- s -

• s_bion : CompNovoIonScoringBase::IonScore
• s_byteorder_ : MzXMLHandler
• s_centroided_ : MzXMLHandler
• s_chargedeconvoluted_ : MzXMLHandler
• s_completiontime_ : MzXMLHandler
• s_compressionType_ : MzXMLHandler
• s_contentType_ : MzXMLHandler
• s_count_ : MzXMLHandler
• s_deisotoped_ : MzXMLHandler
• s_email_ : MzXMLHandler
• s_endmz_ : MzXMLHandler
• s_filename_ : MzXMLHandler
• s_filesha1_ : MzXMLHandler
• s_filetype_ : MzXMLHandler
• s_filterline_ : MzXMLHandler
• s_first_ : MzXMLHandler
• s_intensitycutoff_ : MzXMLHandler
• s_isotope_pattern_1 : CompNovoIonScoringBase::IonScore
• s_isotope_pattern_2 : CompNovoIonScoringBase::IonScore
• s_last_ : MzXMLHandler
• s_list : MSDataAggregatingConsumer
• s_mslevel_ : MzXMLHandler
• s_name_ : MzXMLHandler
• s_num_ : MzXMLHandler
• s_peakscount_ : MzXMLHandler
• s_phone_ : MzXMLHandler
• s_polarity_ : MzXMLHandler
• s_precision_ : MzXMLHandler
• s_precursorcharge_ : MzXMLHandler
• s_precursorintensity_ : MzXMLHandler
• s_retentiontime_ : MzXMLHandler
• s_scantype_ : MzXMLHandler
• s_startmz_ : MzXMLHandler
• s_tmp : MSDataAggregatingConsumer
• s_type_ : MzXMLHandler
• s_uri_ : MzXMLHandler
• s_value_ : MzXMLHandler
• s_version_ : MzXMLHandler
• s_windowwideness_ : MzXMLHandler
• s_witness : CompNovoIonScoringBase::IonScore
• s_yion : CompNovoIonScoringBase::IonScore
• sample : MzTabMetaData
• sample_ : ExperimentalSettings
• sample_processing : MzTabMetaData
• sample_ref : MzTabAssayMetaData
• sample_refs : MzTabStudyVariableMetaData
• samplecomment_ : SampleVisualizer
• sampleconcentration_ : SampleVisualizer
• samplemass_ : SampleVisualizer
• samplename_ : SampleVisualizer
• samplenumber_ : SampleVisualizer
• sampleorganism_ : SampleVisualizer
• samples_ : MzMLHandler
• samples_labels_ : MultiplexDeltaMassesGenerator
• samplestate_ : SampleVisualizer
• samplevolume_ : SampleVisualizer
• sampling_points_per_FWHM_ : RawMSSignalSimulation
• saveallbutton_ : MetaDataBrowser
• sc_charge_ : ProtonDistributionModel
• sc_charge_full_ : ProtonDistributionModel
• sc_charge_ion_c_term_ : ProtonDistributionModel
• sc_charge_ion_n_term_ : ProtonDistributionModel
• scale_ : ContinuousWaveletTransform , EuclideanSimilarity , LinearInterpolation< Key, Value > , PeakPickerCWT , ProductModel< 2 >
• scale_0_ : BilinearInterpolation< Key, Value >
• scale_1_ : BilinearInterpolation< Key, Value >
• scaling_ : InterpolationModel
• scaling_lower : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• scaling_upper : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• scan : MS1Signal , MS2Fragment
• SCAN : MSPeak
• scan : PSLPFormulation::IndexTriple
• scan_apex : SHFeature
• scan_count : MzMLHandler
• scan_count_ : MzXMLHandler
• scan_dir_ : MassAnalyzerVisualizer
• scan_direction_ : MassAnalyzer
• SCAN_END : MS2Info
• scan_end : SHFeature
• scan_index : CsiFingerIdMzTabWriter::CsiAdapterIdentification , SiriusMzTabWriter::SiriusAdapterIdentification
• scan_index_heavy : OPXLDataStructs::CrossLinkSpectrumMatch
• scan_index_light : OPXLDataStructs::CrossLinkSpectrumMatch
• scan_law_ : MassAnalyzer , MassAnalyzerVisualizer
• scan_map_ : PepXMLFile
• scan_mode_ : InstrumentSettings
• scan_number : SpectrumMetaDataLookup::SpectrumMetaData
• scan_rate_ : MassAnalyzer , MassAnalyzerVisualizer
• scan_regexp_ : SpectrumLookup
• SCAN_START : MS2Info
• scan_start : SHFeature
• scan_time_ : MassAnalyzer , MassAnalyzerVisualizer
• scan_windows_ : InstrumentSettings
• scanEnd : MS2Fragment
• scans : IsotopeCluster
• scans_ : SpectrumLookup
• scanStart : MS2Fragment
• scanTRIndex_ : SuperHirnParameters
• scene_ : TOPPASWidget
• schema_location_ : XMLFile
• schema_version_ : MzIdentMLDOMHandler , XMLFile
• scope_path_ : CVMappingRule
• score : CompNovoIonScoringBase::IonScore , CsiFingerIdMzTabWriter::CsiAdapterHit , DeNovoIonScoring::IonScore , FeatureFinderAlgorithmIsotopeWavelet::BoxElement , IDFilter::HasGoodScore< HitType > , IsotopeWaveletTransform< PeakType >::BoxElement
• SCORE : MSPeak
• score : OPXLDataStructs::CrossLinkSpectrumMatch , RNPxlReportRow , SiriusMzTabWriter::SiriusAdapterHit , RateScorePair , RNPxlSearch::AnnotatedHit , SIPPeptide
• score_ : ChargePair , CompNovoIdentificationBase::Permut , DeconvPeak , PeptideHit , ProteinHit
• score_clas_pairs_ : ROCCurve
• SCORE_HOLDER : SHFeature
• score_type : PeptideHit::PepXMLAnalysisResult
• score_type_ : InspectOutfile , PeptideIdentification , PeptideIdentificationVisualizer , ProteinIdentificationVisualizer
• score_type_names : PercolatorOutfile
• scoredistribution_ : MapAlignmentAlgorithmSpectrumAlignment
• scores_ : IsotopeWaveletTransform< PeakType >
• scoring_method_ : ConsensusIDAlgorithmPEPMatrix
• sd_map_ : MzIdentMLDOMHandler
• search_database_ref : MzIdentMLDOMHandler::SpectrumIdentification
• search_engine : MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• search_engine_ : MzIdentMLDOMHandler , PepXMLFile , ProteinIdentification
• search_engine_score : MzTabPSMSectionRow
• search_engine_score_ms_run : MzTabPeptideSectionRow , MzTabProteinSectionRow , MzTabSmallMoleculeSectionRow
• search_engine_version_ : MzIdentMLDOMHandler , ProteinIdentification
• search_id_ : PepXMLFile
• search_number_ : MascotRemoteQuery
• search_param_ : ConsensusXMLFile , FeatureXMLFile
• search_parameters_ : MascotXMLHandler , ProteinIdentification
• search_score_summary_ : PepXMLFile
• search_summary_ : PepXMLFile
• search_title_ : MascotInfile
• search_type_ : MascotInfile
• searched_mass_ : AccurateMassSearchResult
• searchtype : MzIdentMLDOMHandler::SpectrumIdentificationProtocol
• second : ProbablePhosphoSites
• second_nearest_gap_ : StablePairFinder
• secondary_id_ : SpectralMatch
• secondary_types : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• seed_ : UniqueIdGenerator
• seeds_ : FeatureFinderAlgorithmPicked
• seen_experiment_ : PepXMLFile
• selected_ : Annotation1DItem , MultiGradientSelector
• selected_activation_ : IsobaricChannelExtractor
• selected_color_ : MultiGradientSelector
• selected_ion_count_ : MzMLHandler
• selected_peak_ : Spectrum2DCanvas , SpectrumCanvas
• selected_pen_ : Annotations1DContainer
• semi_cleavage_ : XTandemInfile
• sep_ : MzTabStringList , SVOutStream , CSVWriter
• sep_indices_ : BigString
• separator_ : BigString
• seq_1 : ProbablePhosphoSites
• seq_2 : ProbablePhosphoSites
• sequence : FASTAFile::FASTAEntry , MzIdentMLDOMHandler::DBSequence , MzTabPeptideSectionRow , MzTabPSMSectionRow , ProteinResolver::PeptideEntry , Peptide , Protein , LightCompound , LightProtein , Peptide , Protein , RNPxlSearch::AnnotatedHit , SIPPeptide
• sequence_ : IMSElement , PeptideHit , ProteinHit
• sequence_header_filter_ : SequestInfile
• sequences : SVMData
• sequences_ : PrecursorIonSelectionPreprocessing
• seriesposition_regex_ : SpectrumAnnotator
• server_path_ : MascotRemoteQuery
• set : EGHFitter1D::Data , EmgFitter1D::Data
• set_Name_ID_map_ : QcMLFile
• set_to_zero_ : ParentPeakMower
• setQualityAts_ : QcMLFile
• setQualityQPs_ : QcMLFile
• setQualityQPs_members_ : QcMLFile
• setting : MzTabSoftwareMetaData
• settings_ : FullSwathFileConsumer , MSDataWritingConsumer
• sf : RawMSSignalSimulation::ContaminantInfo
• sfIsoDist10 : IsotopicDist
• sfIsoDist50 : IsotopicDist
• sfIsoDist90 : IsotopicDist
• sfIsoMass10 : IsotopicDist
• sfIsoMass50 : IsotopicDist
• sfIsoMass90 : IsotopicDist
• sfMassStep : IsotopicDist
• sfMaxIsotopeIndex : IsotopicDist
• sfMaxMass : IsotopicDist
• sfMaxMassIndex : IsotopicDist
• sfMinMass : IsotopicDist
• sfNrIsotopes : IsotopicDist
• sgolay_frame_length_ : PeakPickerMRM
• sgolay_polynomial_order_ : PeakPickerMRM
• shape : RawMSSignalSimulation::ContaminantInfo
• shift : FragmentAnnotationDetail_
• short_name : MultiplexDeltaMassesGenerator::Label
• short_name_ : Residue
• show_alignment_ : Spectrum1DCanvas
• show_fragment_ions_ : SequestInfile
• show_grid_ : SpectrumCanvas
• show_legend_ : AxisWidget
• show_splitters_ : HistogramWidget
• show_timing_ : SpectrumCanvas
• si_map_ : MzIdentMLDOMHandler
• si_pro_map_ : MzIdentMLDOMHandler
• sigma : GaussFitter::GaussFitResult
• sigma_ : EGHTraceFitter , GaussFilterAlgorithm , GaussTraceFitter , IsotopeWaveletTransform< PeakType > , PrecursorIonSelectionPreprocessing , SVMWrapper
• sigma_5_bound_ : EGHTraceFitter
• sigma_square_ : EGHFitter1D , EGHModel
• sigma_square_2_ : EGHModel
• sigmas_ : SVMWrapper
• signal : OptimizePeakDeconvolution::Data , OptimizePick::Data , TwoDOptimization::Data
• signal2D : TwoDOptimization::Data
• signal_ : ContinuousWaveletTransform
• signal_length_ : ContinuousWaveletTransform
• signal_to_noise : PeakShape
• signal_to_noise_ : PeakPickerCWT , PeakPickerHiRes , PeakPickerIterative , PeakPickerMaxima , PeakPickerMRM
• signal_weight : PSLPFormulation::IndexTriple
• SignalToNoise : MSPeak , SHFeature
• signalToNoise_ : CentroidPeak
• significance_threshold_ : PeptideIdentification
• sil_2_sdat_ : MzIdentMLHandler
• sil_2_sdb_ : MzIdentMLHandler
• sil_2_sip_ : MzIdentMLHandler
• similarities_ : ConsensusIDAlgorithmSimilarity
• simulators_ : SvmTheoreticalSpectrumGeneratorSet
• sine_table_ : IsotopeWavelet
• singleMass_ : Adduct
• singletonRegistryInstance_ : SingletonRegistry
• site : MzTabModificationMetaData
• sites_ : UnimodXMLHandler
• size : ConsensusMap::FileDescription
• SIZE : IMSIsotopeDistribution
• size : MzMLHandlerHelper::BinaryData
• size_ : ClusterProxyKD , SparseVector< Value > , StringView
• size_only_ : FeatureFileOptions , FeatureXMLFile , PeakFileOptions
• size_proportions_ : SaveImageDialog
• size_ratio_ : SaveImageDialog
• size_x_ : SaveImageDialog
• size_y_ : SaveImageDialog
• skip_chromatogram_ : MzMLHandler
• skip_data : MzMLHandler::SpectrumData , MzXMLHandler::SpectrumData
• skip_spectrum_ : MzDataHandler , MzMLHandler , MzXMLHandler
• skip_xml_checks_ : IndexedMzMLFile , MzMLSpectrumDecoder , PeakFileOptions
• slope_ : LinearRegression , TransformationModelLinear
• slope_bound_ : FeatureFinderAlgorithmPicked
• slope_max_ : TransformationModelBSpline
• slope_min_ : TransformationModelBSpline
• sm_ : XMLHandler
• small_molecule_data_ : MzTab
• small_molecule_quantification_unit : MzTabMetaData
• smallest_score_ : PosteriorErrorProbabilityModel
• smallmolecule_abundance_assay : MzTabSmallMoleculeSectionRow
• smallmolecule_abundance_std_error_study_variable : MzTabSmallMoleculeSectionRow
• smallmolecule_abundance_stdev_study_variable : MzTabSmallMoleculeSectionRow
• smallmolecule_abundance_study_variable : MzTabSmallMoleculeSectionRow
• smallmolecule_search_engine_score : MzTabMetaData
• smiles : CsiFingerIdMzTabWriter::CsiAdapterHit , MzTabSmallMoleculeSectionRow
• SMILES : TransitionTSVReader::TSVTransition
• smiles_string : Compound
• smiles_string_ : SpectralMatch
• smoothed_intensities_ : MassTrace
• sn_ : SignalToNoiseOpenMS< ContainerT >
• sn_bin_count_ : PeakPickerIterative , PeakPickerMRM
• sn_ratio : OpenSwath_Scores
• SN_statistics_ : SpectrumAnnotator
• sn_win_len_ : PeakPickerIterative , PeakPickerMRM
• sn_window_length_ : PeakPickerMaxima
• snap_factors_ : SpectrumCanvas
• snd_database_ : SequestInfile
• software : MzTabMetaData , MzTabSoftwareMetaData
• software_ : DataProcessing , Instrument , MzMLHandler , TargetedExperiment
• software_name_ : SoftwareVisualizer
• software_ref : Prediction , RetentionTime
• software_version_ : SoftwareVisualizer
• solver_ : LPWrapper , OfflinePrecursorIonSelection , PrecursorIonSelection , PSLPFormulation , PSProteinInference
• sonar_ : OpenSwathOSWWriter , OpenSwathTSVWriter
• sonar_diff : OpenSwath_Scores
• sonar_lag : OpenSwath_Scores
• sonar_rsq : OpenSwath_Scores
• sonar_shape : OpenSwath_Scores
• sonar_sn : OpenSwath_Scores
• sonar_trend : OpenSwath_Scores
• sonarscoring_ : MRMFeatureFinderScoring
• sort_chromatograms_by_rt_ : PeakFileOptions
• sort_spectra_by_mz_ : PeakFileOptions
• source : MzTabInstrumentMetaData
• SOURCE_DIR : FTPeakDetectController
• source_feature_index_ : AccurateMassSearchResult
• source_file_ : ChromatogramSettings , SpectrumSettings
• source_files_ : ExperimentalSettings , MzMLHandler , TargetedExperiment
• source_out_param_ : TOPPASEdge
• sp_map_ : MzIdentMLDOMHandler
• spacer_ : Spectrum1DWidget
• spacing_ : ContinuousWaveletTransform , GaussFilter , GaussFilterAlgorithm , LinearResampler
• spacing_difference_ : PeakPickerHiRes , PeakPickerIterative , PeakPickerMaxima
• spacing_difference_gap_ : PeakPickerHiRes , PeakPickerMaxima
• spacing_for_spectra_resampling_ : MRMFeatureFinderScoring , OpenSwathScoring
• sparse_element_ : SparseVector< Value >
• sparse_window_percent_ : SignalToNoiseEstimatorMedian< Container >
• spec_ : MzDataHandler , MzMLHandler
• spec_1d_ : IDEvaluationBase
• spec_id_ : MzMLSqliteHandler
• spec_name : LCMS
• spec_ref_ : MzTabSpectraRef
• spec_write_counter_ : MzXMLHandler
• species : MzTabProteinSectionRow , MzTabSampleMetaData , MzTabSmallMoleculeSectionRow
• specificities : MzIdentMLDOMHandler::ModificationParam
• specificity_ : EnzymaticDigestion
• specificity_type_ : Modification
• spectra_ : InspectInfile , MSDataSqlConsumer , MSExperiment , SpectrumAccessOpenMSInMemory
• spectra_all_peaks : OPXLDataStructs::PreprocessedPairSpectra
• spectra_before_chroms_ : IndexedMzMLFile
• spectra_combo_box_ : SpectraViewWidget
• spectra_common_peaks : OPXLDataStructs::PreprocessedPairSpectra
• spectra_data_ref : MzIdentMLDOMHandler::SpectrumIdentification , SpectrumMetaDataLookup
• spectra_expected_ : MSDataWritingConsumer
• spectra_identification_view_widget_ : TOPPViewBase
• spectra_index_ : CachedmzML , SpectrumAccessOpenMSCached
• spectra_meta_ : SpectrumAccessOpenMSInMemory
• spectra_offsets : MzMLHandler
• spectra_offsets_ : IndexedMzMLFile
• spectra_ref : MzTabPeptideSectionRow , MzTabPSMSectionRow , MzTabSmallMoleculeSectionRow
• spectra_search_box_ : SpectraViewWidget
• spectra_treewidget_ : SpectraViewWidget
• spectra_view_widget_ : TOPPViewBase
• spectra_written_ : MSDataCachedConsumer , MSDataWritingConsumer
• spectra_xlink_peaks : OPXLDataStructs::PreprocessedPairSpectra
• spectraview_behavior_ : TOPPViewBase
• spectrum : FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern , FeatureFinderAlgorithmPickedHelperStructs::Seed , MzMLHandler::SpectrumData , MzXMLHandler::SpectrumData , PeakIndex
• spectrum_data_ : MzMLHandler , MzXMLHandler
• spectrum_id : LCMS
• spectrum_ID : SHFeature
• spectrum_id : TOPPViewBase
• spectrum_identification_list_ref : MzIdentMLDOMHandler::SpectrumIdentification
• spectrum_identification_protocol_ref : MzIdentMLDOMHandler::SpectrumIdentification
• spectrum_identifications_ : Identification
• spectrum_ids_ : XTandemXMLFile
• spectrum_widget_ : SpectrumCanvas
• spline_ : BSpline2d , SplinePackage , TransformationModelBSpline
• sprocessing_ptr_ : MSDataTransformingConsumer
• sptr : SwathMap
• sptr_ : SpectrumAccessTransforming
• SQ : MS2Info
• sql_writer_ : MSDataSqlConsumer
• sr_map_ : MzIdentMLDOMHandler
• ss_ : SVOutStream
• ssize_ : DataValue
• st_ : Annotation1DCaret
• stack_ : Param::ParamIterator
• stand_dev_residuals_ : LinearRegression
• stand_error_slope_ : LinearRegression
• start : MzIdentMLDOMHandler::PeptideEvidence , MzTabPSMSectionRow
• start_ : PeptideEvidence
• start_point_ : Annotation1DDistanceItem
• start_secs_ : StopWatch
• start_system_time_ : StopWatch
• start_usecs_ : StopWatch
• start_user_time_ : StopWatch
• started_writing_ : MSDataWritingConsumer
• startScan : MS2ConsensusSpectrum
• startTR : MS2ConsensusSpectrum
• state_ : MzTabNullNaNAndInfAbleBase , Sample
• states : AnnotationStatistics
• states_ : HiddenMarkovModel
• static_intensities : SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
• statistics1_ : BiGaussFitter1D , BiGaussModel
• statistics2_ : BiGaussFitter1D , BiGaussModel
• statistics_ : EGHModel , EmgModel , Fitter1D , GaussModel , PeptideProteinResolution
• stats_ : IsobaricQuantifier , PeptideAndProteinQuant
• status_ : PepXMLFile , TOPPASToolVertex
• status_list_ : MetaDataBrowser
• stdev_ : SignalToNoiseEstimatorMeanIterative< Container >
• stickdata_ : Spectrum3DOpenGLCanvas
• stn_estimates_ : SignalToNoiseEstimator< Container >
• stop : MzIdentMLDOMHandler::PeptideEvidence
• stop_after_feature_ : MRMTransitionGroupPicker
• stop_after_intensity_ratio_ : MRMTransitionGroupPicker
• stop_report_after_feature_ : MRMFeatureFinderScoring
• store_ : DataMatrix
• store_compact_ : MascotGenericFile
• store_peptide_reliability_ : MzTabFile
• store_peptide_uri_ : MzTabFile
• store_protein_goterms_ : MzTabFile
• store_protein_reliability_ : MzTabFile
• store_protein_uri_ : MzTabFile
• store_psm_reliability_ : MzTabFile
• store_psm_uri_ : MzTabFile
• store_smallmolecule_reliability_ : MzTabFile
• store_smallmolecule_uri_ : MzTabFile
• storeAllLowProbabilityMS2Scans_ : SuperHirnParameters
• str_ : DataValue
• str_list_ : DataValue
• strarray_ : TransitionTSVReader
• stream : LogStreamBuf::StreamStruct
• stream_ : LogStreamNotifier
• stream_at_end_ : Bzip2Ifstream , GzipIfstream
• stream_list_ : LogStreamBuf
• stream_type_map_ : LogConfigHandler
• strict_ : MRMFeatureFinderScoring
• string_data_arrays_ : MSChromatogram , MSSpectrum
• stringlist : ParamXMLHandler
• strip_namespaces_ : CVMappingFile
• struct_size_in_datapoints_ : MorphologicalFilter
• study_variable : MzTabMetaData
• su_ : MRMFeatureFinderScoring , OpenSwathScoring
• sub_scores : PeptideHit::PepXMLAnalysisResult
• subordinate_feature_level_ : FeatureXMLFile
• subordinates_ : Feature
• subsamples_ : Sample
• subsections_ : DefaultParamHandler , TOPPBase
• subsections_TOPP_ : TOPPBase
• subspec_to_sequences_ : CompNovoIdentificationBase
• succ_states_ : HMMState
• sum_ : BasicStatistics< RealT >
• sum_formula : LightCompound
• sum_formula_ : SpectralMatch
• SumFormula : TransitionTSVReader::TSVTransition
• superimposer_ : MapAlignmentAlgorithmPoseClustering
• supported_schemes : TOPPASResource
• svm_feat_centers_ : FeatureFindingMetabo
• svm_feat_scales_ : FeatureFindingMetabo
• svm_params_ : SimpleSVM
• swath_assay_ : PepXMLFile
• swath_consumers_ : CachedSwathFileConsumer , MzMLSwathFileConsumer
• swath_map_boundaries_ : FullSwathFileConsumer
• swath_maps_ : FullSwathFileConsumer
• symbol_ : Element
• symbols_ : ElementDB
• symmetric_ : LevMarqFitter1D , TransformationModelLinear
• symmetry_ : EmgFitter1D , EmgModel
• synonym_trans_ : HiddenMarkovModel
• synonym_trans_names_ : HiddenMarkovModel
• synonyms : ControlledVocabulary::CVTerm
• synonyms_ : Enzyme , Residue , ResidueModification