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

- c -

C : ImmoniumIonsInPeptide
c : EmgFitter1D::EgmFitterFunctor
c_ : CubicSpline2d, QuadraticRegression, SpectrumAccessQuadMZTransforming, mean_and_stddev
c_intensity_ : NucleicAcidSpectrumGenerator, TheoreticalSpectrumGenerator, TheoreticalSpectrumGeneratorXLMS
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
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_im_ : MassTrace
centroid_mz_ : MassTrace
centroid_rt_ : MassTrace
centroid_sd_ : MassTrace
centroided_ : FeatureFinderMultiplexAlgorithm
cexp_ : MzDataHandler, MzMLHandler, MzXMLHandler, TraMLHandler
changed_ : QTCluster, TOPPASScene
channel_ : MSstatsFile::MSstatsTMTLine_
channel_count : IsobaricQuantifierStatistics
CHANNEL_COUNT : ItraqConstants
channel_level_abundances : PeptideAndProteinQuant::ProteinData
channel_mz_delta : IsobaricChannelExtractor
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, Biosaur2Algorithm::PatternCandidate, Biosaur2Algorithm::PeptideFeature, ConsensusIDAlgorithm::HitInfo, ObservationMatch, InternalCalibration::LockMass, IsotopeCluster::ChargedIndexSet, MzTabMSmallMoleculeEvidenceSectionRow, MzTabMSmallMoleculeFeatureSectionRow, MzTabOSMSectionRow, MzTabPeptideSectionRow, MzTabPSMSectionRow, MzTabSmallMoleculeSectionRow, NuXLFragmentAnnotationHelper::FragmentAnnotationDetail_, NuXLReportRow, PeptideHit::PeakAnnotation, SimpleTSGXLMS::SimplePeak, SiriusMSFile::CompoundInfo, Summary, LightCompound, Peptide
charge_ : AccurateMassSearchResult, Adduct, AdductInfo, BaseFeature, EmpiricalFormula, ExtendedIsotopeFitter1D, ExtendedIsotopeModel, FeatureHandle, FeatureHypothesis, IdentificationHit, IsotopeFitter1D, IsotopeModel, MultiplexIsotopicPeakPattern, OSWPeptidePrecursor, PeptideHit, PepXMLFile, Precursor, PrecursorVisualizer, PeptideCompound, TraMLProduct
charge_count : FLASHHelperClasses::MassFeature
charge_count_for_DL_scoring_ : PeakGroupScoring
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, ProteinIdentificationVisualizer
check_boxes_ : TheoreticalSpectrumGenerationDialog
check_defaults_ : DefaultParamHandler
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
children_bitset : ACNode
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 >
chromatogram_ranges_ : MSExperiment
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
classification_ : ResidueModification
clearbutton_ : MetaInfoVisualizer
clearData_ : MSDataCachedConsumer
cleavage_regex_ : DigestionEnzyme
cleavage_site_ : XTandemInfile
clipboard_ : TOPPASScene
clipboard_scene_ : TOPPASBase
closebutton_ : MetaDataBrowser
cluster_index_ : MinimumDistance
clusters_ : GridBasedClustering< Metric >
clusters_final_ : GridBasedClustering< Metric >
cm_ : LayerStatisticsConsensusMap, LayerStoreDataConsensusMapVisible
cmap_ : FeatureXMLHandler
cmax_ : Biosaur2Algorithm
cmin_ : Biosaur2Algorithm
cmp : SiriusMSFile::CompoundInfo
cmp_ : Compomer
cmp_bs_ : TargetedSpectraExtractor::BinnedSpectrumComparator
cnt_decal : InternalCalibration::CalibrantStats_
cnt_empty : InternalCalibration::CalibrantStats_
cnt_nomz : InternalCalibration::CalibrantStats_
cnt_nort : InternalCalibration::CalibrantStats_
cnt_total : InternalCalibration::CalibrantStats_
code_ : Ribonucleotide
code_map_ : RibonucleotideDB
coeff_ : MZTrafoModel
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
combined_ranges_ : MSExperiment
combos_ : GridSearch< TupleTypes >
combos_ready_ : GridSearch< TupleTypes >
comet_id_ : DigestionEnzymeProtein
command : TOPPASScene::TOPPProcess
commandline : ToolExternalDetails
comment_ : ChromatogramSettings, ExperimentalSettings, ExperimentalSettingsVisualizer, HPLC, Sample, 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_
config_ : SqMassFile
configuration_list_ : TraMLProduct
configurations_ : IncludeExcludeTarget
conn_ : OSWFile
connection_line_color_ : Annotation1DCaret< DataPoint >
consecutive_missed : MassTraceDetection::TraceExtensionState
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_ : FeatureFinderMultiplexAlgorithm, ConsensusXMLHandler, LayerDataConsensus, MzTab::CMMzTabStream
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
content_ : ExperimentalDesign::SampleSection
context_add_ : PlotCanvas
convex_hull_ : Feature
convex_hull_mode_ : Biosaur2Algorithm
convex_hulls_ : Feature
convex_hulls_modified_ : Feature
cookie_ : MascotRemoteQuery
coordinate_ : DPosition< D, TCoordinateType >
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
cos_cor_isotopes : Biosaur2Algorithm::PatternCandidate
cos_corr : Biosaur2Algorithm::IsotopeCandidate
count : IdentificationSummary::UniqueID, SummaryStatistics< T >, OpenSearchModificationAnalysis::ModificationPattern, OpenSearchModificationAnalysis::ModificationSummary, ProteinModificationSummary::Statistics
count_ : RangeStats< VALUE_TYPE >
count_centroided : MzMLFile::SpecInfo
count_empty_ : ConsensusIDAlgorithm
count_profile : MzMLFile::SpecInfo
count_unknown : MzMLFile::SpecInfo
counter : LogStreamBuf::LogCacheStruct, StatsCounter
coverage : ParentSequence, MzTabNucleicAcidSectionRow, MzTabProteinSectionRow
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_iso_shift_ : OpenPepXLAlgorithm
cross_link_mass_light_ : OpenPepXLAlgorithm
cross_link_mass_mono_link_ : OpenPepXLAlgorithm
cross_link_name_ : OpenPepXLAlgorithm
cross_link_position : OPXLDataStructs::ProteinProteinCrossLink
cross_link_residue1_ : OpenPepXLAlgorithm
cross_link_residue2_ : OpenPepXLAlgorithm
cross_linked_nucleotide : NuXLAnnotatedHit
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_v : IDBoostGraph::dfs_ccsplit_visitor
current_ : GUIProgressLoggerImpl, Param::ParamIterator
current_analysis_result_ : IdXMLFile, PepXMLFile
current_base_name_ : PepXMLFile
current_charge_ : XTandemXMLFile
current_chull_ : FeatureXMLHandler
current_column_pos_ : IndentedStream
current_considered_hits_ : ConsensusIDAlgorithmRanks
current_data_ : DIATreeTab
current_feature_ : FeatureXMLHandler
current_id_ : MzMLHandler, MzMLValidator, XTandemXMLFile
current_id_hit_ : MzIdentMLHandler
current_idx_ : LayerData1DBase
current_layer_ : LayerStack
current_logger_ : ProgressLogger
current_max_charge_ : SpectralDeconvolution
current_max_mass_ : SpectralDeconvolution
current_max_ms_level_ : FLASHDeconvAlgorithm
current_min_mass_ : SpectralDeconvolution
current_min_ms_level_ : FLASHDeconvAlgorithm
current_mod_location_ : MzIdentMLHandler
current_modifications_ : PepXMLFile
current_number_of_runs_ : ConsensusIDAlgorithmRanks
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_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
currently_locked_ : GUILock
currently_valid_ : PythonSelector
custom : MzTabMAssayMetaData, MzTabMetaData, MzTabMMetaData, MzTabSampleMetaData
customizations_ : Instrument, InstrumentVisualizer
cut_off : DBSuitability::SuitabilityData
cut_off_ : BaseModel
cuts_after_regex_ : DigestionEnzymeRNA
cuts_after_regexes_ : RNaseDigestion
cuts_before_regex_ : DigestionEnzymeRNA
cuts_before_regexes_ : RNaseDigestion
cv : MzTabMetaData, MzTabMMetaData
cv_ : MzIdentMLDOMHandler, MzIdentMLHandler, MzMLHandler, SemanticValidator, TraMLHandler
cv_identifier_ref_ : CVMappingTerm, CVTerm
CV_label_ : MzTabParameter
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
cvRef : QcMLFile::Attachment, QcMLFile::QualityParameter
cvs : MzIdentMLDOMHandler::DBSequence
cvs_ : TargetedExperiment
cvt_ptr_ : CVTermListInterface
cwd_ : InputFile, InputFileList, TOPPASInputFileListVertex