataWritingConsumer
• chromatograms_native_ids_ : IndexedMzMLHandler , OnDiscMSExperiment
• chromatograms_offsets_ : IndexedMzMLHandler , MzMLHandler
• chromatograms_written_ : MSDataCachedConsumer , MSDataWritingConsumer
• ChromatogramSettings() : ChromatogramSettings
• ChromatogramTools() : ChromatogramTools
• ChromatogramType : CachedSwathFileConsumer , ChromatogramSettings , FullSwathFileConsumer , IMSDataConsumer , CachedMzMLHandler , MzMLHandler , MSDataCachedConsumer , MSDataSqlConsumer , MSDataWritingConsumer , MSExperiment , MzMLSwathFileConsumer , RegularSwathFileConsumer
• CHROMATOGRAPHY : IonSource
• ChromeleonFile() : ChromeleonFile
• Chunk() : MSSpectrum::Chunk
• chunk_() : FeatureFinderIdentificationAlgorithm
• chunk_offset_ : FASTAContainer< TFI_File >
• chunkAt() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• Chunks() : MSSpectrum::Chunks
• chunks_ : MSSpectrum::Chunks
• chunkSize() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• CI : IonSource
• CID : IonSource , Precursor
• cid_ : MzIdentMLHandler
• CIon : NASequence , Residue
• citations_ : TOPPBase
• cite_openms_ : TOPPBase
• class_models : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• classification_ : ResidueModification
• classifyFeatures_() : FeatureFinderIdentificationAlgorithm
• classifyIsotopes_() : CompNovoIonScoringBase
• clean_all_charge_states_ : ParentPeakMower
• 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
• clearbutton_ : MetaInfoVisualizer
• clearCache() : LogStreamBuf
• clearCurrentProcessingStep() : IdentificationData
• clearData_ : MSDataCachedConsumer
• 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
• cleavage_ : MascotInfile
• cleavage_regex_ : DigestionEnzyme
• cleavage_site_ : XTandemInfile
• cleavageCorrectionTerm() : PScore
• CleavageModel_() : EnzymaticDigestionLogModel::CleavageModel_
• clicked() : TOPPASVertex
• clipboard_ : TOPPASScene
• clipboard_scene_ : TOPPASBase
• clockTime() : StopWatch::TimeDiff_
• clone() : Digestion , Modification , SampleTreatment , Tagging
• close() : Bzip2Ifstream , GzipIfstream , HDF5Connector
• closebutton_ : MetaDataBrowser
• closeByTab() : TOPPASBase , TOPPViewBase
• closed_boxes_ : IsotopeWaveletTransform< PeakType >
• closeEvent() : INIFileEditorWindow , SpectrumWidget , TOPPASBase , TOPPASWidget , TOPPViewBase
• closeFile() : TOPPASBase , TOPPViewBase
• closeListEditor_() : ParamEditorDelegate
• cluster() : ClusterHierarchical , GridBasedClustering< Metric > , MultiplexClustering
• cluster_index_ : MinimumDistance
• ClusterAnalyzer() : ClusterAnalyzer
• ClusterCenter : HashGrid< Cluster >
• ClusteredMS2ConsensusSpectrum() : ClusteredMS2ConsensusSpectrum
• ClusterFunctor() : ClusterFunctor
• ClusterHierarchical() : ClusterHierarchical
• clusterIndistProteinsAndPeptides() : IDBoostGraph
• clusterIndistProteinsAndPeptidesAndExtendGraph() : IDBoostGraph
• ClusteringGrid() : ClusteringGrid
• ClusterPointType : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• ClusterProxyKD() : ClusterProxyKD
• clusters_ : GridBasedClustering< Metric >
• clusters_final_ : GridBasedClustering< Metric >
• clusterSeeds_() : IsotopeWaveletTransform< PeakType >
• cm_cf_ids_ : MzQuantMLHandler
• CMD : ProgressLogger
• CMMzTabStream() : MzTab::CMMzTabStream
• cmp : SiriusMSFile::CompoundInfo
• cmp1_ : LexicographicComparator< Cmp1, Cmp2 >
• cmp2_ : LexicographicComparator< Cmp1, Cmp2 >
• cmp_ : Compomer , PointerComparator< Cmp > , ReverseComparator< Cmp >
• cmp_bs_ : TargetedSpectraExtractor::BinnedSpectrumComparator
• cmpOligos_() : LibSVMEncoder
• cmsq_ : MzQuantMLHandler
• CNG : InstrumentSettings
• CNL : InstrumentSettings
• cnt_decal : InternalCalibration::CalibrantStats_
• cnt_empty : InternalCalibration::CalibrantStats_
• cnt_nomz : InternalCalibration::CalibrantStats_
• cnt_nort : InternalCalibration::CalibrantStats_
• cnt_total : InternalCalibration::CalibrantStats_
• CoarseIsotopePatternGenerator() : CoarseIsotopePatternGenerator
• code_ : LocalLinearMap , Ribonucleotide
• code_map_ : RibonucleotideDB
• coeff_ : MZTrafoModel
• coeff_quad_fit_ : TOFCalibration
• coeffs_ : GaussFilterAlgorithm , SavitzkyGolayFilter
• cohesion() : ClusterAnalyzer
• col() : Matrix< Value >
• colIndex() : Matrix< Value >
• collapseStringVector() : TOPPViewIdentificationViewBehavior
• collect_annotations_ : QTCluster
• collectDecompositionsRecursively_() : IntegerMassDecomposer< ValueType, DecompositionValueType >
• collected_protein_hits_ : IDMergerAlgorithm
• collectFragmentScansInArea() : Spectrum2DCanvas
• collectPrecursorCandidates() : OPXLHelper
• collectRatios_() : IsobaricNormalizer
• collectSetParameter() : QcMLFile
• COLLISION_QUADRUPOLE : Instrument
• colnames() : CSVWriter , DataMatrix , IDataFrameWriter
• colnames_ : DataMatrix
• color() : MultiGradient
• color_ : Annotation1DCaret , Annotation1DPeakItem , ColorSelector , TOPPASEdge
• ColorSelector() : ColorSelector
• cols() : Matrix< Value >
• cols_ : Matrix< Value >
• colTypes : QcMLFile::Attachment
• column_ : HPLC
• column_description_ : ConsensusMap
• columnExists() : SqliteConnector
• ColumnHeader() : ConsensusMap::ColumnHeader
• ColumnHeaders : ConsensusMap
• columnname_to_columnindex_ : ExperimentalDesign::SampleSection
• colunit_peptide : MzTabMetaData
• colunit_protein : MzTabMetaData
• colunit_psm : MzTabMetaData
• colunit_small_molecule : MzTabMetaData
• combinations_logic_ : CVMappingRule
• CombinationsLogic : CVMappingRule
• combineMods() : ResidueModification
• combinePrecursorPurities() : PrecursorPurity
• combineTopRanksFromPairs() : OPXLHelper
• combos_ : GridSearch< TupleTypes >
• combos_ready_ : GridSearch< TupleTypes >
• comet_id_ : DigestionEnzymeProtein
• command : TOPPASScene::TOPPProcess
• commandline : ToolExternalDetails
• comment_ : ChromatogramSettings , ExperimentalSettings , ExperimentalSettingsVisualizer , HPLC , MetaInfoDescription , Sample , SampleTreatment , SpectrumSettings , SpectrumSettingsVisualizer
• comment_rows_ : MzTab
• commitAndCloseComboBox_() : ParamEditorDelegate
• commitAndCloseLineEdit_() : ParamEditorDelegate
• commitAndCloseListEditor_() : ParamEditorDelegate
• common_name_ : SpectralMatch
• 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
• 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
• component_group_name : MRMFeaturePicker::ComponentGroupParams , MRMFeaturePicker::ComponentParams , MRMFeatureQC::ComponentGroupPairQCs , MRMFeatureQC::ComponentGroupQCs
• component_group_pair_qcs : MRMFeatureQC
• component_group_qcs : MRMFeatureQC
• component_name : AbsoluteQuantitationStandards::runConcentration , MRMFeaturePicker::ComponentParams , MRMFeatureQC::ComponentQCs
• component_name_ : AbsoluteQuantitationMethod
• component_qcs : MRMFeatureQC
• composition_ : PTMXMLHandler
• Compound : TargetedExperiment , Compound , LightTargetedExperiment
• compound_adduct : MetaboTargetedAssay
• compound_count : TargetedExperiment::SummaryStatistics
• compound_name : MetaboTargetedAssay , LightCompound
• compound_ref_ : IncludeExcludeTarget , ReactionMonitoringTransition
• compound_reference_map_ : TargetedExperiment , LightTargetedExperiment
• compound_reference_map_dirty_ : TargetedExperiment , LightTargetedExperiment
• compound_timeout_ : SiriusAdapterAlgorithm
• CompoundName : TransitionTSVFile::TSVTransition
• CompoundReferenceMapType : TargetedExperiment
• compounds : LightTargetedExperiment
• compounds_ : TargetedExperiment
• compoundspectrumpair : MetaboTargetedAssay::CompoundSpectrumPair
• CompoundTransitionMapType : MRMAssay
• CompoundType : IonMobilityScoring , OpenSwathScoring
• CompoundVectorType : MRMAssay
• compress() : ConvexHull2D
• CompressedInputSource() : CompressedInputSource
• compression : MzMLHandlerHelper::BinaryData
• compressionType_ : MzXMLHandler::SpectrumData
• compressSignals_() : RawMSSignalSimulation
• compressString() : ZlibCompression
• compressTrieDB() : InspectOutfile
• compute() : AScore , Contaminants , DBSuitability , FeatureDeconvolution , FragmentMassError , FWHM , HyperScore , ILPDCWrapper , MassExplainer , MetaboliteFeatureDeconvolution , MissedCleavages , MorpheusScore , Ms2IdentificationRate , Ms2SpectrumStats , MzCalibration , PeptideMass , RTAlignment , TIC
• compute_additional_points_ : EmgGradientDescent
• compute_CHRG() : LCElutionPeak
• compute_delta_area() : LCElutionPeak
• compute_F() : SpectraSTSimilarityScore
• compute_peak_quality_ : MRMTransitionGroupPicker
• compute_peak_shape_metrics_ : MRMTransitionGroupPicker
• compute_total_mi_ : MRMTransitionGroupPicker
• compute_z() : EmgGradientDescent , EmgGradientDescent_friend
• computeApexSNR() : ElutionPeakDetection
• computeAveragineSimScore_() : FeatureFindingMetabo
• computeBaseProbability_() : AScore
• computeBestClusterForCenter_() : FeatureGroupingAlgorithmKD
• computeBinnedCoverage() : MRMRTNormalizer
• 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
• concentration_ : Sample
• concentration_units : AbsoluteQuantitationStandards::featureConcentration , AbsoluteQuantitationStandards::runConcentration
• concentration_units_ : AbsoluteQuantitationMethod
• condensIsotopePattern() : ConsensusIsotopePattern
• condition_ : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_
• conditional_prob : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• ConfidenceScoring() : ConfidenceScoring
• config_ : SqMassFile
• Configuration : IncludeExcludeTarget , ReactionMonitoringTransition
• configuration_list_ : TraMLProduct
• ConfigurationListType : TraMLHandler
• configurations_ : IncludeExcludeTarget
• configure() : LogConfigHandler
• ConnectedComponent() : ConnectedComponent
• connectEdgeSignals() : TOPPASScene
• connection_line_color_ : Annotation1DCaret
• connectMergerVertexSignals() : TOPPASScene
• connectOutputVertexSignals() : TOPPASScene
• connectToolVertexSignals() : TOPPASScene
• connectVertexSignals() : TOPPASScene
• connectVisualizer_() : MetaDataBrowser
• consensus : LayerData
• Consensus : ProteinResolver::ResolverResult
• consensus_ : BaseLabeler
• consensus_feature_filenames : MSstatsFile::AggregatedConsensusInfo
• consensus_feature_intensities : MSstatsFile::AggregatedConsensusInfo
• consensus_feature_labels : MSstatsFile::AggregatedConsensusInfo
• consensus_feature_peptide_hit_user_value_keys_ : MzTab::CMMzTabStream
• consensus_feature_retention_times : MSstatsFile::AggregatedConsensusInfo
• consensus_feature_user_value_keys_ : MzTab::CMMzTabStream
• consensus_map : ProteinResolver::ResolverResult
• consensus_map_ : ConsensusXMLFile , FeatureFinderMultiplexAlgorithm , MSSim , MzTab::CMMzTabStream
• consensus_maps_ : MSQuantifications
• ConsensusFeature() : ConsensusFeature
• ConsensusIDAlgorithm() : ConsensusIDAlgorithm
• ConsensusIDAlgorithmAverage() : ConsensusIDAlgorithmAverage
• ConsensusIDAlgorithmBest() : ConsensusIDAlgorithmBest
• ConsensusIDAlgorithmIdentity() : ConsensusIDAlgorithmIdentity
• ConsensusIDAlgorithmPEPIons() : ConsensusIDAlgorithmPEPIons
• ConsensusIDAlgorithmPEPMatrix() : ConsensusIDAlgorithmPEPMatrix
• ConsensusIDAlgorithmRanks() : ConsensusIDAlgorithmRanks
• ConsensusIDAlgorithmSimilarity() : ConsensusIDAlgorithmSimilarity
• ConsensusIDAlgorithmWorst() : ConsensusIDAlgorithmWorst
• ConsensusIsotopePattern() : ConsensusIsotopePattern
• ConsensusIterator_ : LayerStatisticsDialog
• ConsensusMap() : ConsensusMap
• ConsensusMapMergerAlgorithm() : ConsensusMapMergerAlgorithm
• ConsensusMapNormalizerAlgorithmMedian() : ConsensusMapNormalizerAlgorithmMedian
• ConsensusMapNormalizerAlgorithmQuantile() : ConsensusMapNormalizerAlgorithmQuantile
• ConsensusMapNormalizerAlgorithmThreshold : ConsensusMapNormalizerAlgorithmMedian , ConsensusMapNormalizerAlgorithmThreshold
• ConsensusMapSharedPtrType : LayerData , SpectrumCanvas , TOPPViewBase , TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• ConsensusMapType : LayerData , SpectrumCanvas , TOPPViewBase , TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
• CONSENSUSXML : FileTypes
• ConsensusXMLFile() : ConsensusXMLFile , IdXMLFile
• consider_H2O_loss_ : ParentPeakMower
• consider_NH3_loss_ : ParentPeakMower
• considered_hits_ : ConsensusIDAlgorithm
• console_width_ : ConsoleUtils
• ConsoleUtils() : ConsoleUtils
• const_abundances_iterator : IMSIsotopeDistribution
• const_cell_iterator : HashGrid< Cluster >
• CONST_CONT_IT : MatchedIterator< CONT_T, TRAIT, CONST_T >
• const_enzymes_ : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• const_grid_iterator : HashGrid< Cluster >
• const_iterator : _Iterator< _Val, _Ref, _Ptr > , KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , CalibrationData , ConsensusFeature , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType > , EmpiricalFormula , FeatureFinderAlgorithmPickedHelperStructs::MassTraces , HashGrid< Cluster > , IMSAlphabet , IsotopeDistribution , MassTrace , Matrix< Value > , MSExperiment , XCorrArrayType
• const_mass_iterator : IMSAlphabet
• const_masses_iterator : IMSIsotopeDistribution
• const_modified_residues_ : ResidueDB
• const_name_iterator : IMSAlphabet
• const_peaks_iterator : IMSIsotopeDistribution
• const_pointer : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , AASequence::ConstIterator , AASequence::Iterator , NASequence::ConstIterator , NASequence::Iterator
• const_reference : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , AASequence::ConstIterator , AASequence::Iterator , ConstRefVector< ContainerT > , Matrix< Value > , NASequence::ConstIterator , NASequence::Iterator
• const_residues_ : ResidueDB
• const_reverse_iterator : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , IsotopeDistribution , MassTrace , Matrix< Value >
• const_weights_ : SequestOutfile
• CONSTANT : MassAnalyzer
• ConstAreaIterator : MSExperiment
• ConstEdgeIterator : TOPPASScene , TOPPASVertex
• ConstEntryIterator : Param::ParamNode
• ConstEnzymeIterator : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• ConstExperimentSharedPtrType : LayerData , SpectrumCanvas
• ConstIterator() : AASequence::ConstIterator , Annotations1DContainer , ConsensusMap , ConstRefVector< ContainerT > , DPosition< D, TCoordinateType > , EmpiricalFormula , FeatureMap , HashGrid< Cluster >::ConstIterator , IsotopeDistribution , Map< Key, T > , Histogram< ValueType, BinSizeType > , Matrix< Value > , MSChromatogram , MSExperiment , MSSpectrum , NASequence::ConstIterator , RibonucleotideDB , String , StringListUtils , TextFile
• ConstNodeIterator : Param::ParamNode
• ConstPeakIterator : PeakPickerCWT
• constraints_type : RealMassDecomposer
• ConstReference : FeatureMap , Matrix< Value >
• ConstRefVector() : ConstRefVector< ContainerT > , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
• ConstRefVectorConstIterator() : ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
• ConstRefVectorIterator() : ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
• ConstReverseIterator : ConsensusMap , ConstRefVector< ContainerT > , FeatureMap , IsotopeDistribution , Map< Key, T > , Matrix< Value > , MSChromatogram , MSSpectrum , String , StringListUtils , TextFile
• ConstRibonucleotidePtr : NucleicAcidSearchEngine , ModifiedNASequenceGenerator , NASequence , RibonucleotideDB
• constructClusteredConsenusSpectraFragments() : ClusteredMS2ConsensusSpectrum
• constructConsusPattern() : ConsensusIsotopePattern
• constructFile_() : MSstatsFile
• constructHeader_() : IBSpectraFile
• constructMS1FeatureFromMS2Feature() : FTPeakDetectController
• constructTargTransList_() : MRMFeatureSelector , MRMFeatureSelector_test
• ConstVertexIterator : TOPPASScene
• consumeChromatogram() : FullSwathFileConsumer , IMSDataConsumer , MSDataAggregatingConsumer , MSDataCachedConsumer , MSDataChainingConsumer , MSDataSqlConsumer , MSDataStoringConsumer , MSDataTransformingConsumer , MSDataWritingConsumer , NoopMSDataConsumer , NoopMSDataWritingConsumer
• consumeCVTerms() : CVTermList , CVTermListInterface
• consumeMS1Spectrum_() : CachedSwathFileConsumer , FullSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• consumer_ : MzMLHandler , MzXMLHandler
• consumers_ : MSDataChainingConsumer
• consumeSpectrum() : FullSwathFileConsumer , IMSDataConsumer , MSDataAggregatingConsumer , MSDataCachedConsumer , MSDataChainingConsumer , MSDataSqlConsumer , MSDataStoringConsumer , MSDataTransformingConsumer , MSDataWritingConsumer , NoopMSDataConsumer , NoopMSDataWritingConsumer
• consumeSwathSpectrum_() : CachedSwathFileConsumer , FullSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
• consuming_possible_ : FullSwathFileConsumer
• CONT_IT : MatchedIterator< CONT_T, TRAIT, CONST_T >
• contact : MzTabMetaData
• Contact : TargetedExperiment , Contact
• contact_info_ : ContactPerson , ContactPersonVisualizer
• contact_ref : Configuration , Prediction
• ContactPerson() : ContactPerson
• ContactPersonVisualizer() : ContactPersonVisualizer
• contacts_ : ExperimentalSettings , TargetedExperiment
• container : IMSAlphabet
• container_type : BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value > , Matrix< Value >
• ContainerType : AcquisitionInfo , ConstRefVector< ContainerT > , EGHModel , EmgModel , IMSAlphabetParser< AlphabetElementType, Container, InputSource > , IsotopeDistribution , LevMarqFitter1D , BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value > , Matrix< Value > , MSChromatogram , MSSpectrum
• contains() : EmpiricalFormula , ListUtils
• contains_invalid_references : TargetedExperiment::SummaryStatistics
• containsIMData() : MSSpectrum
• containsInvalidReferences() : TargetedExperiment
• containsMSLevel() : PeakFileOptions
• containsScanOfLevel() : MSExperiment
• containsTag() : MassDecomposition
• Contaminants() : Contaminants
• contaminants_ : RawMSSignalSimulation
• contaminants_loaded_ : RawMSSignalSimulation
• contaminants_map_ : MSSim
• content_ : ExperimentalDesign::SampleSection
• context_add_ : SpectrumCanvas
• contextMenuEvent() : EnhancedTabBar , MultiGradientSelector , Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , TOPPASEdge , TOPPASLogWindow , TOPPASScene , TOPPASTabBar , 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() : StringManager , MapConversion , TransitionHelper
• convert_ms_peaks() : ProcessData
• convert_to_LC_elution_peak() : ProcessData
• convertChromatogramsToSpectra() : ChromatogramTools
• convertData_() : SimpleSVM
• convertModificationSet_() : XTandemInfile
• convertPeptideIdScores_() : PrecursorIonSelection
• convertPeptideToAASequence() : OpenSwathDataAccessHelper
• convertPQPToTargetedExperiment() : TransitionPQPFile
• convertSeedList() : SeedListGenerator
• convertSpectraToChromatograms() : ChromatogramTools
• convertTargetedCompound() : OpenSwathDataAccessHelper
• convertTargetedExp() : OpenSwathDataAccessHelper
• convertTargetedExperimentToPQP() : TransitionPQPFile
• convertTargetedExperimentToTSV() : TransitionTSVFile
• convertToChromatogramPtr() : OpenSwathDataAccessHelper
• convertToFeatureMap() : FIAMSDataProcessor
• convertToOpenMSChromatogram() : OpenSwathDataAccessHelper
• convertToOpenMSChromatogramFilter() : OpenSwathDataAccessHelper
• convertToOpenMSSpectrum() : OpenSwathDataAccessHelper
• convertToSpectrumPtr() : OpenSwathDataAccessHelper
• convertTransition_() : TransitionTSVFile
• convertTSVToTargetedExperiment() : TransitionTSVFile
• convex_hull_ : Feature
• convex_hulls_ : Feature
• convex_hulls_modified_ : Feature
• ConvexHull2D() : ConvexHull2D
• convolve_() : CoarseIsotopePatternGenerator
• convolvePow_() : CoarseIsotopePatternGenerator
• convolveSquare_() : CoarseIsotopePatternGenerator
• cookie_ : MascotRemoteQuery
• Coordinate : MSstatsFile
• coordinate_ : DPosition< D, TCoordinateType >
• coordinate_container : BasicStatistics< RealT >
• CoordinateType : Annotation1DItem , Annotations1DContainer , BaseModel< D > , BiGaussModel , ChromatogramPeak , DBoundingBox< D > , DPosition< D, TCoordinateType > , DRange< D > , EGHModel , EmgModel , ExtendedIsotopeModel , FeatureDeconvolution , FeatureFinderAlgorithm , Fitter1D , GaussModel , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , DIntervalBase< D > , InterpolationModel , IsotopeModel , AveragePosition< D > , MetaboliteFeatureDeconvolution , MSChromatogram , MSExperiment , MSSpectrum , Peak1D , Peak2D
• copy() : Param
• copy_() : HiddenMarkovModel , TOPPASOutputFileListVertex
• copyBatchTransitions_() : OpenSwathWorkflow
• copyDirRecursively() : File
• copyLayer() : TOPPViewBase
• CopyOptions : File
• copySearchParams_() : IDMergerAlgorithm
• copySelected() : TOPPASScene
• copySubset() : Param
• cord_ : LocalLinearMap
• cores_ : SiriusAdapterAlgorithm
• corner_ : Spectrum3DOpenGLCanvas
• corr_max : Summary
• corr_mean : Summary
• corr_min : Summary
• correct_window_counter_ : FullSwathFileConsumer
• correctAreaToObeyMinMaxRanges_() : SpectrumWidget
• correctIM() : SwathMapMassCorrection
• correctIsotopicImpurities() : IsobaricIsotopeCorrector
• correctly_assigned_fit_param_ : PosteriorErrorProbabilityModel
• correctMass_() : CoarseIsotopePatternGenerator
• correctMZ() : SwathMapMassCorrection
• correctPeptideIntensities_() : FeatureFinderMultiplexAlgorithm
• correctToHighestIntensityMS1Peak() : PrecursorCorrection
• correctToNearestFeature() : PrecursorCorrection
• correctToNearestMS1Peak() : PrecursorCorrection
• correlate_() : PeakPickerCWT
• correlation_coefficient_ : AbsoluteQuantitationMethod
• COTRANSLATIONAL : ResidueModification
• count() : squared_difference_counted< _Tp, _Dist > , LayerStatisticsDialog::MetaStatsValue_ , ROCCurve , SummaryStatistics< T > , mean_and_stddev
• count_empty_ : ConsensusIDAlgorithm
• count_trans_ : HiddenMarkovModel
• count_trans_all_ : HiddenMarkovModel
• count_within_range() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• counter : LogStreamBuf::LogCacheStruct
• counter_ : PrecursorIonSelectionPreprocessing
• countFreeIDs() : DocumentIDTagger
• countHits() : IDFilter
• countIntensities_() : SvmTheoreticalSpectrumGeneratorTrainer
• countIonizedResidues_() : IonizationSimulation
• countLabelsAndTransitionTypes() : MRMFeatureFilter
• countMissedCleavages_() : EnzymaticDigestion
• countMissedCleavagesTryptic_() : CompNovoIdentificationBase
• countPeptides_() : PeptideAndProteinQuant
• countScansInSwath_() : SwathFile
• countTargetDecoy() : ProteinResolver
• countTreatments() : Sample
• coverage : ParentMolecule , MzTabNucleicAcidSectionRow , MzTabProteinSectionRow , ProteinResolver::ProteinEntry
• coverage_ : ProteinHit
• COVERAGE_UNKNOWN : ProteinHit
• cpep_id_ : MzIdentMLDOMHandler , MzIdentMLHandler , XQuestResultXMLHandler
• cpro_id_ : MzIdentMLDOMHandler , MzIdentMLHandler , XQuestResultXMLHandler
• cpu_speed_ : StopWatch
• create() : AverageLinkage , BiGaussFitter1D , BiGaussModel , BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSumAgreeingIntensities , ComplementFilter , ComplementMarker , CompleteLinkage , EGHFitter1D , EGHModel , EmgFitter1D , EmgModel , ExtendedIsotopeFitter1D , ExtendedIsotopeModel , Factory< FactoryProduct > , FeatureFinderAlgorithmIsotopeWavelet , FeatureFinderAlgorithmMRM , FeatureFinderAlgorithmPicked , FeatureFinderAlgorithmSH , FeatureGroupingAlgorithmKD , FeatureGroupingAlgorithmLabeled , FeatureGroupingAlgorithmQT , FeatureGroupingAlgorithmUnlabeled , GaussFitter1D , GaussModel , GoodDiffFilter , GUIProgressLoggerImpl , ICPLLabeler , IntensityBalanceFilter , IsotopeDiffFilter , IsotopeFitter1D , IsotopeMarker , IsotopeModel , ITRAQLabeler , LabeledPairFinder , LabelFreeLabeler , ListUtils , MapAlignmentEvaluationAlgorithmPrecision , MapAlignmentEvaluationAlgorithmRecall , NeutralLossDiffFilter , NeutralLossMarker , O18Labeler , PeakAlignment , PoseClusteringAffineSuperimposer , PoseClusteringShiftSuperimposer , ProductModel< 2 > , ProteinIdentification::Mapping , QTClusterFinder , SILACLabeler , SimplePairFinder , SingleLinkage , SpectraSTSimilarityScore , SpectrumAlignmentScore , SpectrumCheapDPCorr , SpectrumPrecursorComparator , StablePairFinder , SteinScottImproveScore , TICFilter , VersionInfo::VersionDetails , ZhangSimilarityScore
• create_rows_for_commmon_metavalue_ : SpectraIdentificationViewWidget
• createAdduct_() : MassExplainer
• createAndSolveCombinedLPFeatureBased_() : PSLPFormulation
• createAndSolveCombinedLPForKnownLCMSMapFeatureBased() : PSLPFormulation
• createAndSolveILP_() : PSLPFormulation
• createAndSolveILPForInclusionListCreation() : PSLPFormulation
• createAndSolveILPForKnownLCMSMapFeatureBased() : PSLPFormulation
• createAssayLibrary_() : FeatureFinderIdentificationAlgorithm
• createBFPeptideProbabilisticAdderFactor() : MessagePasserFactory< Label >
• createChargeFactor() : MessagePasserFactory< Label >
• createCompound_() : TransitionTSVFile
• createCompoundReferenceMap_() : TargetedExperiment
• createConsensIsotopPattern() : LCElutionPeak
• createConsensusFeature_() : QTClusterFinder
• createConsensusMapCache() : MasstraceCorrelator
• createContaminants_() : RawMSSignalSimulation
• createDirs() : TOPPASToolVertex
• createEditor() : ListEditorDelegate , ParamEditorDelegate
• createExperiment() : RTSimulation
• createFeatureElutionProfiles() : SuperHirnParameters
• createFeatureElutionProfiles_ : SuperHirnParameters
• createFeatureMap_() : MSSim
• createFlankingAAXMLString_() : IdXMLFile
• createHRData() : FeatureFinderAlgorithmIsotopeWavelet
• createIfNotExists_() : CVTermListInterface , MetaInfoInterface
• createIndices_() : MzMLSqliteHandler
• createINI_() : ToolsDialog
• createIntensityDistribution_() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
• createMemdumpIndex() : CachedMzMLHandler
• createMetaDistribution_() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
• createModel() : ModelDescription< D >
• createMRMFeature() : MRMTransitionGroupPicker
• createMZFeatureClusters() : MS1FeatureMerger
• createNewRow() : ListTable
• createOutputDir() : TOPPASOutputFileListVertex
• createPeptide_() : TransitionTSVFile
• createPeptideEvidenceFactor() : MessagePasserFactory< Label >
• createPeptideProbabilisticAdderFactor() : MessagePasserFactory< Label >
• createPeptideReferenceMap_() : TargetedExperiment , LightTargetedExperiment
• createPositionXMLString_() : IdXMLFile
• createProtein_() : TransitionTSVFile
• createProteinFactor() : MessagePasserFactory< Label >
• createProteinReferenceMap_() : TargetedExperiment
• createProteinSequenceBasedLPInclusionList() : OfflinePrecursorIonSelection
• createProteinToPeptideLinks_() : MzTabFile
• createPseudoSpectra() : MasstraceCorrelator
• createRandomPartitions() : SVMWrapper
• createRegularizingSumEvidenceFactor() : MessagePasserFactory< Label >
• createReplicateFactor() : MessagePasserFactory< Label >
• createResidueModificationToResidueMap_() : ModifiedPeptideGenerator
• createResources() : TOPPASScene
• createSpec_() : MSExperiment
• createStream_() : StreamHandler
• createSumEvidenceFactor() : MessagePasserFactory< Label >
• createSumFactor() : MessagePasserFactory< Label >
• createTables() : MzMLSqliteHandler
• createTheoreticalSpectra_() : AScore
• createTOPPToolsTreeWidget() : TOPPASBase
• createTransition_() : TransitionTSVFile
• createUnknownFromMassString() : ResidueModification
• creation_date_ : Identification
• CRM : InstrumentSettings
• cropFeature_() : FeatureFinderAlgorithmPicked
• CROSS : OPXLDataStructs
• cross_link : OPXLDataStructs::CrossLinkSpectrumMatch
• cross_link_classes_ : XFDRAlgorithm
• cross_link_mass_ : OpenPepXLLFAlgorithm
• cross_link_mass_iso_shift_ : OpenPepXLAlgorithm
• cross_link_mass_light_ : OpenPepXLAlgorithm
• cross_link_mass_mono_link_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
• cross_link_name_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
• cross_link_position : OPXLDataStructs::ProteinProteinCrossLink
• cross_link_residue1_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
• cross_link_residue2_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
• cross_linker_mass : OPXLDataStructs::ProteinProteinCrossLink
• cross_linker_name : OPXLDataStructs::ProteinProteinCrossLink
• cross_linker_name_ : XQuestResultXMLHandler
• crosslink_class_decoys_ : XFDRAlgorithm
• crosslink_class_fulldecoysinterlinks_ : XFDRAlgorithm
• crosslink_class_fulldecoysintralinks_ : XFDRAlgorithm
• crosslink_class_hybriddecoysinterlinks_ : XFDRAlgorithm
• crosslink_class_hybriddecoysintralinks_ : XFDRAlgorithm
• crosslink_class_interdecoys_ : XFDRAlgorithm
• crosslink_class_interlinks_ : XFDRAlgorithm
• crosslink_class_intradecoys_ : XFDRAlgorithm
• crosslink_class_intralinks_ : XFDRAlgorithm
• crosslink_class_monodecoys_ : XFDRAlgorithm
• crosslink_class_monolinks_ : XFDRAlgorithm
• crosslink_class_targets_ : XFDRAlgorithm
• CrossLinksDB() : CrossLinksDB , ModificationsDB
• crux_id_ : DigestionEnzymeProtein
• CSV : FileTypes
• csv_header : PrecursorCorrection
• CsvFile() : CsvFile
• CSVWriter() : CSVWriter
• ct_regex_ : SpectrumAnnotator
• CTERM : Modification
• CTerminal : Residue
• CubicSpline2d() : CubicSpline2d
• curPos() : Bzip2InputStream , GzipInputStream
• curr_region_ : TwoDOptimization
• curr_v : IDBoostGraph::dfs_ccsplit_visitor
• current_ : GUIProgressLoggerImpl , Param::ParamIterator
• current_analysis_result_ : IdXMLFile , PepXMLFile
• current_assay_ : MzQuantMLHandler
• current_base_name_ : PepXMLFile
• current_cf_id_ : MzQuantMLHandler
• current_charge_ : XTandemXMLFile
• current_chull_ : FeatureXMLFile
• current_col_types_ : MzQuantMLHandler
• current_considered_hits_ : ConsensusIDAlgorithmRanks
• current_count_ : MzQuantMLHandler
• current_dm_values_ : MzQuantMLHandler
• current_dp_ : MzQuantMLHandler
• current_feature_ : FeatureXMLFile
• current_files_ : MzQuantMLHandler
• current_id_ : MzMLHandler , MzMLValidator , MzQuantMLHandler , XTandemXMLFile
• current_id_hit_ : MzIdentMLHandler
• current_layer_ : SpectrumCanvas
• current_logger_ : ProgressLogger
• current_mod_location_ : MzIdentMLHandler
• current_modifications_ : PepXMLFile
• current_number_of_runs_ : ConsensusIDAlgorithmRanks
• current_orderedps_ : MzQuantMLHandler
• current_pas_ : MzQuantMLHandler
• current_path_ : INIFileEditorWindow , SwathWizardBase , TOPPASBase , TOPPViewBase
• current_peak_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
• current_peptide_ : PepXMLFile
• current_protein_ : XTandemXMLFile
• current_proteins_ : PepXMLFile
• current_row_ : MzQuantMLHandler
• current_scan_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
• current_sequence_ : PepXMLFile
• current_spectrum_ : LayerData
• current_spectrum_id_ : MzIdentMLHandler
• current_spectrum_search_ : XQuestResultXMLHandler
• current_start_ : XTandemXMLFile
• current_state : Spawn< TNeedle >
• current_step_ref_ : IdentificationData
• current_stop_ : XTandemXMLFile
• current_sws_ : MzQuantMLHandler
• currentChanged_() : EnhancedTabBar , TOPPASTabBar
• currentIdChanged() : EnhancedTabBar , TOPPASTabBar
• currentLayerParametersChanged_() : Spectrum2DCanvas
• currentLayerParamtersChanged_() : Spectrum1DCanvas , Spectrum3DCanvas
• currently_valid_ : PythonSelector
• curve() : ROCCurve
• custom : MzTabMetaData , MzTabSampleMetaData
• customContextMenuRequested_() : FilterList
• customizations_ : Instrument , InstrumentVisualizer
• cut() : ClusterAnalyzer
• cut_off : DBSuitability::SuitabilityData
• cut_off_ : BaseModel< D >
• cutForTime() : FIAMSDataProcessor
• cutoffNeg() : ROCCurve
• cutoffPos() : ROCCurve
• cutoffScore_ : MapAlignmentAlgorithmSpectrumAlignment
• cuts_after_regex_ : DigestionEnzymeRNA , RNaseDigestion
• cuts_before_regex_ : DigestionEnzymeRNA , RNaseDigestion
• cv : MzTabMetaData
• CV : TargetedExperiment , CV
• cv_ : MzIdentMLDOMHandler , MzIdentMLHandler , MzMLHandler , MzQuantMLHandler , SemanticValidator , TraMLHandler
• cv_identifier_ref_ : CVMappingTerm , CVTerm
• CV_label_ : MzTabParameter
• cv_params_ : MSQuantifications::AnalysisSummary
• cv_ref : CVTerm::Unit
• cv_references_ : CVMappingFile , CVMappings
• cv_references_vector_ : CVMappings
• cv_tag_ : SemanticValidator
• cv_term : ScoreType
• cv_terms_ : CVMappingRule , CVTermList , XMLHandler
• cvAcc : QcMLFile::Attachment , QcMLFile::QualityParameter
• CVMappingFile() : CVMappingFile
• CVMappingRule() : CVMappingRule
• CVMappings() : CVMappings
• CVMappingTerm() : CVMappingTerm
• cvp_stack_ : MzQuantMLHandler
• cvParam_() : MzDataHandler
• cvRef : QcMLFile::Attachment , QcMLFile::QualityParameter
• CVReference() : CVReference
• cvs : MzIdentMLDOMHandler::DBSequence
• cvs_ : TargetedExperiment
• cvStringToEnum_() : XMLHandler
• cvt_ptr_ : CVTermListInterface
• CVTerm() : ControlledVocabulary::CVTerm , CVTerm
• CVTermList() : CVTermList
• CVTermListInterface() : CVTermListInterface
• cwd_ : InputFile , InputFileList , TOPPASInputFileListVertex
• CYCLOTRON : MassAnalyzer