- d -

• d : RANSACParam
• d_ : CubicSpline2d
• d_intensity_ : NucleicAcidSpectrumGenerator
• data : BinaryDataArray , MzMLHandler::ChromatogramData , MzMLHandler::SpectrumData
• DATA : LCMSCData
• data : OSBinaryDataArray , XCorrArrayType
• data_ : CalibrationData , DataValue , FASTAContainer< TFI_Vector > , KDTreeFeatureNode , BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value > , ProcessData , SimpleSVM , TransformationDescription , TransformationXMLFile
• data_bg_ : FASTAContainer< TFI_File >
• data_fg_ : FASTAContainer< TFI_File >
• data_given_ : TransformationModelLinear
• data_graph : Pattern< TNeedle, FuzzyAC >
• data_host : Pattern< TNeedle, FuzzyAC >
• data_id : DataQuery
• data_keywordIndex : PatternAuxData< TNeedle >
• data_lastState : PatternAuxData< TNeedle >
• data_length_ : IsotopeWaveletTransform< PeakType >
• data_map_outputNodes : Pattern< TNeedle, FuzzyAC >
• data_needleLength : PatternAuxData< TNeedle >
• data_node_depth : Pattern< TNeedle, FuzzyAC >
• data_processing_ : ChromatogramSettings , ConsensusMap , FeatureMap , MzDataHandler , MzXMLHandler , MetaInfoDescription , SpectrumSettings
• data_processings_ : MSQuantifications
• data_queries_ : IdentificationData
• data_query_lookup_ : IdentificationData
• data_query_ref : MoleculeQueryMatch
• data_to_decode_ : MzDataHandler
• data_to_encode_ : MzDataHandler
• data_type : MzMLHandlerHelper::BinaryData
• database : DBSearchParam , MzTabNucleicAcidSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• database_ : SequestInfile , SiriusAdapterAlgorithm
• database_name_ : AccurateMassSearchEngine
• database_ref : MzIdentMLDOMHandler::DBSequence
• database_version : DBSearchParam , MzTabNucleicAcidSectionRow , MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• database_version_ : AccurateMassSearchEngine
• date : MzIdentMLDOMHandler::DatabaseInput
• date_ : MascotXMLHandler , PepXMLFile , ProteinIdentification
• date_time : DataProcessingStep
• date_time_string_ : MascotXMLHandler
• datetime_ : ExperimentalSettings , ExperimentalSettingsVisualizer
• db : ProteinIdentification::SearchParameters
• db_ : InspectInfile , MascotInfile , ProteinIdentificationVisualizer , SqliteConnector
• db_map_ : MzIdentMLDOMHandler
• db_mapping_file_ : AccurateMassSearchEngine
• db_mass_ : AccurateMassSearchResult
• db_pos_length_ : InspectOutfile
• db_search_params_ : IdentificationData
• db_search_steps_ : IdentificationData
• db_sq_map_ : MzIdentMLDOMHandler
• db_struct_file_ : AccurateMassSearchEngine
• db_version : ProteinIdentification::SearchParameters
• db_version_ : ProteinIdentificationVisualizer
• debug_ : FeatureFinderAlgorithmPicked , MapAlignmentAlgorithmSpectrumAlignment
• debug_im_file_ : SwathMapMassCorrection
• debug_level_ : FeatureFinderIdentificationAlgorithm , SiriusAdapterAlgorithm::SiriusTemporaryFileSystemObjects , TOPPBase
• debug_lvl_ : BayesianProteinInferenceAlgorithm
• DEBUG_MASS_END : LCElutionPeak
• DEBUG_MASS_START : LCElutionPeak
• debug_mz_file_ : SwathMapMassCorrection
• debug_streams_ : LogConfigHandler
• debugmatrix_ : MapAlignmentAlgorithmSpectrumAlignment
• debugscorematrix_ : MapAlignmentAlgorithmSpectrumAlignment
• debugtraceback_ : MapAlignmentAlgorithmSpectrumAlignment
• decoded_char : MzMLHandlerHelper::BinaryData
• decoded_double_list_ : MzDataHandler
• decoded_list_ : MzDataHandler
• decoder_ : Base64
• decomp_ : MassDecomposition
• decomp_cache_ : CompNovoIdentificationBase
• decomp_weights_precision_ : CompNovoIdentificationBase
• decomposer_ : RealMassDecomposer , MassDecompositionAlgorithm
• decon_ms1_mz_tol_ : SwathQC
• deconvolution_ : PeakPickerCWT
• decoy : TransitionTSVFile::TSVTransition , LightTransition
• decoy_index_ : ConfidenceScoring
• decoy_prefix_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
• decoy_string_ : XQuestResultXMLHandler , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , PeptideIndexing , XFDRAlgorithm
• decoy_type_ : ReactionMonitoringTransition
• DEF_COSINE_SIMILARITY : TOPPGNPSExport
• DEF_PRECURSOR_MZ_TOLERANCE : TOPPGNPSExport
• DEF_PRECURSOR_RT_TOLERANCE : TOPPGNPSExport
• default_array_length : MzMLHandler::ChromatogramData , MzMLHandler::SpectrumData
• default_array_length_ : MzMLHandler
• default_baseloss_ : Ribonucleotide
• DEFAULT_BIN_OFFSET_HIRES : BinnedSpectrum
• DEFAULT_BIN_OFFSET_LOWRES : BinnedSpectrum
• DEFAULT_BIN_WIDTH_HIRES : BinnedSpectrum
• DEFAULT_BIN_WIDTH_LOWRES : BinnedSpectrum
• default_charge_ : ParentPeakMower
• default_dir_ : ToolsDialog , TOPPASToolConfigDialog
• default_ms_level_ : DTAFile
• default_nterm_mods_ : XTandemXMLFile
• default_parameters_file_ : XTandemInfile
• default_processing_ : MzMLHandler
• default_scan_regexp : SpectrumLookup
• default_value : ParameterInformation
• defaultArrayLength : Chromatogram , Spectrum , OSChromatogram , OSSpectrum
• defaults_ : DefaultParamHandler
• deisotope_mode_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
• delay_ : AcqusHandler
• delay_in_seconds_ : FileWatcher
• delete_buffer_ : LogStream
• delim_ : MSstatsFile
• DELTA_CN : MS2Info
• delta_cn_weights_ : SequestOutfile
• delta_mass : MultiplexDeltaMasses::DeltaMass , MultiplexDeltaMassesGenerator::Label
• delta_mass_weights_ : SequestOutfile
• delta_masses_ : MultiplexDeltaMasses
• delta_masses_list_ : MultiplexDeltaMassesGenerator
• denominator_ref_ : ConsensusFeature::Ratio
• des : SiriusMSFile::CompoundInfo
• desc_ : TOPPASBase
• description : ControlledVocabulary::CVTerm , FASTAFile::FASTAEntry , ParentMolecule , IsobaricQuantitationMethod::IsobaricChannelInformation , ItraqConstants::ChannelInfo , MultiplexDeltaMassesGenerator::Label , MzTabMetaData , MzTabNucleicAcidSectionRow , MzTabProteinSectionRow , MzTabSampleMetaData , MzTabSmallMoleculeSectionRow , MzTabStudyVariableMetaData , Param::ParamEntry , Param::ParamIterator::TraceInfo , Param::ParamNode , ParameterInformation , PepXMLFile::AminoAcidModification , OSBinaryDataArray
• description_ : ConsensusFeature::Ratio
• description_text_ : TOPPASScene
• descriptions_ : ParamXMLHandler
• descriptors : SvmTheoreticalSpectrumGenerator::DescriptorSet
• detectableIsotopeFactor_ : SuperHirnParameters
• detecting_transition : TransitionTSVFile::TSVTransition , LightTransition
• detector : MzTabInstrumentMetaData
• dfs_color_ : TOPPASVertex
• dh_ : AhoCorasickAmbiguous
• dia_byseries_intensity_min_ : DIAScoring
• dia_byseries_ppm_diff_ : DIAScoring
• dia_centroided_ : DIAScoring , SONARScoring
• dia_extract_window_ : DiaPrescore , DIAScoring , SONARScoring
• dia_extraction_ppm_ : DIAScoring , SONARScoring
• dia_nr_charges_ : DIAScoring
• dia_nr_isotopes_ : DIAScoring
• diascoring_ : MRMFeatureFinderScoring
• diff_average_mass_ : ResidueModification
• diff_exponent_ : SimplePairFinder
• diff_formula_ : UnimodXMLHandler , ResidueModification
• diff_intercept_ : SimplePairFinder
• diff_mono_mass_ : ResidueModification
• diff_score : IDDecoyProbability::Transformation_
• digested_db_ : Contaminants
• digestion_ : IDFilter::DigestionFilter , IDFilter::PeptideDigestionFilter
• digestion_enzyme : DBSearchParam , ProteinIdentification::SearchParameters
• digestion_time_ : Digestion
• digestionenzyme_ : DigestionVisualizer
• digestionPH_ : DigestionVisualizer
• digestiontemperature_ : DigestionVisualizer
• digestiontime_ : DigestionVisualizer
• dilution_factor : AbsoluteQuantitationStandards::featureConcentration , AbsoluteQuantitationStandards::runConcentration
• dim_ : FeatureXMLFile
• dimension_name_full_ : Peak2D
• dimension_name_short_ : Peak2D
• dimension_unit_full_ : Peak2D
• dimension_unit_short_ : Peak2D
• dimensionsize_ : DistanceMatrix< Value >
• disable_parsing_ : FeatureXMLFile
• disease : MzTabSampleMetaData
• dist_ : HistogramWidget , OptimizePeakDeconvolution , UniqueIdGenerator
• distance : BinaryTreeNode
• distance_ : MinimumDistance
• distance_it_for_cluster_idx_ : GridBasedClustering< Metric >
• distances_ : GridBasedClustering< Metric >
• distribution_ : IsotopeDistribution
• distributions_ : ProductModel< 2 >
• dlg_ : GUIProgressLoggerImpl
• dm_elements_2d_ : TOPPViewBase
• dm_hull_2d_ : TOPPViewBase
• dm_hulls_2d_ : TOPPViewBase
• dm_ident_2d_ : TOPPViewBase
• dm_label_2d_ : TOPPViewBase
• dm_precursors_2d_ : TOPPViewBase
• dm_unassigned_2d_ : TOPPViewBase
• document_id_ : IdXMLFile
• doi : Citation
• dotprod_score_dia : OpenSwath_Scores
• doWrite_ : OpenSwathOSWWriter , OpenSwathTSVWriter
• dps_ : MSDataWritingConsumer
• drag_start_pos_ : TOPPASTreeView
• draw_group_1d_ : TOPPViewBase
• draw_interesting_MZs_ : Spectrum1DCanvas
• draw_modes_ : Spectrum1DCanvas
• drift_time : TransitionTSVFile::TSVTransition , LightCompound
• drift_time_ : MSSpectrum , Precursor , PeptideCompound
• drift_time_unit_ : MSSpectrum , Precursor
• drift_window_low_ : Precursor
• drift_window_up_ : Precursor
• dry_run_ : TOPPASScene
• dt_model_file_ : DetectabilitySimulation
• dw_ : AcqusHandler