| OpenMS 2.5.0

### - c -

- c : FeatureFinderAlgorithmIsotopeWavelet::BoxElement , IsotopeWaveletTransform< PeakType >::BoxElement
- c13MassError_ : DeconvPeak
- c1_ : BernNorm , MapAlignmentAlgorithmSpectrumAlignment
- c2_ : BernNorm
- c_ : CubicSpline2d , QuadraticRegression , SpectrumAccessQuadMZTransforming , TOFCalibration , mean_and_stddev
- c_intensity_ : NucleicAcidSpectrumGenerator , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
- c_mzs_ : IsotopeWaveletTransform< PeakType >
- c_spacings_ : IsotopeWaveletTransform< PeakType >
- c_term_gain_ : DigestionEnzymeProtein
- c_term_mod_ : AASequence
- C_TERMINAL_AA : PeptideEvidence
- cache_count_ : FASTAContainer< TFI_Vector >
- cached_spectrum_ : LayerData
- cachedir_ : CachedSwathFileConsumer , MzMLSwathFileConsumer
- cal_data_ : InternalCalibration
- calc_mass_to_charge : MzTabOSMSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
- calculated_mass_to_charge_ : IdentificationHit
- calib_masses_ : TOFCalibration
- calib_peaks_ft_ : TOFCalibration
- CancelButton_ : ListEditor
- cancelbutton_ : MetaDataBrowser
- candidates_ : SiriusAdapterAlgorithm
- candidates_out_ : FeatureFinderIdentificationAlgorithm
- canvas_ : LayerStatisticsDialog , SpectrumWidget
- canvas_3d_ : Spectrum3DOpenGLCanvas
- canvas_coverage_min_ : Spectrum2DCanvas
- capacity_ : ConstRefVector< ContainerT >
- CAPTION_3D_SUFFIX_ : TOPPViewBase
- caret_positions_ : Annotation1DCaret
- category : ToolDescriptionInternal , ToolExternalDetails
- ccs_ : IDBoostGraph
- cd_ : SwathQC
- cd_spectra_ : SwathQC
- CE : TransitionTSVFile::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
- centroided_ : FeatureFinderMultiplexAlgorithm
- centroidWindowWidth_ : SuperHirnParameters
- cexp_ : MzDataHandler , MzMLHandler , MzXMLHandler , TraMLHandler
- cf_cf_obj_ : MzQuantMLHandler
- changed_ : QTCluster , TOPPASScene
- 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
- channels_ : ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
- CHANNELS_EIGHTPLEX : ItraqConstants
- CHANNELS_FOURPLEX : ItraqConstants
- CHANNELS_TMT_SIXPLEX : ItraqConstants
- char_rest_ : MzXMLHandler::SpectrumData
- character_buffer_ : MascotXMLHandler
- charge : NucleicAcidSearchEngine::PrecursorInfo , MoleculeQueryMatch , RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ , InternalCalibration::LockMass , IsotopeCluster::ChargedIndexSet , 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_lower_bound_ : FeatureFindingMetabo
- charge_max_ : FeatureFinderMultiplexAlgorithm
- charge_min_ : FeatureFinderMultiplexAlgorithm
- charge_set_ : PeptideCompound , TraMLProduct
- charge_state : SHFeature
- charge_upper_bound_ : FeatureFindingMetabo
- charges : DBSearchParam , 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
- checkConvertAndFilterPepHits_ : BayesianProteinInferenceAlgorithm
- checked_base_name_ : PepXMLFile
- checksum_ : SourceFile , SourceFileVisualizer
- checksum_type_ : SourceFile , SourceFileVisualizer
- chemical_formula : MzTabSmallMoleculeSectionRow
- chgLLhoods : MessagePasserFactory< Label >
- chi_squared_ : LinearRegression , QuadraticRegression
- children : ControlledVocabulary::CVTerm
- childScan : MSPeak
- 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 : 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_ : IndexedMzMLHandler , MzMLHandler
- chromatograms_written_ : MSDataCachedConsumer , MSDataWritingConsumer
- chunk_offset_ : FASTAContainer< TFI_File >
- cid_ : MzIdentMLHandler
- citations_ : TOPPBase
- cite_openms_ : TOPPBase
- class_models : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- classification_ : ResidueModification
- clean_all_charge_states_ : ParentPeakMower
- clearbutton_ : MetaInfoVisualizer
- clearData_ : MSDataCachedConsumer
- cleavage_ : MascotInfile
- cleavage_regex_ : DigestionEnzyme
- 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
- cmp : SiriusMSFile::CompoundInfo
- cmp1_ : LexicographicComparator< Cmp1, Cmp2 >
- cmp2_ : LexicographicComparator< Cmp1, Cmp2 >
- cmp_ : Compomer , PointerComparator< Cmp > , ReverseComparator< Cmp >
- cmp_bs_ : TargetedSpectraExtractor::BinnedSpectrumComparator
- cmsq_ : MzQuantMLHandler
- code_ : LocalLinearMap , Ribonucleotide
- code_map_ : RibonucleotideDB
- coeff_ : MZTrafoModel
- coeff_quad_fit_ : TOFCalibration
- coeffs_ : GaussFilterAlgorithm , SavitzkyGolayFilter
- collect_annotations_ : QTCluster
- collected_protein_hits_ : IDMergerAlgorithm
- colnames_ : DataMatrix
- color_ : Annotation1DCaret , Annotation1DPeakItem , ColorSelector , TOPPASEdge
- cols_ : Matrix< Value >
- colTypes : QcMLFile::Attachment
- column_ : HPLC
- column_description_ : ConsensusMap
- columnname_to_columnindex_ : ExperimentalDesign::SampleSection
- colunit_peptide : MzTabMetaData
- colunit_protein : MzTabMetaData
- colunit_psm : MzTabMetaData
- colunit_small_molecule : MzTabMetaData
- combinations_logic_ : CVMappingRule
- 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
- common_name_ : SpectralMatch
- completion_time_ : DataProcessing , DataProcessingVisualizer
- compomer_ : ChargePair
- 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_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
- compounds : LightTargetedExperiment
- compounds_ : TargetedExperiment
- compoundspectrumpair : MetaboTargetedAssay::CompoundSpectrumPair
- compression : MzMLHandlerHelper::BinaryData
- compressionType_ : MzXMLHandler::SpectrumData
- compute_additional_points_ : EmgGradientDescent
- compute_peak_quality_ : MRMTransitionGroupPicker
- compute_peak_shape_metrics_ : MRMTransitionGroupPicker
- compute_total_mi_ : MRMTransitionGroupPicker
- concentration_ : Sample
- concentration_units : AbsoluteQuantitationStandards::featureConcentration , AbsoluteQuantitationStandards::runConcentration
- concentration_units_ : AbsoluteQuantitationMethod
- condition_ : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_
- conditional_prob : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
- config_ : SqMassFile
- configuration_list_ : TraMLProduct
- configurations_ : IncludeExcludeTarget
- connection_line_color_ : Annotation1DCaret
- consensus : LayerData
- 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
- consider_H2O_loss_ : ParentPeakMower
- consider_NH3_loss_ : ParentPeakMower
- considered_hits_ : ConsensusIDAlgorithm
- console_width_ : ConsoleUtils
- const_enzymes_ : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
- 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
- content_ : ExperimentalDesign::SampleSection
- context_add_ : SpectrumCanvas
- convex_hull_ : Feature
- convex_hulls_ : Feature
- convex_hulls_modified_ : Feature
- cookie_ : MascotRemoteQuery
- coordinate_ : DPosition< D, TCoordinateType >
- cord_ : LocalLinearMap
- cores_ : SiriusAdapterAlgorithm
- corner_ : Spectrum3DOpenGLCanvas
- corr_max : Summary
- corr_mean : Summary
- corr_min : Summary
- correct_window_counter_ : FullSwathFileConsumer
- correctly_assigned_fit_param_ : PosteriorErrorProbabilityModel
- correlation : SIPIncorporation
- correlation_coefficient_ : AbsoluteQuantitationMethod
- correlation_map : SIPPeptide
- correlation_maxima : SIPPeptide
- count : LayerStatisticsDialog::MetaStatsValue_ , SummaryStatistics< T >
- count_empty_ : ConsensusIDAlgorithm
- count_trans_ : HiddenMarkovModel
- count_trans_all_ : HiddenMarkovModel
- counter : LogStreamBuf::LogCacheStruct
- counter_ : PrecursorIonSelectionPreprocessing
- 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_rows_for_commmon_metavalue_ : SpectraIdentificationViewWidget
- createFeatureElutionProfiles_ : SuperHirnParameters
- creation_date_ : Identification
- 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
- crux_id_ : DigestionEnzymeProtein
- csv_header : PrecursorCorrection
- ct_regex_ : SpectrumAnnotator
- 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
- custom : MzTabMetaData , MzTabSampleMetaData
- customizations_ : Instrument , InstrumentVisualizer
- cut_off_ : BaseModel< D >
- cutoffScore_ : MapAlignmentAlgorithmSpectrumAlignment
- cuts_after_regex_ : DigestionEnzymeRNA , RNaseDigestion
- cuts_before_regex_ : DigestionEnzymeRNA , RNaseDigestion
- 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_term : ScoreType
- 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