- c -

c : EmgFitter1D::EgmFitterFunctor , FeatureFinderAlgorithmIsotopeWavelet::BoxElement , IsotopeWaveletTransform< PeakType >::BoxElement
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_TERM_MODIFICATION_INDEX : ModifiedPeptideGenerator
C_TERMINAL_AA : PeptideEvidence
cache_count_ : FASTAContainer< TFI_Vector >
cached_terms_ : MzMLHandler
cachedir_ : CachedSwathFileConsumer , MzMLSwathFileConsumer
cal_data_ : InternalCalibration
calc_mass_to_charge : MzTabMSmallMoleculeEvidenceSectionRow , MzTabOSMSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
calculated_mass_to_charge_ : IdentificationHit
calib_masses_ : TOFCalibration
calib_peaks_ft_ : TOFCalibration
callbackStdErr_ : ExternalProcess
callbackStdOut_ : ExternalProcess
CancelButton_ : ListEditor
cancelbutton_ : MetaDataBrowser
candidates_out_ : FeatureFinderAlgorithmMetaboIdent , FeatureFinderIdentificationAlgorithm
canvas_ : PlotWidget
canvas_3d_ : Plot3DOpenGLCanvas
canvas_coverage_min_ : Plot2DCanvas
capacity_ : ConstRefVector< ContainerT >
CAPTION_3D_SUFFIX_ : TOPPViewBase
caret_positions_ : Annotation1DCaret< DataPoint >
category : ToolDescriptionInternal , ToolExternalDetails
category_ : ToolInfo
cconsensus_map_ : ConsensusXMLHandler
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::BulkData
centre_ : GridBasedCluster
centroid_mz_ : MassTrace
centroid_position : PeakPickerCWT::PeakArea_
centroid_rt_ : MassTrace
centroid_sd_ : MassTrace
centroided_ : FeatureFinderMultiplexAlgorithm
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_map_ : ITRAQLabeler
channel_names_ : TMTEighteenPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
channels_ : ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTEighteenPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
CHANNELS_EIGHTPLEX : ItraqConstants
CHANNELS_FOURPLEX : ItraqConstants
CHANNELS_TMT_SIXPLEX : ItraqConstants
char_rest_ : MzXMLHandler::SpectrumData
character_buffer_ : MascotXMLHandler
charge : NucleicAcidSearchEngine::PrecursorInfo , ConsensusIDAlgorithm::HitInfo , ObservationMatch , RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_ , InternalCalibration::LockMass , IsotopeCluster::ChargedIndexSet , MzTabMSmallMoleculeEvidenceSectionRow , MzTabMSmallMoleculeFeatureSectionRow , MzTabOSMSectionRow , MzTabPeptideSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow , OptimizePeakDeconvolution::Data , PeptideHit::PeakAnnotation , RNPxlReportRow , SimpleTSGXLMS::SimplePeak , SiriusMSFile::CompoundInfo , Summary , SvmTheoreticalSpectrumGenerator::IonType , LightCompound , Peptide
charge_ : AccurateMassSearchResult , Adduct , AdductInfo , BaseFeature , EmpiricalFormula , ExtendedIsotopeFitter1D , ExtendedIsotopeModel , FeatureHandle , FeatureHypothesis , IdentificationHit , IsotopeFitter1D , IsotopeModel , MultiplexIsotopicPeakPattern , OptimizePeakDeconvolution , OSWPeptidePrecursor , PeptideHit , PepXMLFile , Precursor , PrecursorVisualizer , PeptideCompound , TraMLProduct
charge_count : FLASHDeconvHelperStructs::MassFeature
charge_lower_bound_ : FeatureFindingMetabo
charge_max_ : FeatureFinderMultiplexAlgorithm
charge_min_ : FeatureFinderMultiplexAlgorithm
charge_score_ : PeakGroup
charge_set_ : PeptideCompound , TraMLProduct
charge_upper_bound_ : FeatureFindingMetabo
charges : DBSearchParam , ProteinIdentification::SearchParameters
charges_ : FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound , HasPrecursorCharge< SpectrumType > , XQuestResultXMLHandler , MascotInfile , ProteinIdentificationVisualizer
check_boxes_ : TheoreticalSpectrumGenerationDialog
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 : MzTabMSmallMoleculeEvidenceSectionRow , MzTabMSmallMoleculeSectionRow , MzTabSmallMoleculeSectionRow
chemical_name : MzTabMSmallMoleculeEvidenceSectionRow , MzTabMSmallMoleculeSectionRow
chgLLhoods : MessagePasserFactory< Label >
chi_squared_ : LinearRegression , QuadraticRegression
children : ControlledVocabulary::CVTerm
chrom_annotation_ : LayerDataChrom
chrom_count_total_ : MzMLHandler
chrom_data_ : FeatureFinderAlgorithmMetaboIdent , 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_ : LayerDataChrom , MRMTransitionGroup< ChromatogramType, TransitionType >
ChromatogramNames : ChromatogramSettings
chromatograms_ : MRMTransitionGroup< ChromatogramType, TransitionType > , MSDataSqlConsumer , MSExperiment , SpectrumAccessOpenMSInMemory
chromatograms_expected_ : MSDataWritingConsumer
chromatograms_native_ids_ : IndexedMzMLHandler , OnDiscMSExperiment
chromatograms_offsets_ : IndexedMzMLHandler , MzMLHandler
chromatograms_written_ : MSDataCachedConsumer , MSDataWritingConsumer
chunk_offset_ : FASTAContainer< TFI_File >
chunks_ : MSSpectrum::Chunks
cid_ : MzIdentMLHandler
citations_ : ToolInfo , 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_ : LayerStatisticsConsensusMap , LayerStoreDataConsensusMapVisible
cm_cf_ids_ : MzQuantMLHandler
cmap_ : FeatureXMLHandler
cmp : SiriusMSFile::CompoundInfo
cmp_ : Compomer
cmp_bs_ : TargetedSpectraExtractor::BinnedSpectrumComparator
cmsq_ : MzQuantMLHandler
cnt_decal : InternalCalibration::CalibrantStats_
cnt_empty : InternalCalibration::CalibrantStats_
cnt_nomz : InternalCalibration::CalibrantStats_
cnt_nort : InternalCalibration::CalibrantStats_
cnt_total : InternalCalibration::CalibrantStats_
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< DataPoint > , Annotation1DPeakItem< DataPoint > , Annotation1DVerticalLineItem , Colorizer , ColorSelector , TOPPASEdge
color_undo_all_ : Colorizer
colorizer_ : LogStreamBuf
colors_ : Colorizer
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 , MzTabMMetaData
colunit_small_molecule_evidence : MzTabMMetaData
colunit_small_molecule_feature : MzTabMMetaData
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 , MzTabM
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_qcs : MRMFeatureQC
component_name : AbsoluteQuantitationStandards::runConcentration , MRMFeaturePicker::ComponentParams , MRMFeatureQC::ComponentQCs
component_name_ : AbsoluteQuantitationMethod
component_qcs : MRMFeatureQC
composition_ : PTMXMLHandler
compound_adduct : MetaboTargetedAssay
compound_count : TargetedExperiment::SummaryStatistics
compound_file : MetaboTargetedAssay
compound_info : MetaboTargetedAssay::CompoundSpectrumPair , MetaboTargetedAssay::CompoundTargetDecoyPair
compound_name : MetaboTargetedAssay , LightCompound
compound_ref_ : IncludeExcludeTarget , ReactionMonitoringTransition
compound_reference_map_ : TargetedExperiment , LightTargetedExperiment
compound_reference_map_dirty_ : TargetedExperiment , LightTargetedExperiment
compound_rt : MetaboTargetedAssay
CompoundName : TransitionTSVFile::TSVTransition
compounds : LightTargetedExperiment
compounds_ : TargetedExperiment
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_ , TriqlerFile::TriqlerLine_
conditional_prob : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
config_ : SqMassFile
configuration_list_ : TraMLProduct
configurations_ : IncludeExcludeTarget
conn_ : OSWFile
connection_line_color_ : Annotation1DCaret< DataPoint >
consensus_ : BaseLabeler
consensus_feature_filenames : MSstatsFile::AggregatedConsensusInfo , TriqlerFile::AggregatedConsensusInfo
consensus_feature_intensities : MSstatsFile::AggregatedConsensusInfo , TriqlerFile::AggregatedConsensusInfo
consensus_feature_labels : MSstatsFile::AggregatedConsensusInfo , TriqlerFile::AggregatedConsensusInfo
consensus_feature_peptide_hit_user_value_keys_ : MzTab::CMMzTabStream
consensus_feature_peptide_identification_user_value_keys_ : MzTab::CMMzTabStream
consensus_feature_retention_times : MSstatsFile::AggregatedConsensusInfo , TriqlerFile::AggregatedConsensusInfo
consensus_feature_user_value_keys_ : MzTab::CMMzTabStream
consensus_map : ProteinResolver::ResolverResult
consensus_map_ : FeatureFinderMultiplexAlgorithm , ConsensusXMLHandler , LayerDataConsensus , MSSim , MzTab::CMMzTabStream
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 , MzTabMMetaData
contact_info_ : ContactPerson , ContactPersonVisualizer
contact_ref : Configuration , Prediction
contacts_ : ExperimentalSettings , TargetedExperiment
contains_invalid_references : TargetedExperiment::SummaryStatistics
contaminants_ : RawMSSignalSimulation
contaminants_loaded_ : RawMSSignalSimulation
contaminants_map_ : MSSim
content_ : ExperimentalDesign::SampleSection
context_add_ : PlotCanvas
convex_hull_ : Feature
convex_hulls_ : Feature
convex_hulls_modified_ : Feature
cookie_ : MascotRemoteQuery
coordinate_ : DPosition< D, TCoordinateType >
cord_ : LocalLinearMap
corner_ : Plot3DOpenGLCanvas
corr_factor : DBSuitability::SuitabilityData
corr_max : Summary
corr_mean : Summary
corr_min : Summary
correct_window_counter_ : FullSwathFileConsumer
correctly_assigned_fit_param_ : PosteriorErrorProbabilityModel
correlation_coefficient_ : AbsoluteQuantitationMethod
count : IdentificationSummary::UniqueID , SummaryStatistics< T >
count_ : RangeStats< VALUE_TYPE >
count_centroided : MzMLFile::SpecInfo
count_empty_ : ConsensusIDAlgorithm
count_profile : MzMLFile::SpecInfo
count_trans_ : HiddenMarkovModel
count_trans_all_ : HiddenMarkovModel
count_unknown : MzMLFile::SpecInfo
counter : LogStreamBuf::LogCacheStruct , StatsCounter
counter_ : PrecursorIonSelectionPreprocessing
coverage : ParentSequence , 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_ : SpectraIDViewTab
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
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_ : FeatureXMLHandler
current_col_types_ : MzQuantMLHandler
current_column_pos_ : IndentedStream
current_considered_hits_ : ConsensusIDAlgorithmRanks
current_count_ : MzQuantMLHandler
current_data_ : DIATreeTab
current_dm_values_ : MzQuantMLHandler
current_dp_ : MzQuantMLHandler
current_feature_ : FeatureXMLHandler
current_files_ : MzQuantMLHandler
current_id_ : MzMLHandler , MzMLValidator , MzQuantMLHandler , XTandemXMLFile
current_id_hit_ : MzIdentMLHandler
current_idx_ : LayerData1DBase
current_layer_ : LayerStack
current_logger_ : ProgressLogger
current_max_charge_ : FLASHDeconvAlgorithm
current_max_mass_ : FLASHDeconvAlgorithm
current_min_mass_ : FLASHDeconvAlgorithm
current_mod_location_ : MzIdentMLHandler
current_modifications_ : PepXMLFile
current_number_of_runs_ : ConsensusIDAlgorithmRanks
current_orderedps_ : MzQuantMLHandler
current_pas_ : MzQuantMLHandler
current_path_ : FLASHDeconvWizardBase , INIFileEditorWindow , SwathWizardBase , TOPPASBase , TOPPViewBase
current_peak_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::Param
current_peptide_ : PepXMLFile
current_protein_ : XTandemXMLFile
current_proteins_ : PepXMLFile
current_psm_idx_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
current_row_ : MzQuantMLHandler
current_scan_ : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::Param
current_sequence_ : PepXMLFile
current_spectrum_id_ : MzIdentMLHandler
current_spectrum_search_ : XQuestResultXMLHandler
current_start_ : XTandemXMLFile
current_step_ref_ : IdentificationData
current_stop_ : XTandemXMLFile
current_sws_ : MzQuantMLHandler
currently_locked_ : GUILock
currently_valid_ : PythonSelector
custom : MzTabMAssayMetaData , MzTabMetaData , MzTabMMetaData , MzTabSampleMetaData
customizations_ : Instrument , InstrumentVisualizer
cut_off : DBSuitability::SuitabilityData
cut_off_ : BaseModel< D >
cutoffScore_ : MapAlignmentAlgorithmSpectrumAlignment
cuts_after_regex_ : DigestionEnzymeRNA
cuts_after_regexes_ : RNaseDigestion
cuts_before_regex_ : DigestionEnzymeRNA
cuts_before_regexes_ : RNaseDigestion
cv : MzTabMetaData , MzTabMMetaData
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_ : InputFile , InputFileList , TOPPASInputFileListVertex