| OpenMS 2.5.0

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
- 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
- calculateDecompositionWeightsIsotopicPatterns() : MetaProSIPDecomposition
- calculateDIAIdScores() : OpenSwathScoring
- calculateDIAScores() : OpenSwathScoring
- calculateEmissionProbabilities() : HiddenMarkovModel
- calculateEstimatedQVal_() : FalseDiscoveryRate
- calculateFDR_() : FeatureFinderIdentificationAlgorithm
- calculateFDRBasic_() : FalseDiscoveryRate
- calculateFDRs_() : FalseDiscoveryRate
- calculateFitQuality_() : ElutionModelFitter
- calculateForwardPart_() : HiddenMarkovModel
- calculateGaussTable() : SVMWrapper
- calculateGB() : AAIndex
- calculateGridLines_() : Spectrum3DOpenGLCanvas
- calculateIntensityRankInMZWindow() : PScore
- calculateIonRatio() : MRMFeatureFilter
- calculateIsotopePatternsFor13CRange() : MetaProSIPDecomposition
- calculateIsotopePatternsFor13CRangeOfAveraginePeptide() : MetaProSIPDecomposition
- calculateIsotopePatternsFor15NRange() : MetaProSIPDecomposition
- calculateIsotopePatternsFor15NRangeOfAveraginePeptide() : MetaProSIPDecomposition
- calculateIsotopePatternsFor18ORange() : MetaProSIPDecomposition
- calculateIsotopePatternsFor18ORangeOfAveraginePeptide() : MetaProSIPDecomposition
- calculateIsotopePatternsFor2HRange() : MetaProSIPDecomposition
- calculateIsotopePatternsFor2HRangeOfAveraginePeptide() : MetaProSIPDecomposition
- calculateLibraryScores() : OpenSwathScoring
- calculateMap() : QCBase::SpectraMap
- calculateMonoWeight_() : ElementDB
- calculateMT_() : RTSimulation
- calculatePeakLevelSpectra() : PScore
- calculatePeakShapeMetrics() : PeakIntegrator
- calculatePeakShapeMetrics_() : PeakIntegrator
- calculatePermutationPeptideScores_() : AScore
- calculatePrecursorDIAScores() : OpenSwathScoring
- calculatePrecursorMass_() : NucleicAcidSearchEngine
- calculateProteinProbabilities() : PSProteinInference
- calculateProtonDistribution_() : ProtonDistributionModel
- calculateProtonDistributionCharge1_() : ProtonDistributionModel
- calculateProtonDistributionCharge2_() : ProtonDistributionModel
- calculateProtonDistributionGreater2_() : ProtonDistributionModel
- calculateProtonDistributionIonPair_() : ProtonDistributionModel
- calculateRankMap() : PScore
- calculateRatio() : AbsoluteQuantitation
- calculateResolution() : MRMFeatureFilter
- calculateRTDifference() : MRMFeatureFilter
- calculateSeeds_() : UTILProteomicsLFQ
- calculateTheoreticalIsotopesNumber() : EmpiricalFormula
- calculateXICs_() : OfflinePrecursorIonSelection , PSLPFormulation
- calcXcorrCoelutionScore() : MRMScoring
- calcXcorrCoelutionWeightedScore() : MRMScoring
- calcXcorrContrastCoelutionScore() : MRMScoring
- calcXcorrContrastShapeScore() : MRMScoring
- calcXcorrPrecursorCoelutionScore() : MRMScoring
- calcXcorrPrecursorCombinedCoelutionScore() : MRMScoring
- calcXcorrPrecursorCombinedShapeScore() : MRMScoring
- calcXcorrPrecursorContrastCoelutionScore() : MRMScoring
- calcXcorrPrecursorContrastShapeScore() : MRMScoring
- calcXcorrPrecursorShapeScore() : MRMScoring
- calcXcorrShapeScore() : MRMScoring
- calcXcorrShapeWeightedScore() : MRMScoring
- CalDataType : CalibrationData
- calib_masses_ : TOFCalibration
- calib_peaks_ft_ : TOFCalibration
- calibrate() : InternalCalibration , TOFCalibration
- CALIBRATION : DataProcessing
- CalibrationData() : CalibrationData
- callSiriusQProcess() : SiriusAdapterAlgorithm
- CancelButton_ : ListEditor
- cancelbutton_ : MetaDataBrowser
- candidateEdges_() : MetaboliteFeatureDeconvolution
- candidates_ : SiriusAdapterAlgorithm
- candidates_out_ : FeatureFinderIdentificationAlgorithm
- canModificationBeApplied_() : SILACLabeler
- CANNOT_WRITE_OUTPUT_FILE : TOPPBase
- canRun() : JavaInfo
- 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
- centerOfBin() : Histogram< ValueType, BinSizeType >
- centre_ : GridBasedCluster
- CENTROID : SpectrumSettings
- centroid_mz_ : MassTrace
- centroid_position : PeakPickerCWT::PeakArea_
- centroid_rt_ : MassTrace
- centroid_sd_ : MassTrace
- centroidAndCorrectPrecursors_() : UTILProteomicsLFQ
- 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
- 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 , SIPPeptide
- 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
- 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
- checkExtremePSMScores_() : Epifany
- checkFeatureQuality_() : FeatureFinderAlgorithmPicked
- checkFeatureSpectraNumber() : SiriusAdapterAlgorithm
- checkFormula_() : Adduct
- checkForRequiredUserParams_() : PrecursorIonSelection
- checkForSignificantPeak_() : MultiplexFiltering
- checkHits_() : IDMapper
- checkIds_() : BaseGroupFinder
- checkIfFeatureExtractionExists() : FTPeakDetectController
- checkIfIniParametersAreApplicable_() : TOPPBase
- checkIfWeAreDone() : TOPPASScene
- checkIsotopeBelongingAndAdjustMass() : MSPeak
- checkLOD() : AbsoluteQuantitationMethod
- checkLOQ() : AbsoluteQuantitationMethod
- checkMassRanges_() : OfflinePrecursorIonSelection
- checkMassType_() : IDMapper
- checkMaximalRTSpan() : EGHTraceFitter , GaussTraceFitter , TraceFitter
- checkMetaValue() : MRMFeatureFilter
- checkMinimalRTSpan() : EGHTraceFitter , GaussTraceFitter , TraceFitter
- checkName_() : ControlledVocabulary
- checkNumObservations_() : FeatureFinderIdentificationAlgorithm
- checkOldRunConsistency_() : ConsensusMapMergerAlgorithm , IDMergerAlgorithm
- checkParam_() : TOPPBase
- checkParameters_() : MapAlignmentAlgorithmIdentification
- checkParentMatches_() : IdentificationData
- checkPositionForPlausibility_() : IsotopeWaveletTransform< PeakType >
- checkPPMTheoModel_() : IsotopeWaveletTransform< PeakType >
- checkPreferences_() : TOPPViewBase
- checkRange() : MRMFeatureFilter
- checkRDependencies() : RIntegration
- checkRunSettings_() : ConsensusMapMergerAlgorithm
- checkSatellite() : MultiplexFilteredPeak
- checkScoreTypes_() : IdentificationData
- checkSequenceUniqueness_() : MzTab
- checkSize() : SaveImageDialog
- checkSolution_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
- 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_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_() : FeatureFinderIdentificationAlgorithm
- chunk_offset_ : FASTAContainer< TFI_File >
- chunkAt() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
- 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
- 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 >
- clusterSIPPeptides() : MetaProSIPClustering
- cm_cf_ids_ : MzQuantMLHandler
- CMD : ProgressLogger
- 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
- 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
- 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_qc_report_ : MRMFeatureFilter
- component_group_qcs : MRMFeatureQC
- component_name : AbsoluteQuantitationStandards::runConcentration , MRMFeaturePicker::ComponentParams , MRMFeatureQC::ComponentQCs
- component_name_ : AbsoluteQuantitationMethod
- component_qc_report_ : MRMFeatureFilter
- component_qcs : MRMFeatureQC
- composition_ : PTMXMLHandler
- Compound : TargetedExperiment , Compound , LightTargetedExperiment
- compound_adduct : MetaboTargetedAssay
- 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 , FeatureDeconvolution , FragmentMassError , HyperScore , ILPDCWrapper , MassExplainer , MetaboliteFeatureDeconvolution , MissedCleavages , MorpheusScore , Ms2IdentificationRate , Ms2SpectrumStats , MzCalibration , 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_retention_times : MSstatsFile::AggregatedConsensusInfo
- consensus_map : ProteinResolver::ResolverResult
- consensus_map_ : ConsensusXMLFile , FeatureFinderMultiplexAlgorithm , MSSim
- 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
- containsIMData() : TOPPViewBase
- containsInvalidReferences() : TargetedExperiment
- containsMS1Scans() : TOPPViewBase
- containsMSLevel() : PeakFileOptions
- 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
- convertPSMScores_() : Epifany
- convertSeedList() : SeedListGenerator
- convertSpectraToChromatograms() : ChromatogramTools
- convertTargetedCompound() : OpenSwathDataAccessHelper
- convertTargetedExp() : OpenSwathDataAccessHelper
- convertTargetedExperimentToPQP() : TransitionPQPFile
- convertTargetedExperimentToTSV() : TransitionTSVFile
- convertToChromatogramPtr() : OpenSwathDataAccessHelper
- convertToFeatureMap() : FIAMSDataProcessor
- convertToOpenMSChromatogram() : OpenSwathDataAccessHelper
- convertToOpenMSChromatogramFilter() : OpenSwathDataAccessHelper
- convertToOpenMSSpectrum() : OpenSwathDataAccessHelper
- convertToSpectrumPtr() : OpenSwathDataAccessHelper
- convertTransition_() : TransitionTSVFile
- convertTSVToTargetedExperiment() : TransitionTSVFile
- 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
- correlateXICsToMono() : MetaProSIPXICExtraction
- correlation : SIPIncorporation
- correlation_coefficient_ : AbsoluteQuantitationMethod
- correlation_map : SIPPeptide
- correlation_maxima : SIPPeptide
- 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 > , 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 >
- createBinnedPeptideRIAData_() : MetaProSIPReporting
- createChargeFactor() : MessagePasserFactory< Label >
- createCompound_() : TransitionTSVFile
- createCompoundReferenceMap_() : TargetedExperiment
- createConsensIsotopPattern() : LCElutionPeak
- createConsensusMapCache() : MasstraceCorrelator
- createContaminants_() : RawMSSignalSimulation
- createCSVReport() : MetaProSIPReporting
- createDirs() : TOPPASToolVertex
- createEditor() : ListEditorDelegate , ParamEditorDelegate
- createExperiment() : RTSimulation
- createFeatureElutionProfiles() : SuperHirnParameters
- createFeatureElutionProfiles_ : SuperHirnParameters
- createFeatureMap_() : MSSim
- createFlankingAAXMLString_() : IdXMLFile
- createHRData() : FeatureFinderAlgorithmIsotopeWavelet
- createIfNotExists_() : CVTermListInterface , MetaInfoInterface
- createIndices_() : MzMLSqliteHandler
- createINI_() : ToolsDialog
- createIntensityDistribution_() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
- createMemdumpIndex() : CachedMzMLHandler
- createMetaDistribution_() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
- createModel() : ModelDescription< D >
- createMRMFeature() : MRMTransitionGroupPicker
- createMZFeatureClusters() : MS1FeatureMerger
- createNewRow() : ListTable
- createOutputDir() : TOPPASOutputFileListVertex
- createPeptide_() : TransitionTSVFile
- createPeptideCentricCSVReport() : MetaProSIPReporting
- createPeptideEvidenceFactor() : MessagePasserFactory< Label >
- createPeptideProbabilisticAdderFactor() : MessagePasserFactory< Label >
- createPeptideReferenceMap_() : TargetedExperiment , LightTargetedExperiment
- createPositionXMLString_() : IdXMLFile
- createProtein_() : TransitionTSVFile
- createProteinFactor() : MessagePasserFactory< Label >
- createProteinReferenceMap_() : TargetedExperiment
- createProteinSequenceBasedLPInclusionList() : OfflinePrecursorIonSelection
- createProteinToPeptideLinks_() : MzTabFile
- createPseudoSpectra() : MasstraceCorrelator
- createQualityReport() : MetaProSIPReporting
- createRandomPartitions() : SVMWrapper
- createRegularizingSumEvidenceFactor() : MessagePasserFactory< Label >
- createReplicateFactor() : MessagePasserFactory< Label >
- createResidueModificationToResidueMap_() : ModifiedPeptideGenerator
- createResources() : TOPPASScene
- createSpec_() : MSExperiment
- createStream_() : StreamHandler
- createSumEvidenceFactor() : MessagePasserFactory< Label >
- createSumFactor() : MessagePasserFactory< Label >
- createTables() : MzMLSqliteHandler
- createTheoreticalSpectra_() : AScore
- createTOPPToolsTreeWidget() : TOPPASBase
- createTransition_() : TransitionTSVFile
- 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 , 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_secs_ : StopWatch
- 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
- current_system_time_ : StopWatch
- current_usecs_ : StopWatch
- current_user_time_ : StopWatch
- currentChanged_() : EnhancedTabBar , TOPPASTabBar
- currentIdChanged() : EnhancedTabBar , TOPPASTabBar
- currentLayerParametersChanged_() : Spectrum2DCanvas
- currentLayerParamtersChanged_() : Spectrum1DCanvas , Spectrum3DCanvas
- curve() : ROCCurve
- custom : MzTabMetaData , MzTabSampleMetaData
- customizations_ : Instrument , InstrumentVisualizer
- cut() : ClusterAnalyzer
- 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_ : TOPPASInputFileListVertex , TOPPASInputFilesDialog
- CYCLOTRON : MassAnalyzer