- c -

• c : FeatureFinderAlgorithmIsotopeWavelet::BoxElement , IsotopeWaveletTransform< PeakType >::BoxElement
• c13MassError_ : DeconvPeak
• c1_ : BernNorm , MapAlignmentAlgorithmSpectrumAlignment
• c2_ : BernNorm
• c_ : CubicSpline2d , QuadraticRegression , SpectrumAccessQuadMZTransforming , TOFCalibration , mean_and_stddev
• c_intensity_ : TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• c_mzs_ : IsotopeWaveletTransform< PeakType >
• c_spacings_ : IsotopeWaveletTransform< PeakType >
• c_strings_ : StringManager
• c_term_gain_ : Enzyme
• c_term_mod_ : AASequence
• C_TERMINAL_AA : PeptideEvidence
• cachedir_ : CachedSwathFileConsumer , MzMLSwathFileConsumer
• cal_data_ : InternalCalibration
• calc_correct_ : PosteriorErrorProbabilityModel
• calc_incorrect_ : PosteriorErrorProbabilityModel
• calc_mass_to_charge : MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• calculated_mass_to_charge_ : IdentificationHit
• calib_masses_ : TOFCalibration
• calib_peaks_ft_ : TOFCalibration
• CancelButton_ : ListEditor
• cancelbutton_ : MetaDataBrowser
• canvas_ : LayerStatisticsDialog , SpectrumWidget
• canvas_3d_ : Spectrum3DOpenGLCanvas
• canvas_coverage_min_ : Spectrum2DCanvas
• capacity_ : ConstRefVector< ContainerT >
• CAPTION_3D_SUFFIX_ : TOPPViewBase
• caret_positions_ : Annotation1DCaret
• category : ToolDescriptionInternal , ToolExternalDetails
• CE : TransitionTSVReader::TSVTransition
• cell_dimension : HashGrid< Cluster >
• cell_it_ : HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator
• cell_type : MzTabSampleMetaData
• cells_ : ClusteringGrid , HashGrid< Cluster >
• center : IsobaricQuantitationMethod::IsobaricChannelInformation , ItraqConstants::ChannelInfo , SwathMap
• center_index_ : ClusterProxyKD
• center_point_ : QTCluster
• centre_ : GridBasedCluster
• centroid_mz_ : MassTrace
• centroid_position : PeakPickerCWT::PeakArea_
• centroid_rt_ : MassTrace
• centroid_sd_ : MassTrace
• centroidDataModus_ : CentroidData , SuperHirnParameters
• centroidWindowWidth_ : SuperHirnParameters
• cexp_ : MzDataHandler , MzMLHandler , MzXMLHandler , TraMLHandler
• cf_cf_obj_ : MzQuantMLHandler
• changed_ : QTCluster , TOPPASScene
• 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 , TMTTenPlexQuantitationMethod
• channels_ : ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• CHANNELS_EIGHTPLEX : ItraqConstants
• CHANNELS_FOURPLEX : ItraqConstants
• CHANNELS_TMT_SIXPLEX : ItraqConstants
• char_rest_ : MzXMLHandler::SpectrumData
• character_buffer_ : MascotXMLHandler
• charge : FragmentAnnotationDetail_ , InternalCalibration::LockMass , IsotopeCluster::ChargedIndexSet , MS1Signal , MzTabPeptideSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow , OptimizePeakDeconvolution::Data , PeptideHit::PeakAnnotation , RNPxlReportRow , 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 , Compound , Peptide , TraMLProduct
• charge_lower_bound_ : FeatureFindingMetabo
• charge_set_ : Compound , Peptide , TraMLProduct
• charge_state : SHFeature
• charge_upper_bound_ : FeatureFindingMetabo
• charges : ProteinIdentification::SearchParameters
• charges_ : HasPrecursorCharge< SpectrumType > , XQuestResultXMLHandler , MascotInfile , ProteinIdentificationVisualizer
• check_defaults_ : DefaultParamHandler
• check_PPMs_ : FeatureFinderAlgorithmIsotopeWavelet
• check_term_value_types_ : SemanticValidator
• check_units_ : SemanticValidator
• check_width_internally_ : PeakPickerIterative
• checked_base_name_ : PepXMLFile
• checksum_ : SourceFile , SourceFileVisualizer
• checksum_type_ : SourceFile , SourceFileVisualizer
• chemical_formula : MzTabSmallMoleculeSectionRow
• chi_squared_ : LinearRegression , QuadraticRegression
• children : ControlledVocabulary::CVTerm
• childScan : MSPeak
• CHRG : MS2Info , MSPeak
• CHRG_MAP : LCElutionPeak
• chrom_fwhm_ : ElutionPeakDetection , FeatureFindingMetabo
• chrom_id_ : MzMLSqliteHandler
• chrom_index_ : CachedmzML , SpectrumAccessOpenMSCached
• chrom_peak_snr_ : ElutionPeakDetection , MassTraceDetection
• chromatogram : MzMLHandler::ChromatogramData
• chromatogram_ : MzMLHandler , SignalToNoiseOpenMS< ContainerT >
• chromatogram_count : MzMLHandler
• chromatogram_data_ : MzMLHandler
• chromatogram_ids_ : SpectrumAccessOpenMSInMemory
• chromatogram_map_ : MRMTransitionGroup< ChromatogramType, TransitionType >
• ChromatogramNames : ChromatogramSettings
• chromatograms : LayerData
• chromatograms_ : MRMTransitionGroup< ChromatogramType, TransitionType > , MSDataSqlConsumer , MSExperiment , SpectrumAccessOpenMSInMemory
• chromatograms_expected_ : MSDataWritingConsumer
• chromatograms_offsets : MzMLHandler
• chromatograms_offsets_ : IndexedMzMLFile
• chromatograms_written_ : MSDataCachedConsumer , MSDataWritingConsumer
• cid_ : MzIdentMLHandler
• class_models : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• classification_ : ResidueModification
• clean_all_charge_states_ : ParentPeakMower
• clearbutton_ : MetaInfoVisualizer
• clearData_ : MSDataCachedConsumer , MSDataSqlConsumer
• cleavage_ : MascotInfile
• cleavage_regex_ : Enzyme
• cleavage_site_ : XTandemInfile
• clipboard_ : TOPPASScene
• clipboard_scene_ : TOPPASBase
• closebutton_ : MetaDataBrowser
• closed_boxes_ : IsotopeWaveletTransform< PeakType >
• cluster_index_ : MinimumDistance
• clusters_ : GridBasedClustering< Metric >
• clusters_final_ : GridBasedClustering< Metric >
• cm_cf_ids_ : MzQuantMLHandler
• cmp1_ : LexicographicComparator< Cmp1, Cmp2 >
• cmp2_ : LexicographicComparator< Cmp1, Cmp2 >
• cmp_ : Compomer , PointerComparator< Cmp > , ReverseComparator< Cmp >
• cmsq_ : MzQuantMLHandler
• code_ : LocalLinearMap
• coeff_ : MZTrafoModel
• coeff_quad_fit_ : TOFCalibration
• coeffs_ : GaussFilterAlgorithm , SavitzkyGolayFilter
• collect_annotations_ : QTCluster
• colnames_ : DataMatrix
• color_ : Annotation1DCaret , Annotation1DPeakItem , ColorSelector , TOPPASEdge
• cols_ : Matrix< Value >
• colTypes : QcMLFile::Attachment
• column_ : HPLC
• colunit_peptide : MzTabMetaData
• colunit_protein : MzTabMetaData
• colunit_psm : MzTabMetaData
• colunit_small_molecule : MzTabMetaData
• combinations_logic_ : CVMappingRule
• comet_id_ : Enzyme
• command : TOPPASScene::TOPPProcess
• commandline : ToolExternalDetails
• comment_ : ChromatogramSettings , ExperimentalSettings , ExperimentalSettingsVisualizer , HPLC , MetaInfoDescription , Sample , SampleTreatment , SpectrumSettings , SpectrumSettingsVisualizer
• comment_rows_ : MzTab
• common_name_ : SpectralMatch
• completion_time_ : DataProcessing , DataProcessingVisualizer
• compomer_ : ChargePair
• composition_ : PTMXMLHandler
• compound_name : LightCompound
• compound_ref_ : IncludeExcludeTarget , ReactionMonitoringTransition
• compound_reference_map_ : TargetedExperiment , LightTargetedExperiment
• compound_reference_map_dirty_ : TargetedExperiment , LightTargetedExperiment
• CompoundName : TransitionTSVReader::TSVTransition
• compounds : LightTargetedExperiment
• compounds_ : TargetedExperiment
• compression : MzMLHandlerHelper::BinaryData
• compressionType_ : MzXMLHandler::SpectrumData
• compute_peak_quality_ : MRMTransitionGroupPicker
• concentration_ : Sample
• conditional_prob : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• configuration_list_ : TraMLProduct
• configurations_ : IncludeExcludeTarget
• connection_line_color_ : Annotation1DCaret
• consensus : LayerData
• consensus_ : BaseLabeler
• consensus_map : ProteinResolver::ResolverResult
• consensus_map_ : ConsensusXMLFile , MSSim
• consensus_maps_ : MSQuantifications
• consider_H2O_loss_ : ParentPeakMower
• consider_NH3_loss_ : ParentPeakMower
• considered_hits_ : ConsensusIDAlgorithm
• console_width_ : ConsoleUtils
• const_enzymes_ : EnzymesDB
• const_modified_residues_ : ResidueDB
• const_residues_ : ResidueDB
• const_weights_ : SequestOutfile
• consumer_ : MzMLHandler , MzXMLHandler
• consumers_ : MSDataChainingConsumer
• consuming_possible_ : FullSwathFileConsumer
• contact : MzTabMetaData
• contact_info_ : ContactPerson , ContactPersonVisualizer
• contact_ref : Configuration , Prediction
• contacts_ : ExperimentalSettings , TargetedExperiment
• contaminants_ : RawMSSignalSimulation
• contaminants_loaded_ : RawMSSignalSimulation
• contaminants_map_ : MSSim
• context_add_ : SpectrumCanvas
• convex_hull_ : Feature
• convex_hulls_ : Feature
• convex_hulls_modified_ : Feature
• cookie_ : MascotRemoteQuery
• coordinate_ : DPosition< D, TCoordinateType >
• cord_ : LocalLinearMap
• corner_ : Spectrum3DOpenGLCanvas
• corr_max : Summary
• corr_mean : Summary
• corr_min : Summary
• correct_window_counter_ : FullSwathFileConsumer
• correctly_assigned_fit_param_ : PosteriorErrorProbabilityModel
• correlation : SIPIncorporation
• correlation_map : SIPPeptide
• correlation_maxima : SIPPeptide
• count : LayerStatisticsDialog::MetaStatsValue_ , SummaryStatistics< T >
• count_ : BigString
• count_empty_ : ConsensusIDAlgorithm
• count_trans_ : HiddenMarkovModel
• count_trans_all_ : HiddenMarkovModel
• counter : LogStreamBuf::LogCacheStruct
• counter_ : PrecursorIonSelectionPreprocessing
• coverage : ProteinResolver::ProteinEntry
• coverage_ : ProteinHit
• COVERAGE_UNKNOWN : ProteinHit
• cpep_id_ : MzIdentMLDOMHandler , MzIdentMLHandler
• cpro_id_ : MzIdentMLDOMHandler , MzIdentMLHandler
• cprocessing_ptr_ : MSDataTransformingConsumer
• cpu_speed_ : StopWatch
• create_rows_for_commmon_metavalue_ : SpectraIdentificationViewWidget
• createFeatureElutionProfiles_ : SuperHirnParameters
• creation_date_ : Identification
• cross_link : OPXLDataStructs::CrossLinkSpectrumMatch
• cross_link_position : OPXLDataStructs::ProteinProteinCrossLink
• cross_linker_mass : OPXLDataStructs::ProteinProteinCrossLink
• cross_linker_name : OPXLDataStructs::ProteinProteinCrossLink
• csms_ : XQuestResultXMLHandler
• ct_regex_ : SpectrumAnnotator
• curr_region_ : TwoDOptimization
• current_ : Param::ParamIterator
• current_analysis_result_ : 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_ : IDEvaluationBase , 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_stop_ : XTandemXMLFile
• current_sws_ : MzQuantMLHandler
• current_system_time_ : StopWatch
• current_usecs_ : StopWatch
• current_user_time_ : StopWatch
• custom : MzTabMetaData , MzTabSampleMetaData
• customizations_ : Instrument , InstrumentVisualizer
• cut_off_ : BaseModel< D >
• cutoffScore_ : MapAlignmentAlgorithmSpectrumAlignment
• cv : MzTabMetaData
• 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_terms_ : CVMappingRule , CVTermList , XMLHandler
• cvAcc : QcMLFile::Attachment , QcMLFile::QualityParameter
• cvp_stack_ : MzQuantMLHandler
• cvRef : QcMLFile::Attachment , QcMLFile::QualityParameter
• cvs : MzIdentMLDOMHandler::DBSequence
• cvs_ : TargetedExperiment
• cvt_ptr_ : CVTermListInterface
• cwd_ : TOPPASInputFileListVertex , TOPPASInputFilesDialog