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

- g -

• GAMMA : SVMWrapper
• gamma_table_ : IsotopeWavelet
• gamma_table_max_index_ : IsotopeWavelet
• gamma_table_new_ : IsotopeWavelet
• GammaDistributionFitResult() : GammaDistributionFitter::GammaDistributionFitResult
• GammaDistributionFitter() : GammaDistributionFitter
• gap_ : MapAlignmentAlgorithmSpectrumAlignment
• GAS : Sample
• gauss_ : PeakPickerMRM
• gauss_algo_ : GaussFilter
• gauss_table_ : SVMWrapper
• gauss_tables_ : SVMWrapper
• gauss_width_ : PeakPickerMRM
• GaussFilter() : GaussFilter
• GaussFilterAlgorithm() : GaussFilterAlgorithm
• GaussFitResult() : GaussFitter::GaussFitResult
• GaussFitter() : GaussFitter
• GaussFitter1D() : GaussFitter1D
• GaussianEstimate : SignalToNoiseEstimatorMeanIterative< Container > , SignalToNoiseEstimatorMedian< Container >
• GaussModel() : GaussModel
• GaussTraceFitter() : GaussTraceFitter
• GaussTraceFunctor() : GaussTraceFitter::GaussTraceFunctor
• gb_bb_l_ : Residue
• gb_bb_r_ : Residue
• gb_sc_ : Residue
• GBdeltaright_() : AAIndex
• GBleft_() : AAIndex
• GBsidechain_() : AAIndex
• GD_MS : IonSource
• GELML : FileTypes
• genCord_() : LocalLinearMap
• generateCandidates() : DeNovoAlgorithm
• generateDecoyAssays_() : MRMAssay
• generateDecoyInSilicoMap_() : MRMAssay
• generateDecoys() : MRMDecoy
• generateDecoySequences_() : MRMAssay
• generateDescriptorSet_() : SvmTheoreticalSpectrumGenerator
• generateDistributionImage_() : IDDecoyProbability
• generateKnockoutDeltaMasses() : MultiplexDeltaMassesGenerator
• generateMapsCentroided_() : FeatureFinderMultiplexAlgorithm
• generateMapsProfile_() : FeatureFinderMultiplexAlgorithm
• generateMSESpectra_() : RawTandemMSSignalSimulation
• generateMzTabMetaDataSection_() : MzTabFile
• generateMzTabPeptideHeader_() : MzTabFile
• generateMzTabPeptideSection_() : MzTabFile
• generateMzTabPeptideSectionRow_() : MzTabFile
• generateMzTabProteinHeader_() : MzTabFile
• generateMzTabProteinSection_() : MzTabFile
• generateMzTabProteinSectionRow_() : MzTabFile
• generateMzTabPSMHeader_() : MzTabFile
• generateMzTabPSMSection_() : MzTabFile
• generateMzTabPSMSectionRow_() : MzTabFile
• generateMzTabSmallMoleculeHeader_() : MzTabFile
• generateMzTabSmallMoleculeSection_() : MzTabFile
• generateMzTabSmallMoleculeSectionRow_() : MzTabFile
• generatePartialLossSpectrum() : RNPxlSearch::RNPxlFragmentIonGenerator
• generatePeakPatterns_() : FeatureFinderMultiplexAlgorithm
• generatePrecursorSpectra_() : RawTandemMSSignalSimulation
• generateRawSignals() : RawMSSignalSimulation
• generateRawTandemSignals() : RawTandemMSSignalSimulation
• generateScores() : TargetedSpectraExtractor::BinnedSpectrumComparator , TargetedSpectraExtractor::Comparator
• generateSeedList() : SeedListGenerator
• generateSeedLists() : SeedListGenerator
• generateSequenceDiagram_() : TOPPViewIdentificationViewBehavior
• generateSequenceRow_() : TOPPViewIdentificationViewBehavior
• generateTargetAssays_() : MRMAssay
• generateTargetInSilicoMap_() : MRMAssay
• generateTargetSequences() : RNPxlModificationsGenerator
• generateTransitions_() : FeatureFinderIdentificationAlgorithm
• generateTrieDB() : InspectOutfile
• generator : DIAScoring
• generator_ : ConfidenceScoring
• GenericFunctor() : LevMarqFitter1D::GenericFunctor , TraceFitter::GenericFunctor
• get() : _Alloc_base< _Tp, _Alloc >::NoLeakAlloc , CentroidData , Date , DateTime , MzTabBoolean , MzTabDouble , MzTabDoubleList , MzTabInteger , MzTabIntegerList , MzTabModificationList , MzTabParameterList , MzTabString , MzTabStringList , RawData , TOPPASResources , TOPPASVertex::TOPPASFilenames
• get1stLayerIndex() : SpectrumAlignmentDialog
• get2DData() : MSExperiment
• get2ndLayerIndex() : SpectrumAlignmentDialog
• get3CharsNumber_() : TOPPASVertex
• get_AC() : MS2Info , SHFeature
• get_alignment_error() : LCMS
• get_alignment_error_down() : SHFeature
• get_alignment_error_up() : SHFeature
• get_ALL_AC() : MS2Info
• get_ALL_AC_END() : MS2Info
• get_ALL_AC_START() : MS2Info
• get_ALL_peak() : LCMSCData
• get_ALL_peak_ordered() : LCMSCData
• get_allocator() : _Alloc_base< _Tp, _Alloc > , KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
• get_apex_intensity() : LCElutionPeak
• get_apex_MZ() : LCElutionPeak
• get_apex_peak_intensity() : SHFeature
• get_apex_retention_time() : LCElutionPeak
• get_best_MS2_SCAN() : SHFeature
• get_charge_state() : LCElutionPeak , MSPeak , SHFeature
• get_CHRG() : MS2Info
• get_Chrg() : MSPeak
• get_DATA_end() : LCMSCData
• get_DATA_start() : LCMSCData
• get_DELTA_CN() : MS2Info
• get_end_retention_time() : LCElutionPeak
• get_end_scan() : LCElutionPeak
• get_feature() : SHFeature
• get_feature_ID() : SHFeature
• get_feature_list() : LCMS
• get_feature_list_begin() : LCMS
• get_feature_list_end() : LCMS
• get_feature_list_reference() : LCMS
• get_feature_match_status() : SHFeature
• get_FEATURE_PI() : SHFeature
• get_feature_profile() : SHFeature
• get_ID() : MS2Info
• get_intensity() : LCElutionPeak , MSPeak
• get_isotopic_peaks() : MSPeak
• get_isotopic_peaks_end() : MSPeak
• get_isotopic_peaks_start() : MSPeak
• get_LC_elution_peak_counter() : ProcessData
• get_MASTER_ID() : LCMS , SHFeature
• get_match_list() : SHFeature
• get_match_list_end() : SHFeature
• get_match_list_REFERENCE() : SHFeature
• get_match_list_start() : SHFeature
• get_MATCHED_peak_area() : SHFeature
• get_matching_nb() : SHFeature
• get_MOD_SQ() : MS2Info , SHFeature
• get_Modification_list() : MS2Info
• get_Modification_list_end() : MS2Info
• get_Modification_list_start() : MS2Info
• get_Molecular_Mass() : SHFeature
• get_MONO_AA_MASS() : MS2Info
• get_MONO_H() : SHFeature
• get_MONO_MZ() : MS2Info
• get_MS2_info() : SHFeature
• get_MS2_scan() : SHFeature
• get_MS2_SCAN_LIST() : SHFeature
• get_MS2_SCAN_LIST_END() : SHFeature
• get_MS2_SCAN_LIST_START() : SHFeature
• get_MS2_SCAN_MAP() : SHFeature
• get_MS2_SCANS_END() : SHFeature
• get_MS2_SCANS_SIZE() : SHFeature
• get_MS2_SCANS_START() : SHFeature
• get_MS2_TYPE_TAG() : MS2Info , SHFeature
• get_MZ() : LCElutionPeak , MSPeak , ProcessData , SHFeature
• get_MZ_by_iterator() : LCMSCData
• get_MZ_END() : SHFeature
• get_MZ_list() : LCMSCData
• get_MZ_LIST_end() : ProcessData
• get_MZ_LIST_start() : ProcessData
• get_MZ_lower_bound() : ProcessData
• get_MZ_START() : SHFeature
• get_nb_common_match() : SHFeature
• get_nb_common_peaks() : LCMS
• get_nb_features() : LCMS
• get_nb_identified_features() : LCMS
• get_nb_ms_peaks() : LCElutionPeak
• get_nb_MZ_cluster_elements() : ProcessData
• get_nb_raw_specs() : LCMS
• get_NEUTRAL_MR() : MS2Info
• get_noise_even() : SignalToNoiseEstimatorMedianRapid::NoiseEstimator
• get_noise_odd() : SignalToNoiseEstimatorMedianRapid::NoiseEstimator
• get_noise_value() : SignalToNoiseEstimatorMedianRapid::NoiseEstimator
• get_nr_isotopes() : MSPeak
• get_peak_area() : SHFeature
• get_peak_score() : SHFeature
• get_PEP_PROB() : MS2Info
• get_pep_prob() : SHFeature
• get_PREV_AA() : MS2Info
• get_profile_Molecular_Mass() : SHFeature
• get_profile_retention_time() : SHFeature
• get_PROTEO_TYPE() : MS2Info
• get_quick_lda_score() : OpenSwath_Scores
• get_raw_MZ() : SHFeature
• get_raw_node() : _Iterator< _Val, _Ref, _Ptr >
• get_raw_retention_time_apex() : SHFeature
• get_raw_spec_name() : LCMS
• get_raw_spec_name_end() : LCMS
• get_raw_spec_name_map() : LCMS
• get_raw_spec_name_start() : LCMS
• get_replicate_intensity_sum() : SHFeature
• get_replicate_match_nb() : SHFeature
• get_retention_time() : MSPeak , SHFeature
• get_retention_time_END() : SHFeature
• get_retention_time_START() : SHFeature
• get_SCAN() : MS2Info
• get_Scan() : MSPeak
• get_scan_apex() : LCElutionPeak
• get_SCAN_END() : MS2Info
• get_scan_end() : SHFeature
• get_scan_number() : MSPeak , SHFeature
• get_SCAN_START() : MS2Info
• get_scan_start() : SHFeature
• get_score() : MSPeak
• get_SCORE_HOLDER() : SHFeature
• get_signal_list_end() : LCElutionPeak
• get_signal_list_start() : LCElutionPeak
• get_spec_name() : LCMS
• get_spectrum_ID() : LCMS , SHFeature
• get_SQ() : MS2Info , SHFeature
• get_start_retention_time() : LCElutionPeak
• get_start_scan() : LCElutionPeak
• get_target_file() : FTPeakDetectController
• get_THEO_MZ() : MS2Info , SHFeature
• get_total_peak_area() : LCElutionPeak
• get_TOTAL_SQ() : MS2Info , SHFeature
• get_TRYPTIC_STATE() : MS2Info
• get_XCORR() : MS2Info
• getA() : QuadraticRegression
• getAAAfter() : PeptideEvidence
• getAABefore() : PeptideEvidence
• getAAFrequencies() : AASequence
• getAbsoluteMZTolerance_() : IDMapper
• getAbundance() : IMSIsotopeDistribution
• getAbundances() : IMSIsotopeDistribution
• getACAndACType() : InspectOutfile , SequestOutfile
• getAcceptableAbsolute() : FuzzyStringComparator
• getAcceptableRelative() : FuzzyStringComparator
• getAccession() : CVMappingTerm , CVTerm , MzTabParameter , ProteinHit
• getAccession_() : PeptideAndProteinQuant
• getAccuracy() : MassAnalyzer
• getAcquisitionInfo() : ChromatogramSettings , SpectrumSettings
• getAcquisitionMode() : IonDetector
• getActionMode() : SpectrumCanvas , SpectrumWidget , TOPPASScene
• getActivationEnergy() : Precursor
• getActivationMethod_() : IsobaricChannelExtractor
• getActivationMethods() : Precursor
• getActive1DWidget() : TOPPViewBase
• getActive2DWidget() : TOPPViewBase
• getActive3DWidget() : TOPPViewBase
• getActiveCanvas() : TOPPViewBase
• getActiveSpectrumWidget() : TOPPViewBase
• getADCSamplingFrequency() : IonDetector
• getAddedSpectra_() : OpenSwathScoring
• getAddress() : ContactPerson
• getAdductBase() : MassExplainer
• getAdductsAsString() : Compomer
• getAffectedAminoAcids() : Modification
• getAggregateScore_() : ConsensusIDAlgorithmAverage , ConsensusIDAlgorithmBest , ConsensusIDAlgorithmIdentity , ConsensusIDAlgorithmRanks , ConsensusIDAlgorithmWorst
• getAlignedPeaksIndices() : Spectrum1DCanvas
• getAlignmentScore() : Spectrum1DCanvas
• getAlignmentSize() : Spectrum1DCanvas
• getAlignmentTraceback() : PeakAlignment
• getAllCentroidMZ() : FeatureHypothesis
• getAllCentroidRT() : FeatureHypothesis
• getAllChildTerms() : ControlledVocabulary
• getAllCometNames() : ProteaseDB
• getAllCruxNames() : ProteaseDB
• getAllDecompositions() : IntegerMassDecomposer< ValueType, DecompositionValueType > , MassDecomposer< ValueType, DecompositionValueType >
• getAllFeasibleFragmentAdducts() : RNPxlSearch::RNPxlParameterParsing
• getAllIntensities() : FeatureHypothesis
• getAllMSGFNames() : ProteaseDB
• getAllNames() : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• getAllNeighbors() : QTCluster
• getAllOMSSANames() : ProteaseDB
• getAllowChildren() : CVMappingTerm
• getAllSearchModifications() : CrossLinksDB , ModificationsDB
• getAllSpectra() : SpectrumAccessSqMass
• getAllXTandemNames() : ProteaseDB
• getAlphabetMass() : Weights
• getAlphaBoundaries_() : EGHTraceFitter
• getAlwaysAppendData() : PeakFileOptions
• getAmount() : Adduct
• getAnalysisResults() : PeptideHit
• getAnalysisSummary() : MSQuantifications
• getAnnotatedImmoniumIon() : RNPxlFragmentAnnotationHelper
• getAnnotation_() : PeptideAndProteinQuant
• getAnnotations() : GridFeature , LayerData , QTCluster
• getAnnotationState() : BaseFeature
• getAnnotationStatistics() : FeatureMap
• getApexScan() : MS2ConsensusSpectrum , MS2Fragment
• getArchAsString() : OpenMSOSInfo
• getArea() : EGHTraceFitter , GaussTraceFitter , TraceFitter
• getARGP820102() : AAIndex
• getAssayRT_() : ConfidenceScoring
• getAssays() : MSQuantifications
• getAtomicNumber() : Element
• getAtomicNumbers() : ElementDB
• getAverageMass() : IMSElement , IMSIsotopeDistribution , ResidueModification
• getAverageMasses() : IMSAlphabet
• getAverageMS1CycleTime() : MassTrace
• getAverageWeight() : AASequence , Element , EmpiricalFormula , Residue
• getAveragine() : IsotopeWavelet
• getAvgDistance() : ClusterProxyKD
• getAvgMZ() : FeatureFinderAlgorithmPickedHelperStructs::MassTrace
• getAvIntens_() : IsotopeWaveletTransform< PeakType >
• getAvMZSpacing_() : IsotopeWaveletTransform< PeakType >
• getAxisMaximum() : AxisWidget
• getAxisMinimum() : AxisWidget
• getB() : QuadraticRegression
• getBackboneBasicityLeft() : Residue
• getBackboneBasicityRight() : Residue
• getBackgroundIntensityBinsIntens() : SuperHirnParameters
• getBackgroundIntensityBinsMinBinCount() : SuperHirnParameters
• getBackgroundIntensityBinsMZ() : SuperHirnParameters
• getBackgroundIntensityBinsTR() : SuperHirnParameters
• getBackgroundLevel() : BackgroundControl
• getBackgroundNoiseLevel() : SHFeature
• getBackwardLosses_() : TheoreticalSpectrumGeneratorXLMS
• getBackwardVariable_() : HiddenMarkovModel
• getBase_() : UniqueIdIndexer< RandomAccessContainer >
• getBaseName() : PeptideIdentification
• getBestFeature() : MRMTransitionGroup< ChromatogramType, TransitionType >
• getBestHit() : IDFilter
• getBestHitSequence_() : StablePairFinder
• getBestModificationByDiffMonoMass() : ModificationsDB
• getBestModificationByMonoMass() : ModificationsDB
• getBestRateScorePair() : TOPPMetaProSIP
• getBinIndex() : BinnedSpectrum
• getBinIntensity() : BinnedSpectrum
• getBinLowerMZ() : BinnedSpectrum
• getBins() : BinnedSpectrum
• getBinSize() : BinnedSpectrum
• getBinSpread() : BinnedSpectrum
• getBiologicalRng() : SimRandomNumberGenerator
• getBlind() : InspectInfile
• getBothGnuplotFormula() : PosteriorErrorProbabilityModel
• getBoundary() : MascotInfile
• getBoundingBox() : ConvexHull2D , GridBasedCluster
• getBranch() : VersionInfo
• getC() : QuadraticRegression
• getC13MassError() : DeconvPeak
• getCalculatedMassToCharge() : IdentificationHit
• getCalculatedMZ() : AccurateMassSearchResult
• getCalibrationPoints() : InternalCalibration
• getCaretPositions() : Annotation1DCaret
• getCastValue_() : MRMFeatureQCFile
• getCategory() : ToolHandler
• getCCs_() : MapAlignmentAlgorithmKD
• getCellCount() : ClusteringGrid
• getCenter() : BiGaussModel , EGHModel , EGHTraceFitter , EmgModel , ExtendedIsotopeModel , GaussModel , GaussTraceFitter , InterpolationModel , IsotopeModel , TraceFitter
• getCenterIndex() : ClusterProxyKD
• getCenterMZ() : QTCluster
• getCenterPoint() : QTCluster
• getCenterRT() : QTCluster
• getCentre() : GridBasedCluster
• getCentroidMZ() : FeatureHypothesis , MassTrace
• getCentroidRT() : FeatureHypothesis , MassTrace
• getCentroidSD() : MassTrace
• getCentroidWindowWidth() : SuperHirnParameters
• getChannelInformation() : IsobaricQuantitationMethod , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• getChannelIntensityName() : BaseLabeler
• getCharge() : AccurateMassSearchResult , Adduct , AdductInfo , BaseFeature , ChargePair , DeconvPeak , EmpiricalFormula , ExtendedIsotopeModel , FeatureHandle , FeatureHypothesis , IdentificationHit , IsotopeModel , MultiplexIsotopicPeakPattern , OptimizePeakDeconvolution , PeptideHit , Precursor
• getChargeConsensus() : MSSim
• getChargeContribution_() : RTSimulation
• getCharges() : MascotInfile
• getChargeState() : PeptideCompound , TraMLProduct , LightCompound , Peptide
• getChargeStateIntensities() : ProtonDistributionModel
• getChecksum() : SourceFile
• getChecksumType() : SourceFile
• getChildWithName_() : MzIdentMLDOMHandler , MzIdentMLHandler , MzMLHandler , MzQuantMLHandler , TraMLHandler
• getChiSquared() : LinearRegression , QuadraticRegression
• getCHRG() : MS2Fragment
• getChromatogram() : CachedmzML , MRMTransitionGroup< ChromatogramType, TransitionType > , MSExperiment , OnDiscMSExperiment
• getChromatogramById() : IChromatogramsReader , IndexedMzMLHandler , OnDiscMSExperiment , SpectrumAccessOpenMS , SpectrumAccessOpenMSCached , SpectrumAccessOpenMSInMemory , SpectrumAccessSqMass , SpectrumAccessTransforming , ISpectrumAccess
• getChromatogramById_helper_() : IndexedMzMLHandler
• getChromatogramByPrecursorMZ() : IChromatogramsReader
• getChromatogramData() : LayerData
• getChromatogramIndex() : CachedMzMLHandler
• getChromatogramMetaById() : IChromatogramsReader
• getChromatogramMetaInfo() : SpectrumAccessOpenMS , SpectrumAccessOpenMSCached
• getChromatogramNativeID() : SpectrumAccessOpenMS , SpectrumAccessOpenMSCached , SpectrumAccessOpenMSInMemory , SpectrumAccessSqMass , SpectrumAccessTransforming , ISpectrumAccess
• getChromatograms() : FeatureFinderIdentificationAlgorithm , FeatureHypothesis , MRMTransitionGroup< ChromatogramType, TransitionType > , MSExperiment
• getChromatogramType() : ChromatogramSettings
• getChunkOffset() : FASTAContainer< TFI_File > , FASTAContainer< TFI_Vector >
• getCIDSpectrum_() : CompNovoIdentificationBase
• getCIDSpectrumLight_() : CompNovoIdentificationBase
• getCleavage() : MascotInfile
• getCleavageSite() : XTandemInfile
• getClockTime() : StopWatch
• getClosedBoxes() : IsotopeWaveletTransform< PeakType >
• getClusterIndex() : MinimumDistance
• getClusters() : ClusteringGrid
• getCodebooks() : LocalLinearMap
• getCoefficients() : MZTrafoModel
• getColor() : Annotation1DCaret , Annotation1DPeakItem , ColorSelector
• getColumn() : HPLC
• getColumnHeaders() : ConsensusMap
• getColumnIndex() : LPWrapper
• getColumnLowerBound() : LPWrapper
• getColumnName() : LPWrapper
• getColumns() : SequestOutfile
• getColumnType() : LPWrapper
• getColumnUpperBound() : LPWrapper
• getColumnValue() : LPWrapper
• getCombinationsLogic() : CVMappingRule
• getComboBox() : SpectraViewWidget
• getCometID() : DigestionEnzymeProtein
• getComment() : ChromatogramSettings , ExperimentalSettings , HPLC , Sample , SampleTreatment , SpectrumSettings
• getCommentRows() : MzTab
• getCommonName() : SpectralMatch
• getCompletionTime() : DataProcessing
• getCompomer() : ChargePair
• getCompomerById() : MassExplainer
• getComponent() : Compomer
• getComponentFeatureConcentrations() : AbsoluteQuantitationStandards
• getComponentName() : AbsoluteQuantitationMethod
• getCompoundByRef() : TargetedExperiment , LightTargetedExperiment
• getCompoundRef() : IncludeExcludeTarget , ReactionMonitoringTransition , LightTransition
• getCompounds() : TargetedExperiment , LightTargetedExperiment
• getCompression() : PeakFileOptions
• getCompressionTerm_() : MzMLHandlerHelper
• getConcentration() : Sample
• getConcentrationUnits() : AbsoluteQuantitationMethod
• getConditionalFragmentIsotopeDist() : EmpiricalFormula
• getConfigSetByName_() : LogConfigHandler
• getConfigurationList() : TraMLProduct
• getConfigurations() : IncludeExcludeTarget
• getConsensIsotopeIteratorEnd() : ConsensusIsotopePattern
• getConsensIsotopeIteratorStart() : ConsensusIsotopePattern
• getConsensus() : BaseLabeler
• getConsensusMap() : FeatureFinderMultiplexAlgorithm , LayerData
• getConsensusMaps() : MSQuantifications
• getContactInfo() : ContactPerson
• getContacts() : ExperimentalSettings , TargetedExperiment
• getContainer() : IsotopeDistribution
• getContaminants() : MSSim
• getContentType() : Bzip2InputStream , GzipInputStream
• getConvexHull() : Feature
• getConvexhull() : FeatureFinderAlgorithmPickedHelperStructs::MassTrace , MassTrace
• getConvexHulls() : Feature , FeatureHypothesis
• getCord() : LocalLinearMap
• getCorrectlyAssignedFitResult() : PosteriorErrorProbabilityModel
• getCorrelationCoefficient() : AbsoluteQuantitationMethod
• getCounts() : MzMLHandler
• getCoverage() : ProteinHit
• getCPUTime() : StopWatch
• getCreationDate() : Identification
• getCruxID() : DigestionEnzymeProtein
• getCTermGain() : DigestionEnzymeProtein
• getCTerminalModification() : AASequence
• getCTerminalModificationName() : AASequence
• getCumulativeHistogram() : Histogram< ValueType, BinSizeType >
• getCurrentAnnotations() : LayerData
• getCurrentLayer() : SpectrumCanvas , TOPPViewBase
• getCurrentLayer_() : SpectrumCanvas
• getCurrentLayerIndex() : SpectrumCanvas
• getCurrentMaxIntensity() : SpectrumCanvas
• getCurrentMinIntensity() : SpectrumCanvas
• getCurrentSpectrum() : LayerData
• getCurrentSpectrumIndex() : LayerData
• getCustomizations() : Instrument
• getCutOff() : BaseModel< D >
• getCVIdentifierRef() : CVMappingTerm , CVTerm
• getCVLabel() : MzTabParameter
• getCVReferences() : CVMappings
• getCVs() : TargetedExperiment
• getCVTerm_() : SemanticValidator
• getCVTerms() : CVMappingRule , CVTermList , CVTermListInterface
• getCWD() : TOPPASInputFilesDialog
• getData() : BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value > , MSDataStoringConsumer , ScoringMatrixData_< int, AminoAcid, AdaptedIdentity > , ScoringMatrixData_< int, AminoAcid, PAM30MS >
• getDataArrays() : OSChromatogram , OSSpectrum
• getDatabase() : SequestInfile
• getDataPoints() : TransformationDescription
• getDataProcessing() : ChromatogramSettings , ConsensusMap , FeatureMap , MetaInfoDescription , SpectrumSettings
• getDataProcessingList() : MSQuantifications
• getDataRange() : MSExperiment , SpectrumCanvas
• getDate() : DateTime
• getDateTime() : ExperimentalSettings , ProteinIdentification
• getDb() : InspectInfile
• getDB() : MascotInfile
• getDecisionValues() : SVMWrapper
• getDecomposition() : IntegerMassDecomposer< ValueType, DecompositionValueType > , MassDecomposer< ValueType, DecompositionValueType >
• getDecompositions() : RealMassDecomposer , MassDecompositionAlgorithm
• getDecompositions_() : CompNovoIdentificationBase
• getDecompositionsDAC_() : CompNovoIdentification , CompNovoIdentificationCID
• getDeconvPeaks() : Deisotoper
• getDecoyString() : PeptideIndexing
• getDecoyTransitionType() : ReactionMonitoringTransition
• getDefaultGradientLinearIntensityMode() : MultiGradient
• getDefaultGradientLogarithmicIntensityMode() : MultiGradient
• getDefaultParameters() : BaseLabeler , EmgGradientDescent , FeatureFinderAlgorithm , MSPGenericFile , PeakIntegrator , TargetedSpectraExtractor , TransformationModel , TransformationModelBSpline , TransformationModelInterpolated , TransformationModelLinear , TransformationModelLowess
• getDefaultParameters_() : TOPPBase
• getDefaultParametersFilename() : XTandemInfile
• getDefaults() : DefaultParamHandler , EmgScoring
• getDeltaMasses() : MultiplexDeltaMasses
• getDeltaMassesList() : MultiplexDeltaMassesGenerator
• getDescription() : BaseLabeler , MetaInfoRegistry , Param , ProteinHit , TOPPASScene
• getDetectableIsotopeFactor() : SuperHirnParameters
• getDeviations() : TransformationDescription
• getDFSColor() : TOPPASVertex
• getDFSParent() : TOPPASVertex
• getDiffAverageMass() : ResidueModification
• getDiffFormula() : ResidueModification
• getDiffMonoMass() : ResidueModification
• getDigestionTime() : Digestion
• getDirectory() : TOPPASOutputFilesDialog
• getDistance_() : QTClusterFinder
• getDoubleList_() : TOPPBase
• getDoubleOption_() : TOPPBase
• getDoubleParameter() : SVMWrapper
• getDrawMode() : Spectrum1DCanvas
• getDriftTime() : MSSpectrum , Precursor , PeptideCompound , LightCompound
• getDriftTimeWindowLowerOffset() : Precursor
• getDriftTimeWindowUpperOffset() : Precursor
• getEdgeScore() : ChargePair
• getEdgeStatus() : TOPPASEdge
• getElement() : ElementDB , IMSAlphabet , LPWrapper
• getElementIndex() : ChargePair
• getElementPath() : CVMappingRule
• getElements() : IMSAlphabetParser< AlphabetElementType, Container, InputSource > , IMSAlphabetTextParser , QTCluster
• getEluents() : Gradient
• getElutionPeakDistance() : ProcessData
• getElutionPeakExtraInfo() : LCElutionPeak
• getEmail() : ContactPerson
• getEmptyRows() : MzTab
• getEnd() : PeptideEvidence
• getEndPoint() : Annotation1DDistanceItem
• getEndScan() : MS2ConsensusSpectrum , MS2Fragment
• getEndTR() : MS2ConsensusSpectrum , MS2Fragment
• getEntry() : Param
• getEntry_() : Param
• getEnzyme() : Digestion , DigestionEnzymeDB< DigestionEnzymeType, InstanceType > , InspectInfile
• getEnzymeByRegEx() : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• getEnzymeInfo_() : SequestInfile
• getEnzymeInfoAsString() : SequestInfile
• getEnzymeName() : EnzymaticDigestion , EnzymaticDigestionLogModel , SequestInfile
• getEnzymeNumber() : SequestInfile
• getError() : CalibrationData
• getErrorMessage() : MascotRemoteQuery
• getErrorString() : NetworkGetRequest
• getETDSpectrum_() : CompNovoIdentification
• getExcludeTargets() : TargetedExperiment
• getExecutablePath() : File
• getExperiment() : InspectOutfile , MSSim
• getExperimentalMassToCharge() : IdentificationHit
• getExperimentalSettings() : MSExperiment , OnDiscMSExperiment
• getExperimentLabel() : PeptideIdentification
• getExperimentType() : ConsensusMap
• getExpTableMaxIndex() : IsotopeWavelet
• getExternalToolConfigFiles_() : ToolHandler
• getExternalTools_() : ToolHandler
• getExternalToolsPath() : ToolHandler
• getExtraPeakInfo() : CentroidPeak , MSPeak
• getFactor_() : ZhangSimilarityScore
• getFactors() : ExperimentalDesign::SampleSection
• getFactorValue() : ExperimentalDesign::SampleSection
• getFactory() : SingletonRegistry
• getFAUJ880111() : AAIndex
• getFeasibleFragmentAdducts() : RNPxlSearch::RNPxlParameterParsing
• getFeature() : FeatureEditDialog , GridFeature , MRMFeature , MRMFeatureOpenMS , PeakIndex , IMRMFeature , MockMRMFeature
• getFeatureExtraInformation() : SHFeature
• getFeatureIdentifications() : MSSim
• getFeatureIDs() : MRMFeature
• getFeatureIndex() : GridFeature
• getFeatureList() : ConsensusFeature
• getFeatureMap() : FeatureFinderMultiplexAlgorithm , LayerData
• getFeatureMaps() : MSQuantifications
• getFeatureMassErrorAtPPMLevel() : SHFeature
• getFeatureName() : AbsoluteQuantitationMethod
• getFeatureNumber() : Spectrum2DGoToDialog
• getFeatures() : ConsensusFeature , MRMFeature , MRMTransitionGroup< ChromatogramType, TransitionType >
• getFeatureScaledIntensity_() : RawMSSignalSimulation
• getFeaturesMuteable() : MRMTransitionGroup< ChromatogramType, TransitionType >
• getFeatureWeights() : SimpleSVM
• getFile() : BaseException
• getFileList_() : TOPPViewBase
• getFilename() : TOPPASInputFileDialog
• getFilenames() : TOPPASInputFilesDialog
• getFileNames() : TOPPASVertex
• getFileNames_() : ExperimentalDesign
• getFilenamesOfOpenFiles_() : TOPPViewBase
• getFileSize() : SourceFile
• getFileType() : SourceFile
• getFillData() : PeakFileOptions
• getFilterNr_() : ChromatogramExtractor , ChromatogramExtractorAlgorithm
• getFINA770101() : AAIndex
• getFinalMSExponent() : MassAnalyzer
• getFirstColumn() : FuzzyStringComparator
• getFirstIsotopeRelativeIntensities_() : DIAScoring
• getFirstName() : ContactPerson
• getFittedIntensity() : CentroidPeak
• getFivePrimeGain() : DigestionEnzymeRNA
• getFixedModificationNames() : ModificationDefinitionsSet
• getFixedModifications() : ModificationDefinitionsSet , PrecursorIonSelectionPreprocessing
• getFlag_() : TOPPBase
• getFlags() : Annotation1DTextItem
• getFloatDataArrays() : MSChromatogram , MSSpectrum
• getFlux() : HPLC
• getForceMQCompatability() : PeakFileOptions
• getForceTPPCompatability() : PeakFileOptions
• getFormat() : SaveImageDialog
• getFormula() : AASequence , Adduct , IsotopeModel , Residue , ResidueModification
• getFormulaString() : AccurateMassSearchResult
• getFormVersion() : MascotInfile
• getForwardLosses_() : TheoreticalSpectrumGeneratorXLMS
• getForwardVariable_() : HiddenMarkovModel
• getFoundAdduct() : AccurateMassSearchResult
• getFoundMass() : AccurateMassSearchResult
• getFoundPrecursorCharge() : SpectralMatch
• getFoundPrecursorMass() : SpectralMatch
• getFractionIdentifier() : ExperimentalSettings
• getFractions_() : ExperimentalDesign
• getFractionToMSFilesMapping() : ExperimentalDesign
• getFragmentMassErrorUnit() : XTandemInfile
• getFragmentMassTolerance() : XTandemInfile
• getFragmentMz() : MS2Fragment
• getFragmentPeakArea() : MS2Fragment
• getFullId() : ResidueModification
• getFullName() : ResidueModification
• getFullOutputDirectory() : TOPPASOutputFileListVertex , TOPPASToolVertex
• getFunction() : BaseException
• getFWHM() : EGHTraceFitter , FeatureHypothesis , GaussTraceFitter , MassTrace , PeakShape , TraceFitter
• getFWHMborders() : MassTrace
• getGammaTableMaxIndex() : IsotopeWavelet
• getGaussGnuplotFormula() : PosteriorErrorProbabilityModel
• getGaussMu() : PrecursorIonSelectionPreprocessing
• getGaussSigma() : PrecursorIonSelectionPreprocessing
• getGnuplotFormula() : EGHTraceFitter , GaussTraceFitter , TraceFitter
• getGradient() : HPLC
• getGradientTime() : RTSimulation
• getGridSpacingX() : ClusteringGrid
• getGridSpacingY() : ClusteringGrid
• getGroup() : CalibrationData
• getGumbel_() : PosteriorErrorProbabilityModel
• getGumbelGnuplotFormula() : PosteriorErrorProbabilityModel
• getHeight() : EGHTraceFitter , GaussTraceFitter , TraceFitter
• getHighPoints() : MetaProSIPInterpolation
• getHistogramRightmostPercent() : SignalToNoiseEstimatorMedian< Container >
• getHitDBIndex() : AhoCorasickAmbiguous
• getHitKey() : IDFilter::GetMatchingItems< HitType, Entry >
• getHitProteinPosition() : AhoCorasickAmbiguous
• getHits() : MascotInfile , PeptideIdentification , ProteinIdentification , SpectrumIdentification
• getHorizontalProjection() : Spectrum2DWidget
• getHoveringEdge() : TOPPASScene
• getHPLC() : ExperimentalSettings
• getHTTPPeakListEnclosure() : MascotGenericFile
• getHullPoints() : ConvexHull2D
• getID() : Compomer , GridFeature
• getId() : IdentificationHit
• getID() : MS2Feature
• getId() : ResidueModification
• getID_() : DocumentIDTagger
• getIDDetails_() : IDMapper
• getIdentification() : CompNovoIdentification , CompNovoIdentificationCID , DeNovoIdentification
• getIdentificationMZ_() : SpectrumCanvas
• getIdentifications() : CompNovoIdentification , CompNovoIdentificationBase , CompNovoIdentificationCID , DeNovoIdentification , MSSim
• getIdentifier() : Acquisition , CVMappingRule , CVReference , DocumentIdentifier , PeptideIdentification , ProteinIdentification
• getInchiString() : SpectralMatch
• getIncludeTargets() : TargetedExperiment
• getIncorrectlyAssignedFitResult() : PosteriorErrorProbabilityModel
• getIndex() : ClusteringGrid , FidHandler , IsotopicDist , KDTreeFeatureNode , ListUtils , MetaInfoRegistry
• getIndistinguishableProteins() : ProteinIdentification
• getIndividualIntensities() : AccurateMassSearchResult
• getIniLocation_() : TOPPBase
• getInitialTrTolerance() : SuperHirnParameters
• getInletType() : IonSource
• getInput() : ToolsDialog
• getInputFilename() : XTandemInfile
• getInputParameters() : TOPPASToolVertex
• getInsideReferencePoint() : LinearInterpolation< Key, Value >
• getInsideReferencePoint_0() : BilinearInterpolation< Key, Value >
• getInsideReferencePoint_1() : BilinearInterpolation< Key, Value >
• getInstance() : CrossLinksDB , DigestionEnzymeDB< DigestionEnzymeType, InstanceType > , ElementDB , GlobalExceptionHandler , IsotopeWavelet , LogConfigHandler , ModificationsDB , ResidueDB
• getInstance_() : UniqueIdGenerator
• getInstitution() : ContactPerson
• getInstrument() : ExperimentalSettings , HPLC , InspectInfile , MascotInfile
• getInstruments() : TargetedExperiment
• getInstrumentSettings() : ChromatogramSettings , SpectrumSettings
• getIntegerDataArrays() : MSChromatogram , MSSpectrum
• getIntensity() : BaseModel< D > , CalibrationData , CentroidPeak , ChromatogramPeak , FeatureOpenMS , FidHandler , InterpolationModel , MassTrace , MRMFeatureOpenMS , MultiplexSatelliteProfile , Peak1D , Peak2D , ProductModel< 2 > , IFeature , IMRMFeature , MockFeature , MockMRMFeature
• getIntensity32Bit() : PeakFileOptions
• getIntensityArray() : Chromatogram , Spectrum , OSChromatogram , OSSpectrum
• getIntensityCV() : SuperHirnParameters
• getIntensityFloor() : SuperHirnParameters
• getIntensityHist() : BackgroundIntensityBin
• getIntensityMap() : BackgroundIntensityBin
• getIntensityMode() : SpectrumCanvas
• getIntensityRange() : ConsensusFeature , FeatureFileOptions , PeakFileOptions
• getIntensityThreshold() : SuperHirnParameters
• getIntercept() : LinearRegression
• getIntermediateProducts() : ReactionMonitoringTransition
• getInternalToAIon() : Residue
• getInternalToBIon() : Residue
• getInternalToCIon() : Residue
• getInternalToCTerm() : Residue
• getInternalToFull() : Residue
• getInternalToNTerm() : Residue
• getInternalToolConfigFiles_() : ToolHandler
• getInternalTools_() : ToolHandler
• getInternalToolsPath() : ToolHandler
• getInternalToXIon() : Residue
• getInternalToYIon() : Residue
• getInternalToZIon() : Residue
• getInterpolatedValue_() : ContinuousWaveletTransform
• getInterpolation() : InterpolationModel
• getInterpolationMode() : MultiGradient , MultiGradientSelector
• getInterpretationList() : TraMLProduct
• getInterpretations() : IncludeExcludeTarget
• getIntList_() : TOPPBase
• getIntOption_() : TOPPBase
• getIntParameter() : SVMWrapper
• getInvTableSteps() : IsotopeWavelet
• getIon() : MRMIonSeries
• getIonCutoffPercentage() : SequestInfile
• getIonDetectors() : Instrument
• getIonizationMethod() : IonSource
• getIonMass() : IMSElement
• getIonOptics() : Instrument
• getIonScores() : DeNovoIonScoring
• getIonSeries() : MRMIonSeries
• getIonSeriesWeights() : SequestInfile
• getIonSources() : Instrument
• getIonTypes() : SvmTheoreticalSpectrumGenerator
• getISName() : AbsoluteQuantitationMethod
• getIsolationWidth() : MassAnalyzer
• getIsolationWindowLowerOffset() : Precursor , Product
• getIsolationWindowUpperOffset() : Precursor , Product
• getIsOpen() : Bzip2InputStream , GzipInputStream
• getIsotopeCorrectionMatrix() : IsobaricQuantitationMethod , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• getIsotopeDistances() : FeatureHypothesis
• getIsotopeDistribution() : Element , EmpiricalFormula , IMSElement , IsotopeDistributionCache , IsotopeModel
• getIsotopeDistribution_() : FeatureFinderAlgorithmPicked
• getIsotopeMatrixAsStringList() : ItraqConstants
• getIsotopesSimScore() : AccurateMassSearchResult
• getIsotopicPeaks() : DeconvPeak
• getIsotopIdx() : CentroidPeak
• getIsRepeatable() : CVMappingTerm
• getItemAt() : Annotations1DContainer
• getItraqIntensity_() : ITRAQLabeler
• getKey() : IDFilter::GetMatchingItems< HitType, Entry > , TOPPASInputFileListVertex
• getKeys() : MetaInfo , MetaInfoInterface
• getKHAG800101() : AAIndex
• getLabel() : Adduct , FeatureHypothesis , MassTrace
• getLabelingConsensus() : MSSim
• getLabelLong() : MultiplexDeltaMassesGenerator
• getLabels() : Compomer , FeatureHypothesis , InspectOutfile , SVMWrapper
• getLabels_() : ExperimentalDesign
• getLabelShort() : MultiplexDeltaMassesGenerator
• getLambdaL() : IsotopeWavelet
• getLastLCelutionSignal() : FeatureLCProfile
• getLastName() : ContactPerson
• getLayer() : SpectraIdentificationViewWidget , SpectrumCanvas
• getLayer_() : SpectrumCanvas
• getLayerCount() : SpectrumCanvas
• getLayerFlag() : SpectrumCanvas
• getLayerName() : SpectrumCanvas
• getLCElutionPeakSimilarity() : MS2ConsensusSpectrum
• getLCelutionProfile() : SHFeature
• getLCelutionSignalMap() : FeatureLCProfile
• getLCelutionSignalsEnd() : FeatureLCProfile
• getLCelutionSignalsStart() : FeatureLCProfile
• getLCMS() : FTPeakDetectController
• getLeftAndRightGBValues_() : ProtonDistributionModel
• getLeftEndpoint() : PeakShape
• getLeftPaddingIndex() : ContinuousWaveletTransform
• getLeftSplitter() : HistogramDialog , HistogramWidget
• getLegend() : AxisWidget
• getLevel() : LogStream , LogStreamBuf
• getLibrary() : FeatureFinderIdentificationAlgorithm , TargetedSpectraExtractor::Comparator
• getLibraryIntensities() : TransitionGroupOpenMS< SpectrumT, TransitionT > , ITransitionGroup , MockTransitionGroup
• getLibraryIntensity() : MRMTransitionGroup< ChromatogramType, TransitionType > , ReactionMonitoringTransition , LightTransition
• getLine() : BaseException
• getLinearInterpolation() : IsotopeWaveletTransform< PeakType >
• getLinearIonSpectrum() : TheoreticalSpectrumGeneratorXLMS
• getLinkPosition_() : XQuestResultXMLHandler
• getList() : ListTable , ListEditor
• getListToolStatus_() : TOPPASEdge
• getLLMParam() : LocalLinearMap
• getLLOD() : AbsoluteQuantitationMethod
• getLLOQ() : AbsoluteQuantitationMethod
• getLoadConvexHull() : FeatureFileOptions
• getLoadDetail() : MzMLHandler , MzXMLHandler , XMLHandler
• getLoadedFilePath() : DocumentIdentifier
• getLoadedFileType() : DocumentIdentifier
• getLoadSubordinates() : FeatureFileOptions
• getLocalFile() : TOPPASResource
• getLogDestination() : FuzzyStringComparator
• getLogP() : Compomer
• getLogProb() : Adduct
• getLogScore_() : ILPDCWrapper
• getLogStreamByName_() : LogConfigHandler
• getLogThreshold() : EnzymaticDigestionLogModel
• getLogType() : ProgressLogger
• getLossFormulas() : Residue
• getLossNames() : Residue
• getLower() : LinearRegression
• getLowerRTBound() : EGHTraceFitter , GaussTraceFitter , TraceFitter
• getLowIntensityMSSignalThreshold() : SuperHirnParameters
• getLowMassIons() : Residue
• getLPSolver() : OfflinePrecursorIonSelection , PrecursorIonSelection , PSLPFormulation
• getMagneticFieldStrength() : MassAnalyzer
• getMapIndex() : FeatureHandle , GridFeature
• getMappingRules() : CVMappings
• getMascotXMLResponse() : MascotRemoteQuery
• getMass() : CentroidPeak , Compomer , IMSAlphabet , IMSElement , IMSIsotopeDistribution , Modification , Sample
• getMassAnalyzers() : Instrument
• getMassDiff() : ChargePair
• getMassErrorAtPPMLevel() : SuperHirnUtil
• getMasses() : IMSAlphabet , IMSIsotopeDistribution , PrecursorIonSelectionPreprocessing
• getMassRanges() : OfflinePrecursorIonSelection
• getMassShift() : Tagging
• getMassShiftAt() : MultiplexIsotopicPeakPattern
• getMassShiftCount() : MultiplexIsotopicPeakPattern
• getMassShiftIndex() : MultiplexIsotopicPeakPattern
• getMassShifts() : MultiplexIsotopicPeakPattern
• getMassTolDa() : SuperHirnParameters
• getMassTolPpm() : SuperHirnParameters
• getMasstraceIntensities() : AccurateMassSearchResult
• getMassType() : MascotInfile
• getMassTypeFragment() : SequestInfile
• getMassTypeParent() : SequestInfile
• getMatchedWhitelist() : FuzzyStringComparator
• getMatchingHMDBids() : AccurateMassSearchResult
• getMatchingIndex() : AccurateMassSearchResult
• GetMatchingItems() : IDFilter::GetMatchingItems< HitType, Entry >
• getMatchingPeaks() : IsotopicDist
• getMatchingPeptidoforms_() : MRMAssay
• getMatchingScore() : SpectralMatch
• getMatchingSpectrumIndex() : SpectralMatch
• getMatchPeakAllowedError() : SequestInfile
• getMatchPeakCount() : SequestInfile
• getMatchPeakTolerance() : SequestInfile
• getMatrixA() : LocalLinearMap
• getMatrixRow() : LPWrapper
• getMax() : IsotopeDistribution , RangeManager< D > , Spectrum1DGoToDialog
• getMaxAAPerModPerPeptide() : SequestInfile
• getMaxCharge() : IsotopeWavelet
• getMaxDataPoolSize() : PeakFileOptions
• getMaxFeatureChrg() : SuperHirnParameters
• getMaxFeatureMZ() : SuperHirnParameters
• getMaxInt() : RangeManager< D >
• getMaxIntensity() : MassTrace , SpectrumCanvas
• getMaxInternalCleavageSites() : SequestInfile
• getMaxInterScanRetentionTimeDistance() : SuperHirnParameters
• getMaxIsotope() : CoarseIsotopePatternGenerator
• getMaxIterations() : TwoDOptimization
• getMaxModifications() : ModificationDefinitionsSet
• getMaxModsPerPeptide() : SequestInfile
• getMaxMZ() : MSExperiment , Spectrum2DGoToDialog
• getMaxOccurrences() : ModificationDefinition
• getMaxPeakDistance() : TwoDOptimization
• getMaxPosition_() : PeakPickerCWT
• getMaxPrecursorCharge() : XTandemInfile
• getMaxPTMsize() : InspectInfile
• getMaxRoundingError() : Weights
• getMaxRT() : MSExperiment , Spectrum2DGoToDialog
• getMaxScanDistance() : ProcessData
• getMaxScanSize() : IsotopeWaveletTransform< PeakType >
• getMaxScore() : XQuestResultXMLHandler , PrecursorIonSelection , XQuestResultXMLFile
• getMaxTR() : SuperHirnParameters
• getMaxValidEValue() : XTandemInfile
• getMean() : BackgroundIntensityBin
• getMeanRes() : LinearRegression
• getMergeLayer() : TOPPViewOpenDialog
• getMessage() : BaseException
• getMetaData() : CachedmzML , MzTab , OnDiscMSExperiment
• getMetadataOnly() : FeatureFileOptions , PeakFileOptions
• getMetaValue() : MetaInfoInterface
• getMetaValues() : CalibrationData
• getMethodOfCombination() : AcquisitionInfo
• getMIMatrix() : MRMScoring
• getMin() : IsotopeDistribution , RangeManager< D > , Spectrum1DGoToDialog
• getMinElementCoordinates() : DistanceMatrix< Value >
• getMinFeatureChrg() : SuperHirnParameters
• getMinFeatureMZ() : SuperHirnParameters
• getMinimalIntensityLevel() : ProcessData
• getMinInt() : RangeManager< D >
• getMinIntensity() : SpectrumCanvas , SuperHirnParameters
• getMinMZ() : MSExperiment , Spectrum2DGoToDialog
• getMinNbClusterMembers() : SuperHirnParameters
• getMinPeakGroupSize() : Deisotoper
• getMinRoundingError() : Weights
• getMinRT() : MSExperiment , Spectrum2DGoToDialog
• getMinScore() : XQuestResultXMLHandler , XQuestResultXMLFile
• getMinSpacing() : IsotopeWaveletTransform< PeakType >
• getMinTR() : SuperHirnParameters
• getMissedCleavages() : EnzymaticDigestion , MascotInfile
• getML1s() : TOFCalibration
• getML2s() : TOFCalibration
• getML3s() : TOFCalibration
• getModel() : Instrument , ProductModel< 2 >
• getModelParameters() : TransformationDescription
• getModelType() : TransformationDescription
• getModelTypes() : TransformationDescription
• getModification() : ModificationDefinition , ModificationsDB , Residue
• getModificationName() : ModificationDefinition , Residue
• getModificationNames() : ModificationDefinitionsSet
• getModifications() : InspectInfile , MascotInfile , ModificationDefinitionsSet , PepNovoInfile , SequestInfile , XTandemInfile , RNPxlSearch::RNPxlParameterParsing
• getModifications_() : SimpleSearchEngine , TOPPOpenPepXLLF
• getModificationsFromStringList() : OPXLHelper
• getModificationsPerPeptide() : InspectInfile
• getModifiedAASequence_() : CompNovoIdentificationBase
• getModifiedResidue() : ResidueDB
• getModifiedStringFromAASequence_() : CompNovoIdentificationBase
• getModifString_() : IBSpectraFile
• getModOrSubstIdentifier() : MzTabModification
• getMonoisotopicFeatureIntensity() : FeatureHypothesis
• getMonoisotopicPeaks_() : TOFCalibration
• getMonoMass() : ResidueModification
• getMonoWeight() : AASequence , Element , EmpiricalFormula , Residue
• getMostAbundant() : IsotopeDistribution
• getMs1FeatureMergingTrTolerance() : SuperHirnParameters
• getMs1PeakAreaTrResolution() : SuperHirnParameters
• getMS1TRResolution() : SuperHirnParameters
• getMS2Feature() : SHFeature
• getMS2FragmentMap() : MS2ConsensusSpectrum
• getMS2FragmentPeakEnd() : MS2ConsensusSpectrum
• getMS2FragmentPeakStart() : MS2ConsensusSpectrum
• getMS2Identifications() : MSSim
• getMSChromatogramById() : IndexedMzMLHandler
• getMSData() : FeatureFinderIdentificationAlgorithm
• getMSFile() : MzTabSpectraRef
• getMSFileSection() : ExperimentalDesign
• getMSGFID() : DigestionEnzymeProtein
• getMSLevel() : MSSpectrum
• getMSLevels() : MSExperiment , PeakFileOptions
• getMSSpectrumById() : IndexedMzMLHandler
• getMulticharge() : InspectInfile
• getMZ() : AdductInfo , CalibrationData , ChromatogramPeak , GridFeature , IsotopeWaveletTransform< PeakType >::TransSpectrum , MSChromatogram , MultiplexFilteredMSExperiment , MultiplexFilteredPeak , MultiplexSatelliteProfile , Peak1D , Peak2D , PeptideIdentification , Product , TraMLProduct
• getMz32Bit() : PeakFileOptions
• getMZArray() : Spectrum , OSSpectrum
• getMZErrorPPM() : AccurateMassSearchResult
• getMZidx() : MultiplexFilteredPeak , MultiplexSatelliteCentroided
• getMzMax() : SplinePackage , SplineSpectrum
• getMzMin() : SplinePackage , SplineSpectrum
• getMzPeakCutOffAtMonoPos() : IsotopeWavelet
• getMZRange() : FeatureFileOptions , PeakFileOptions
• getMZShiftAt() : MultiplexIsotopicPeakPattern
• getMZShiftCount() : MultiplexIsotopicPeakPattern
• getMzStepWidth() : SplinePackage
• getMZTolerance() : TwoDOptimization
• getMzTolPpm() : SuperHirnParameters
• getNADH010106() : AAIndex
• getNADH010107() : AAIndex
• getName() : AdductInfo , CVReference , CVTerm , DefaultParamHandler , DigestionEnzyme , Element , BaseException , HMMState , IdentificationHit , IMSAlphabet , IMSElement , IncludeExcludeTarget , Instrument , IsobaricQuantitationMethod , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , MetaInfoDescription , MetaInfoRegistry , ModelDescription< D > , MSChromatogram , MSSpectrum , MzTabParameter , Param::ParamIterator , ReactionMonitoringTransition , Residue , ResidueModification , Sample , Software , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTTenPlexQuantitationMethod , TOPPASInputFileListVertex , TOPPASMergerVertex , TOPPASOutputFileListVertex , TOPPASSplitterVertex , TOPPASToolVertex , TOPPASVertex , TOPPASVertexNameDialog
• getNameMapping() : INIUpdater
• getNameOfFile() : SourceFile
• getNames() : ElementDB
• getNativeID() : ChromatogramSettings , ReactionMonitoringTransition , SpectrumSettings , LightTransition
• getNativeIDs() : MRMFeatureOpenMS , TransitionGroupOpenMS< SpectrumT, TransitionT > , IMRMFeature , ITransitionGroup , MockMRMFeature , MockTransitionGroup
• getNativeIDType() : SourceFile
• getNativeIDTypeAccession() : SourceFile
• getNativeScanId() : FeatureFinderAlgorithmSH
• getNavigator() : SplineSpectrum
• getNbLCelutionSignals() : FeatureLCProfile
• getNbMS2Fragments() : MS2ConsensusSpectrum
• getNbMSTraces() : ProcessData
• getNearestNeighbourIndex() : MinimumDistance
• getNegativeCharges() : Compomer
• getNegativeGnuplotFormula_ : PosteriorErrorProbabilityModel
• getNegativePrior() : PosteriorErrorProbabilityModel
• getNeighborhood() : KDTreeFeatureMaps
• getNetCharge() : Compomer
• getNeutralLossAverageMass() : ResidueModification
• getNeutralLossDiffFormula() : ResidueModification
• getNeutralLossesForIons() : SequestInfile
• getNeutralLossMonoMass() : ResidueModification
• getNeutralMass() : AdductInfo
• getNewToolName() : INIUpdater
• getNextLogCounter_() : LogStreamBuf
• getNextMz() : SplineSpectrum::Navigator
• getNextPeakGroup() : CentroidData
• getNextPrecursors() : PrecursorIonSelection
• getNextPrecursorsSeq() : PrecursorIonSelection
• getNextSpectrum_() : MascotGenericFile , MascotInfile
• getNoise() : CentroidData
• getNoiseSuppression() : XTandemInfile
• getNominalMass() : IMSElement , IMSIsotopeDistribution
• getNormalized_library_intensities_() : OpenSwathScoring
• getNormalizeXcorr() : SequestInfile
• getNPoints() : AbsoluteQuantitationMethod
• getNrChromatograms() : CachedmzML , IChromatogramsReader , IndexedMzMLHandler , MzMLSqliteHandler , MSExperiment , OnDiscMSExperiment , SpectrumAccessOpenMS , SpectrumAccessOpenMSCached , SpectrumAccessOpenMSInMemory , SpectrumAccessSqMass , SpectrumAccessTransforming , ISpectrumAccess
• getNrChromatogramsWritten() : MSDataWritingConsumer
• getNrIsotopes() : DeconvPeak
• getNrOfGroups() : CalibrationData
• getNrSpectra() : CachedmzML , ISpectraReader , IndexedMzMLHandler , MzMLSqliteHandler , MSExperiment , OnDiscMSExperiment , SpectrumAccessOpenMS , SpectrumAccessOpenMSCached , SpectrumAccessOpenMSInMemory , SpectrumAccessSqMass , SpectrumAccessTransforming , ISpectrumAccess
• getNrSpectraWritten() : MSDataWritingConsumer
• getNTermGain() : DigestionEnzymeProtein
• getNTerminalModification() : AASequence
• getNTerminalModificationName() : AASequence
• getNTermLossFormulas() : Residue
• getNTermLossNames() : Residue
• getNucleotideReadingFrame() : SequestInfile
• getNumber() : Sample
• getNumberIterations() : OptimizePick
• getNumberOf() : EmpiricalFormula
• getNumberOfAtoms() : EmpiricalFormula
• getNumberOfChannels() : IsobaricQuantitationMethod , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• getNumberOfColumns() : LPWrapper
• getNumberOfDecompositions() : IntegerMassDecomposer< ValueType, DecompositionValueType > , MassDecomposer< ValueType, DecompositionValueType > , RealMassDecomposer
• getNumberOfEnclosedPoints_() : SVMWrapper
• getNumberOfFixedModifications() : ModificationDefinitionsSet
• getNumberOfFractionGroups() : ExperimentalDesign
• getNumberOfFractions() : ExperimentalDesign
• getNumberOfHits() : XQuestResultXMLHandler , XQuestResultXMLFile
• getNumberOfLabelingElements() : MetaProSIPDecomposition
• getNumberOfLabels() : ExperimentalDesign
• getNumberOfMaxAA() : MassDecomposition
• getNumberOfMissedCleavages() : XTandemInfile
• getNumberOfModifications() : ModificationDefinitionsSet , ModificationsDB
• getNumberOfModifiedResidues() : ResidueDB
• getNumberOfMSFiles() : ExperimentalDesign
• getNumberOfNonZeroEntriesInRow() : LPWrapper
• getNumberOfPeaks_() : OptimizePeakDeconvolution , PeakPickerCWT
• getNumberOfPrecsInSpectrum_() : PSLPFormulation
• getNumberOfProtIds() : PSProteinInference
• getNumberOfProtIdsPeptideRule() : PSProteinInference
• getNumberOfResidues() : ResidueDB
• getNumberOfRows() : LPWrapper
• getNumberOfSamples() : ExperimentalDesign
• getNumberOfSpectraScan() : ClusteredMS2ConsensusSpectrum
• getNumberOfStates() : HiddenMarkovModel
• getNumberOfThreads() : XTandemInfile
• getNumberOfVariableModifications() : ModificationDefinitionsSet
• getNumFeatPoints() : FeatureHypothesis
• getNumJobs() : TOPPASOutputFilesDialog
• getNumPeakCutOff() : IsotopeWavelet
• getNumpressConfigurationIntensity() : PeakFileOptions
• getNumpressConfigurationMassTime() : PeakFileOptions
• getObjective() : LPWrapper
• getObjectiveSense() : LPWrapper
• getObjectiveValue() : LPWrapper
• getObservedIntensity() : AccurateMassSearchResult
• getObservedMZ() : AccurateMassSearchResult
• getObservedPrecursorMass() : SpectralMatch
• getObservedPrecursorRT() : SpectralMatch
• getObservedRT() : AccurateMassSearchResult
• getObservedSpectrumIndex() : SpectralMatch
• getOffset() : BinnedSpectrum , ExtendedIsotopeModel , IsotopeModel , LinearInterpolation< Key, Value >
• getOffset_0() : BilinearInterpolation< Key, Value >
• getOffset_1() : BilinearInterpolation< Key, Value >
• getOMSSAID() : DigestionEnzymeProtein
• getOnDiscPeakData() : LayerData
• getOneLetterCode() : Residue
• getOOBM850104() : AAIndex
• getOpenMSDataPath() : File
• getOpenMSHomePath() : File
• getOptimizedParameters_() : EGHTraceFitter , GaussTraceFitter , TraceFitter
• getOptions() : ConsensusXMLFile , DTA2DFile , FeatureXMLFile , FileHandler , IndexedMzMLFileLoader , MzMLHandler , MzDataFile , MzMLFile , MzXMLFile
• getOrder() : IonDetector , IonSource , MassAnalyzer
• getOrganism() : Sample
• getOrgIntensity() : CentroidPeak
• getOrigin() : ResidueModification
• getOSAsString() : OpenMSOSInfo
• getOutDir() : TOPPASScene
• getOutlierDetectionAttribute() : MS2Fragment
• getOutput() : ToolsDialog
• getOutputDir() : TOPPASOutputFileListVertex , TOPPASToolVertex
• getOutputFilename() : XTandemInfile
• getOutputFiles() : TOPPASVertex
• getOutputFolderName() : TOPPASOutputFileListVertex
• getOutputLines() : SequestInfile
• getOutputParameters() : TOPPASToolVertex
• getOutputResults() : XTandemInfile
• getOutsideReferencePoint() : LinearInterpolation< Key, Value >
• getOutsideReferencePoint_0() : BilinearInterpolation< Key, Value >
• getOutsideReferencePoint_1() : BilinearInterpolation< Key, Value >
• getOverallQuality() : Feature
• getParam() : AcqusHandler , ModelDescription< D > , TheoreticalSpectrumGenerationDialog , TOPPASToolVertex
• getParam_() : TOPPBase
• getParamArgument_() : TOPPBase
• getParamAsBool_() : TOPPBase
• getParamAsDouble_() : TOPPBase
• getParamAsDoubleList_() : TOPPBase
• getParamAsInt_() : TOPPBase
• getParamAsIntList_() : TOPPBase
• getParamAsString_() : TOPPBase
• getParamAsStringList_() : TOPPBase
• getParameterByName_() : TOPPBase
• getParameters() : DefaultParamHandler , FeatureFinder , MSSim , TransformationModel , TransformationModelLinear
• getParameters_() : TOPPASToolVertex
• getParentMass() : Weights
• getParsingSuccess() : IndexedMzMLHandler
• getPartialSequence() : SequestInfile
• getPassThreshold() : IdentificationHit
• getPath_() : MzMLValidator , SemanticValidator
• getPathLabelToFractionGroupMapping() : ExperimentalDesign
• getPathLabelToFractionMapping() : ExperimentalDesign
• getPathLabelToSampleMapping() : ExperimentalDesign
• getPathToFile() : SourceFile
• getPeak() : MultiplexFilteredMSExperiment , PeakIndex
• getPeakAnnotations() : PeptideHit
• getPeakArea_() : PeakPickerCWT
• getPeakCentroid_() : PeakPickerCWT
• getPeakCount() : FeatureFinderAlgorithmPickedHelperStructs::MassTraces
• getPeakData() : LayerData
• getPeakDataMuteable() : LayerData
• getPeakEndPoints_() : PeakPickerCWT
• getPeakFlag() : FeatureFinder
• getPeakIndex() : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
• getPeakIntensitySum() : ProcessData
• getPeakMap() : MSSim , SpectrumCheapDPCorr
• getPeakMassTolerance() : InspectInfile , MascotInfile , SequestInfile
• getPeakPosition() : Annotation1DPeakItem
• getPeaksPerPeptide() : MultiplexIsotopicPeakPattern
• getPeakWidth() : PeakWidthEstimator
• getPeakWidth_() : RawMSSignalSimulation
• getPen() : Annotations1DContainer
• getPenalties() : OptimizePeakDeconvolution , OptimizePick , TwoDOptimization
• getPeptideByRef() : TargetedExperiment , LightTargetedExperiment
• getPeptideEvidences() : PeptideHit
• getPeptideGroupLabel() : Peptide
• getPeptideHit() : ProteinResolver
• getPeptideIdentification() : ProteinResolver
• getPeptideIdentifications() : BaseFeature , SpectrumSettings
• getPeptideMassUnit() : SequestInfile
• getPeptideOptionalColumnNames() : MzTab
• getPeptideProbabilityThreshold() : SuperHirnParameters
• getPeptideProteinCounter() : PrecursorIonSelection
• getPeptideRef() : IncludeExcludeTarget , ReactionMonitoringTransition , LightTransition
• getPeptideResults() : PeptideAndProteinQuant
• getPeptides() : TargetedExperiment
• getPeptideSectionRows() : MzTab
• getPeptideSequence_() : PercolatorOutfile
• getPercentage() : Gradient
• getPercentageFactor() : SpectrumCanvas
• getPercentageIntensityElutionBorderVariation() : SuperHirnParameters
• getPercentages() : Gradient
• getPermut() : CompNovoIdentificationBase::Permut
• getPh() : Digestion
• getPiValue() : Residue
• getPka() : Residue
• getPkb() : Residue
• getPkc() : Residue
• getPoints() : GridBasedCluster
• getPolarity() : InstrumentSettings , IonSource
• getPoolFile() : DocumentIDTagger
• getPos() : ChromatogramPeak , Peak1D
• getPosition() : Annotation1DCaret , Annotation1DPeakItem , Annotation1DTextItem , ChromatogramPeak , AcqusHandler , AveragePosition< D > , Peak1D , Peak2D
• getPositionRange() : ConsensusFeature
• getPositionsAndParameters() : MzTabModification
• getPositiveCharges() : Compomer
• getPositiveGnuplotFormula_ : PosteriorErrorProbabilityModel
• getPossibleChargeStates() : Precursor
• getPPMs_() : IsotopeWaveletTransform< PeakType >
• getPpmToleranceForMZClustering() : SuperHirnParameters
• getPrecision() : Weights
• getPrecursor() : ChromatogramSettings
• getPrecursorActivation() : MSPeak
• getPrecursorAdduct() : SpectralMatch
• getPrecursorChrg() : MS2ConsensusSpectrum
• getPrecursorCHRG() : MS2Fragment , MSPeak
• getPrecursorChromatogram() : MRMTransitionGroup< ChromatogramType, TransitionType >
• getPrecursorChromatograms() : MRMTransitionGroup< ChromatogramType, TransitionType >
• getPrecursorCVTermList() : IncludeExcludeTarget , ReactionMonitoringTransition
• getPrecursorErrorType() : XTandemInfile
• getPrecursorFeature() : MRMFeature , MRMFeatureOpenMS , IMRMFeature , MockMRMFeature
• getPrecursorFeatureIDs() : MRMFeature
• getPrecursorIDs() : MRMFeatureOpenMS , IMRMFeature , MockMRMFeature
• getPrecursorMassErrorUnit() : XTandemInfile
• getPrecursorMassTolerance() : InspectInfile , MascotInfile , SequestInfile
• getPrecursorMassToleranceMinus() : XTandemInfile
• getPrecursorMassTolerancePlus() : XTandemInfile
• getPrecursorMZ() : IncludeExcludeTarget , MS2ConsensusSpectrum , MS2Fragment , MSPeak , ReactionMonitoringTransition , LightTransition
• getPrecursorRTandMZ() : InspectOutfile
• getPrecursors() : BinnedSpectrum , SpectrumSettings
• getPrecursorSpectrum() : MSExperiment
• getPredecessorStates() : HMMState
• getPrediction() : IncludeExcludeTarget , ReactionMonitoringTransition
• getPrefix() : AASequence
• getPressure() : HPLC
• getPrimaryIdentifier() : SpectralMatch
• getPrimaryMSRunPath() : ConsensusMap , FeatureMap , MSExperiment , ProteinIdentification
• getPrintDuplicateReferences() : SequestInfile
• getProbability_() : IDDecoyProbability
• getProcessedData() : ProcessData
• getProcessingActions() : DataProcessing
• getProcessingInfo_() : TOPPBase
• getProcessMemoryConsumption() : SysInfo
• getProcessPeakMemoryConsumption() : SysInfo
• getProduct() : ChromatogramSettings , ReactionMonitoringTransition
• getProductChargeState() : ReactionMonitoringTransition , LightTransition
• getProductCVTermList() : IncludeExcludeTarget
• getProductMZ() : IncludeExcludeTarget , ReactionMonitoringTransition , LightTransition
• getProductName() : AverageLinkage , BiGaussFitter1D , BiGaussModel , BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSpectrumCompareFunctor , BinnedSumAgreeingIntensities , ComplementFilter , ComplementMarker , CompleteLinkage , EGHFitter1D , EGHModel , EmgFitter1D , EmgModel , ExtendedIsotopeFitter1D , ExtendedIsotopeModel , FeatureFinderAlgorithmIsotopeWavelet , FeatureFinderAlgorithmMRM , FeatureFinderAlgorithmPicked , FeatureFinderAlgorithmSH , FeatureGroupingAlgorithmKD , FeatureGroupingAlgorithmLabeled , FeatureGroupingAlgorithmQT , FeatureGroupingAlgorithmUnlabeled , GaussFitter1D , GaussModel , GoodDiffFilter , GUIProgressLoggerImpl , ICPLLabeler , IntensityBalanceFilter , IsotopeDiffFilter , IsotopeFitter1D , IsotopeMarker , IsotopeModel , ITRAQLabeler , LabeledPairFinder , LabelFreeLabeler , MapAlignmentEvaluationAlgorithmPrecision , MapAlignmentEvaluationAlgorithmRecall , MarkerMower , NeutralLossDiffFilter , NeutralLossMarker , O18Labeler , PeakAlignment , PeakMarker , PeakSpectrumCompareFunctor , PoseClusteringAffineSuperimposer , PoseClusteringShiftSuperimposer , ProductModel< 2 > , QTClusterFinder , SILACLabeler , SimplePairFinder , SingleLinkage , SpectraSTSimilarityScore , SpectrumAlignmentScore , SpectrumCheapDPCorr , SpectrumPrecursorComparator , StablePairFinder , SteinScottImproveScore , TICFilter , ZhangSimilarityScore
• getProducts() : SpectrumSettings
• getProgressLogger() : FeatureFinderIdentificationAlgorithm
• getPropertiesB() : GridBasedCluster
• getPropertyA() : GridBasedCluster
• getPropertyVector_() : PeakIntensityPredictor
• getProteinAccession() : PeptideEvidence
• getProteinAccessions_() : IDRipper
• getProteinByRef() : TargetedExperiment
• getProteinGroups() : ProteinIdentification
• getProteinGroups_() : IdXMLFile
• getProteinHits_() : IDRipper
• getProteinIdentification_() : IDRipper
• getProteinIdentifications() : ConsensusMap , ExperimentalSettings , FeatureMap
• getProteinMassFilter() : SequestInfile
• getProteinOptionalColumnNames() : MzTab
• getProteinPeptideSequenceMap() : PrecursorIonSelectionPreprocessing
• getProteinProbability() : PSProteinInference
• getProteinPTMap() : PrecursorIonSelectionPreprocessing
• getProteinResults() : PeptideAndProteinQuant
• getProteinRTMap() : PrecursorIonSelectionPreprocessing
• getProteins() : TargetedExperiment , LightTargetedExperiment
• getProteinSectionRows() : MzTab
• getProtMasses() : PrecursorIonSelectionPreprocessing
• getProtonDistribution() : ProtonDistributionModel
• getPseudoCounts() : HiddenMarkovModel
• getPSIID() : DigestionEnzymeProtein
• getPSIMODAccession() : ResidueModification
• getPSMOptionalColumnNames() : MzTab
• getPSMSectionRows() : MzTab
• getPT() : PrecursorIonSelectionPreprocessing
• getPublications() : TargetedExperiment
• getPValue() : SVMWrapper
• getQuality() : BaseFeature , Feature , QTCluster
• getQuantMethod() : MassTrace
• getQuantMethods() : AbsoluteQuantitation
• getQuantMethodsAsMap() : AbsoluteQuantitation
• getQueryMass() : AccurateMassSearchResult
• getRandomSample_() : FeatureFinderIdentificationAlgorithm
• getRandomSequence_() : MRMAssay
• getRank() : IdentificationHit , PeptideHit , ProteinHit
• getRatios() : ConsensusFeature
• getReagentName() : Modification
• getReference_() : MapAlignmentAlgorithmIdentification
• getReferenceChannel() : IsobaricQuantitationMethod , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTTenPlexQuantitationMethod
• getReferencingHits() : PeptideIdentification
• getRefIntensity() : IsotopeWaveletTransform< PeakType >::TransSpectrum
• getReflectronState() : MassAnalyzer
• getRefMZ() : CalibrationData
• getRefSpectrum() : IsotopeWaveletTransform< PeakType >::TransSpectrum
• getRegEx() : DigestionEnzyme
• getRegExDescription() : DigestionEnzyme
• getRegionEndpoints_() : TwoDOptimization
• getRemovePrecursorNearPeaks() : SequestInfile
• getRequirementLevel() : CVMappingRule
• getResidue() : AASequence , ResidueDB
• getResidues() : ResidueDB
• getResidueSets() : Residue , ResidueDB
• getResiduesInUpperCase() : SequestInfile
• getResidueTypeName() : Residue
• getResolution() : IonDetector , MassAnalyzer
• getResolution_() : RawMSSignalSimulation
• getResolutionMethod() : MassAnalyzer
• getResolutionType() : MassAnalyzer
• getResponse() : NetworkGetRequest
• getResultMap() : FeatureGroupingAlgorithmUnlabeled
• getResults() : GridBasedClustering< Metric > , MascotRemoteQuery , ProteinResolver
• getRetentionTime() : CentroidPeak , IncludeExcludeTarget , MS2Info , ReactionMonitoringTransition , PeptideCompound
• getRetentionTimes_() : MapAlignmentAlgorithmIdentification
• getRetentionTimeType() : PeptideCompound
• getRetentionTimeUnit() : PeptideCompound
• getRevision() : VersionInfo
• getRIAClusterCenter() : MetaProSIPClustering
• getRightEndpoint() : PeakShape
• getRightPaddingIndex() : ContinuousWaveletTransform
• getRightSplitter() : HistogramDialog , HistogramWidget
• getROBB760107() : AAIndex
• getRoundMasses() : CoarseIsotopePatternGenerator
• getRow() : CsvFile
• getRowIndex() : LPWrapper
• getRowLowerBound() : LPWrapper
• getRowName() : LPWrapper
• getRowUpperBound() : LPWrapper
• getRSD() : LinearRegression
• getRSquared() : LinearRegression
• getRT() : CalibrationData , ChromatogramPeak , FeatureOpenMS , GridFeature , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , IsotopeWaveletTransform< PeakType >::TransSpectrum , MRMFeatureOpenMS , MSSpectrum , MultiplexFilteredMSExperiment , MultiplexFilteredPeak , MultiplexSatelliteProfile , MZTrafoModel , Peak2D , PeptideIdentification , PrecursorIonSelectionPreprocessing , RetentionTime , IFeature , IMRMFeature , MockFeature , MockMRMFeature
• getRTBounds() : FeatureFinderAlgorithmPickedHelperStructs::MassTraces
• getRTidx() : MultiplexFilteredPeak , MultiplexSatelliteCentroided
• getRTProbability() : PrecursorIonSelectionPreprocessing
• getRTProbability_() : PrecursorIonSelectionPreprocessing
• getRTProfileIntensity_() : ITRAQLabeler
• getRTRange() : FeatureFileOptions , PeakFileOptions
• getRTRegions_() : FeatureFinderIdentificationAlgorithm
• getRTShift() : Adduct , Compomer
• getRunIDs() : QcMLFile
• getRunNames() : QcMLFile
• getSample() : ExperimentalDesign , ExperimentalSettings
• getSamples() : BaseModel< D > , ExperimentalDesign::SampleSection , InterpolationModel , ProductModel< 2 >
• getSampleSection() : ExperimentalDesign
• getSamplesLabelsList() : MultiplexDeltaMassesGenerator
• getSamplingGrid_() : RawMSSignalSimulation
• getSatellites() : MultiplexFilteredPeak
• getSatellitesProfile() : MultiplexFilteredPeak
• getSaveFileName() : TOPPASScene
• getScale() : ContinuousWaveletTransform , LinearInterpolation< Key, Value > , ProductModel< 2 >
• getScale_0() : BilinearInterpolation< Key, Value >
• getScale_1() : BilinearInterpolation< Key, Value >
• getScalingFactor() : InterpolationModel
• getScanCount() : MzXMLHandler
• getScanDirection() : MassAnalyzer
• getScanLaw() : MassAnalyzer
• getScanMergeKey_() : PercolatorFeatureSetHelper
• getScanMode() : InstrumentSettings
• getScanNumber() : Deisotoper
• getScanNumber_() : PrecursorIonSelectionPreprocessing
• getScanRate() : MassAnalyzer
• getScanTime() : MassAnalyzer
• getScanTRIndex() : SuperHirnParameters
• getScanWindows() : InstrumentSettings
• getScene() : TOPPASWidget
• getScene_() : TOPPASToolVertex
• getScopePath() : CVMappingRule
• getScore() : CompNovoIdentificationBase::Permut , DeconvPeak , FeatureHypothesis , MRMFeature , PeptideHit , ProteinHit
• getScores() : MRMFeature
• getScoreType() : PeptideIdentification , PercolatorOutfile , ProteinIdentification
• getSdIntens_() : IsotopeWaveletTransform< PeakType >
• getSearchEngine() : ProteinIdentification
• getSearchEngineAndVersion() : InspectOutfile , PepNovoOutfile
• getSearchEngineVersion() : ProteinIdentification
• getSearchIdentifier() : MascotRemoteQuery
• getSearchIdentifierFromFilePath() : MascotRemoteQuery
• getSearchParameters() : ProteinIdentification
• getSearchType() : MascotInfile
• getSecondaryIdentifier() : SpectralMatch
• getSectionDescription() : Param
• getSeed() : UniqueIdGenerator
• getSelectedItems() : Annotations1DContainer
• getSelectedPen() : Annotations1DContainer
• getSeparator_() : QuantitativeExperimentalDesign
• getSequence() : IMSElement , PeptideHit , ProteinHit , TheoreticalSpectrumGenerationDialog
• getSequenceHeaderFilter() : SequestInfile
• getSequences() : InspectOutfile , SequestOutfile
• getShortenedNumber_() : AxisPainter
• getShortName() : Residue
• getShortReportFlag() : Deisotoper
• getShowFragmentIons() : SequestInfile
• getSideChainBasicity() : Residue
• getSigma() : EGHTraceFitter , GaussTraceFitter , IsotopeWaveletTransform< PeakType >
• getSignal() : ContinuousWaveletTransform
• getSignalLength() : ContinuousWaveletTransform
• getSignalToNoise() : CentroidPeak , LCElutionPeak , MSPeak , SHFeature , SignalToNoiseEstimator< Container >
• getSignalToNoiseBackground() : LCElutionPeak
• getSignificanceBorders() : SVMWrapper
• getSignificanceThreshold() : PeptideIdentification , ProteinIdentification
• getSimilarity() : SpectraMerger::SpectraDistance_
• getSimilarity_() : ConsensusIDAlgorithmPEPIons , ConsensusIDAlgorithmPEPMatrix , ConsensusIDAlgorithmSimilarity
• getSimulatedFeatures() : MSSim
• getSingleMass() : Adduct
• getSites_() : AScore
• getSize() : ClusterProxyKD , ContinuousWaveletTransform , FeatureHypothesis , AcqusHandler , MassTrace , MSExperiment
• getSizeOnly() : FeatureFileOptions
• getSkipXMLChecks() : PeakFileOptions
• getSlope() : LinearRegression , LinearRegressionWithoutIntercept
• getSmallestScore() : PosteriorErrorProbabilityModel
• getSmallMoleculeOptionalColumnNames() : MzTab
• getSmallMoleculeSectionRows() : MzTab
• getSMILESString() : SpectralMatch
• getSmoothedIntensities() : MassTrace
• getSnapFactor() : SpectrumCanvas
• getSoftware() : DataProcessing , Instrument , TargetedExperiment
• getSolver() : LPWrapper , PSProteinInference
• getSortChromatogramsByRT() : PeakFileOptions
• getSortSpectraByMZ() : PeakFileOptions
• getSourceClassification() : ResidueModification
• getSourceClassificationName() : ResidueModification
• getSourceFeatureIndex() : AccurateMassSearchResult
• getSourceFile() : ChromatogramSettings , SpectrumSettings
• getSourceFiles() : ExperimentalSettings , TargetedExperiment
• getSourceOutParam() : TOPPASEdge
• getSourceOutParamName() : TOPPASEdge
• getSourceVertex() : TOPPASEdge
• getSpacing() : ContinuousWaveletTransform
• getSparseWindowPercent() : SignalToNoiseEstimatorMedian< Container >
• getSpecificity() : EnzymaticDigestion
• getSpecificityByName() : EnzymaticDigestion
• getSpecificityType() : Modification
• getSpecRef() : MzTabSpectraRef
• getSpectra() : InspectInfile , MSExperiment
• getSpectraByRT() : ISpectraReader , SpectrumAccessOpenMS , SpectrumAccessOpenMSCached , SpectrumAccessOpenMSInMemory , SpectrumAccessSqMass , SpectrumAccessTransforming , ISpectrumAccess
• getSpectraIdentificationViewWidget() : TOPPViewBase
• getSpectraIndex() : CachedMzMLHandler
• getSpectraIndicesbyRT() : MzMLSqliteHandler
• getSpectraMetaInfo() : SpectrumAccessOpenMS , SpectrumAccessOpenMSCached
• getSpectraScanNumberEnd() : ClusteredMS2ConsensusSpectrum
• getSpectraScanNumberStart() : ClusteredMS2ConsensusSpectrum
• getSpectrum() : CachedmzML , LayerData , MSExperiment , OnDiscMSExperiment , PeakIndex , TheoreticalSpectrumGenerator
• getSpectrumAccessOpenMSPtr() : SimpleOpenMSSpectraFactory
• getSpectrumAlignment() : SpectrumAlignment
• getSpectrumAlignmentFastCharge() : OPXLSpectrumProcessingAlgorithms
• getSpectrumById() : ISpectraReader , IndexedMzMLHandler , OnDiscMSExperiment , SpectrumAccessOpenMS , SpectrumAccessOpenMSCached , SpectrumAccessOpenMSInMemory , SpectrumAccessQuadMZTransforming , SpectrumAccessSqMass , SpectrumAccessTransforming , ISpectrumAccess
• getSpectrumById_helper_() : IndexedMzMLHandler
• getSpectrumDifference_() : AScore
• getSpectrumIdentifications() : Identification
• getSpectrumMetaById() : ISpectraReader , SpectrumAccessOpenMS , SpectrumAccessOpenMSCached , SpectrumAccessOpenMSInMemory , SpectrumAccessSqMass , SpectrumAccessTransforming , ISpectrumAccess
• getSpectrumMetaData() : SpectrumMetaDataLookup
• getSpectrumParameters() : TOPPViewBase
• getSpectrumWidget() : SpectrumCanvas
• getStandDevRes() : LinearRegression
• getStandErrSlope() : LinearRegression
• getStart() : PeptideEvidence
• getStartPoint() : Annotation1DDistanceItem
• getStartScan() : MS2ConsensusSpectrum , MS2Fragment
• getStartTR() : MS2ConsensusSpectrum , MS2Fragment
• getState() : HiddenMarkovModel , Sample
• getStatistics() : PeptideAndProteinQuant
• getStatus() : LPWrapper , TOPPASToolVertex
• getStream() : LogConfigHandler , StreamHandler
• getStreamTypeByName_() : LogConfigHandler
• getString() : RNPxlReportRow , RNPxlReportRowHeader , StringView
• getStringDataArrays() : MSChromatogram , MSSpectrum
• getStringList_() : TOPPBase
• getStringOption_() : TOPPBase
• getSubordinates() : Feature
• getSubsamples() : Sample
• getSubsection_() : TOPPBase
• getSubsectionDefaults_() : TOPPBase
• getSubsections() : DefaultParamHandler
• getSubsequence() : AASequence
• getSubtreeStatus() : TOPPASVertex
• getSuccessorStates() : HMMState
• getSuffix() : AASequence
• getSumFormula() : SpectralMatch
• getSummedFeatureIntensity() : FeatureHypothesis
• getSupportedCharges() : SvmTheoreticalSpectrumGeneratorSet
• getSVCProbabilities() : SVMWrapper
• getSvmModel() : SvmTheoreticalSpectrumGeneratorSet
• getSVRProbability() : SVMWrapper
• getSwath_() : MRMAssay
• getSymbol() : Element
• getSymbols() : ElementDB
• getSymmetricMeasure() : PeakShape
• getSynonyms() : DigestionEnzyme , Residue , ResidueModification
• getSystemParameterDefaults_() : File
• getSystemParameters() : File
• getSystemTime() : StopWatch
• getTableSteps() : IsotopeWavelet
• getTableWidget() : SpectraIdentificationViewWidget
• getTabWidth() : FuzzyStringComparator
• getTagCount() : InspectInfile
• getTags() : Param
• getTargetCVTerms() : TargetedExperiment
• getTargetInParam() : TOPPASEdge
• getTargetInParamName() : TOPPASEdge
• getTargetNucleotideToFragmentAdducts() : RNPxlSearch::RNPxlParameterParsing
• getTargetVertex() : TOPPASEdge
• getTau() : EGHTraceFitter
• getTaxon() : XTandemInfile
• getTaxonomy() : MascotInfile
• getTaxonomyFilename() : XTandemInfile
• getTechnicalRng() : SimRandomNumberGenerator
• getTempDir() : TOPPASScene
• getTempDirectory() : File
• getTemperature() : Digestion , HPLC
• getTemporaryFile() : File
• getTerm() : ControlledVocabulary
• getTermByName() : ControlledVocabulary
• getTermName() : CVMappingTerm
• getTerms() : ControlledVocabulary
• getTermSpecificity() : ResidueModification
• getTermSpecificityName() : ResidueModification
• getText() : Annotation1DItem
• getTheoreticalmaxPosition() : FeatureFinderAlgorithmPickedHelperStructs::MassTraces
• getTheta() : Deisotoper
• getThreeLetterCode() : Residue
• getThreePrimeGain() : DigestionEnzymeRNA
• getThreshold() : ClusterHierarchical
• getTIC() : MSExperiment
• getTime() : DateTime , VersionInfo
• getTimeArray() : Chromatogram , OSChromatogram
• getTimepoints() : Gradient
• getTOFTotalPathLength() : MassAnalyzer
• getTolerance() : SpectrumAlignmentDialog
• getToleranceMZ() : SuperHirnParameters
• getTool() : ToolsDialog
• getToolDescriptions() : ToolDescriptionHandler
• getToolNamesFromINI() : INIUpdater
• getToolToolStatus_() : TOPPASEdge
• getToolUserDefaults_() : TOPPBase
• getTopoNr() : TOPPASVertex
• getTOPPToolList() : ToolHandler
• getTR() : MS2ConsensusSpectrum , MS2Fragment
• getTrace() : Param::ParamIterator
• getTraceLength() : MassTrace
• getTransform() : IsotopeWaveletTransform< PeakType >
• getTransformationModel() : AbsoluteQuantitationMethod
• getTransformationModelParams() : AbsoluteQuantitationMethod
• getTransformHighRes() : IsotopeWaveletTransform< PeakType >
• getTransIntensity() : IsotopeWaveletTransform< PeakType >::TransSpectrum
• getTransition() : MRMTransitionGroup< ChromatogramType, TransitionType >
• getTransitionGroupID() : MRMTransitionGroup< ChromatogramType, TransitionType >
• getTransitionProbability() : HiddenMarkovModel
• getTransitionProbability_() : HiddenMarkovModel
• getTransitions() : MRMTransitionGroup< ChromatogramType, TransitionType > , TargetedExperiment , LightTargetedExperiment
• getTransitionsMuteable() : MRMTransitionGroup< ChromatogramType, TransitionType >
• getTreatment() : Sample
• getTreeWidget() : SpectraViewWidget
• getTrTol() : SuperHirnParameters
• getTSVHeader_() : TransitionTSVFile
• getTValue() : LinearRegression
• getType() : FileHandler , IonDetector , MassAnalyzer , OPXLDataStructs::ProteinProteinCrossLink , SampleTreatment , SpectrumSettings , TOPPASToolVertex
• getTypeByContent() : FileHandler
• getTypeByFileName() : FileHandler
• getTypes() : ToolHandler
• getULOD() : AbsoluteQuantitationMethod
• getULOQ() : AbsoluteQuantitationMethod
• getUnassignedPeptideIdentifications() : ConsensusMap , FeatureMap
• getUnbiasedSample_() : FeatureFinderIdentificationAlgorithm
• getUnchargedMass() : Precursor
• getUniModAccession() : ResidueModification
• getUniModRecordId() : ResidueModification
• getUniqueId() : UniqueIdGenerator , UniqueIdInterface
• getUniqueName() : File
• getUnit() : CVTerm , DataValue , MetaInfoRegistry
• getUnmodifiedAASequence_() : ICPLLabeler
• getUnmodifiedSequence_() : SILACLabeler
• getUpper() : LinearRegression
• getUpperRTBound() : EGHTraceFitter , GaussTraceFitter , TraceFitter
• getURL() : ContactPerson , TOPPASResource
• getUserDirectory() : File
• getUserTime() : StopWatch
• getUseTerm() : CVMappingTerm
• getUseTermName() : CVMappingTerm
• getUtilList() : ToolHandler
• getValidXWeights() : TransformationModel
• getValidYWeights() : TransformationModel
• getValue() : CVTerm , DistanceMatrix< Value > , EGHTraceFitter , GaussTraceFitter , IDFilter::GetMatchingItems< HitType, Entry > , Matrix< Value > , MetaInfo , MzTabParameter , Param , TraceFitter
• getValueAtRT() : SignalToNoiseOpenMS< ContainerT > , ISignalToNoise , MockSignalToNoise
• getValueByLambda() : IsotopeWavelet
• getValueByLambdaExact() : IsotopeWavelet
• getValueByLambdaExtrapol() : IsotopeWavelet
• getValueByMass() : IsotopeWavelet
• getVariableModificationNames() : ModificationDefinitionsSet
• getVariableModifications() : MascotInfile , ModificationDefinitionsSet
• getVariant() : Tagging
• getVASM830103() : AAIndex
• getVectorWout() : LocalLinearMap
• getVendor() : Instrument
• getVerboseLevel() : FuzzyStringComparator
• getVersion() : XMLFile , Software , VersionInfo
• getVersionStruct() : VersionInfo
• getVertexAt_() : TOPPASScene
• getVerticalProjection() : Spectrum2DWidget
• getVisibleArea() : SpectrumCanvas
• getVisibleConsensusData() : SpectrumCanvas
• getVisibleFeatureData() : SpectrumCanvas
• getVisibleIdentifications() : SpectrumCanvas
• getVisiblePeakData() : SpectrumCanvas
• getVolume() : Sample
• getWantedRecords() : InspectOutfile
• getWavelet() : ContinuousWaveletTransform
• getWeight() : CalibrationData , Weights , AveragePosition< D > , PrecursorIonSelectionPreprocessing , WeightWrapper
• getWeightMode() : WeightWrapper
• getWhitelist() : FuzzyStringComparator
• getWidth() : BaseFeature , CentroidData , FeatureHandle
• getWILM950102() : AAIndex
• getWindowId() : EnhancedTabBarWidgetInterface , SpectrumWidget , TOPPASWidget
• getWorkspace() : TOPPViewBase
• getWriteIndex() : PeakFileOptions
• getWriteSupplementalData() : PeakFileOptions
• getX() : DPosition< D, TCoordinateType >
• getXCoord() : QTCluster
• getXCorrMatrix() : MRMScoring
• getXIC_() : PSLPFormulation
• getXIntercept() : LinearRegression
• getXLinkIonSpectrum() : TheoreticalSpectrumGeneratorXLMS
• getxQuestBase64EncodedSpectrum_() : XQuestResultXMLFile
• getXRefTypeName() : ControlledVocabulary::CVTerm
• getXSize() : SaveImageDialog
• getXTandemID() : DigestionEnzymeProtein
• getY() : DPosition< D, TCoordinateType >
• getYCoord() : QTCluster
• getYSize() : SaveImageDialog
• getZoomScan() : InstrumentSettings
• glm_ : ConfidenceScoring
• global_LR : SIPPeptide
• GlobalExceptionHandler() : GlobalExceptionHandler
• go() : Deisotoper
• go_terms : MzTabProteinSectionRow
• GoodDiffFilter() : GoodDiffFilter
• gotRedirect() : MascotRemoteQuery
• gpu_ids_ : FeatureFinderAlgorithmIsotopeWavelet
• Gradient() : Gradient
• gradient : LayerData , MultiGradientSelector
• gradient_ : HPLC , MultiGradientSelector
• gradient_area_width_ : MultiGradientSelector
• gradient_max_ : RTSimulation
• gradient_min_ : RTSimulation
• gradientdata_ : GradientVisualizer
• gradientlabel_ : GradientVisualizer
• GradientVisualizer() : GradientVisualizer
• GREATER_EQUAL : DataFilters
• Grid : HashGrid< Cluster > , QTClusterFinder
• grid_ : GridBasedClustering< Metric > , HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator , RawMSSignalSimulation , SpectrumWidget
• grid_at() : HashGrid< Cluster >
• grid_begin() : HashGrid< Cluster >
• grid_dimension : HashGrid< Cluster >
• grid_dimension_ : HashGrid< Cluster >
• grid_end() : HashGrid< Cluster >
• grid_intensity_ : Spectrum3DOpenGLCanvas
• grid_it_ : HashGrid< Cluster >::ConstIterator , HashGrid< Cluster >::Iterator
• grid_iterator : HashGrid< Cluster >::ConstIterator , HashGrid< Cluster > , HashGrid< Cluster >::Iterator
• grid_line_ : AxisWidget
• grid_mz_ : Spectrum3DOpenGLCanvas
• grid_rt_ : Spectrum3DOpenGLCanvas
• grid_spacing_mz_ : MultiplexClustering
• grid_spacing_rt_ : MultiplexClustering
• grid_spacing_x_ : ClusteringGrid
• grid_spacing_y_ : ClusteringGrid
• GridBasedCluster() : GridBasedCluster
• GridBasedClustering() : GridBasedClustering< Metric >
• GridFeature() : GridFeature
• gridLines() : AxisWidget
• gridlines_ : Spectrum3DOpenGLCanvas
• gridLinesShown() : SpectrumCanvas
• GridVector : AxisPainter , AxisTickCalculator , AxisWidget
• ground_ : Spectrum3DOpenGLCanvas
• group() : FeatureGroupingAlgorithm , FeatureGroupingAlgorithmKD , FeatureGroupingAlgorithmLabeled , FeatureGroupingAlgorithmQT , FeatureGroupingAlgorithmUnlabeled
• group_() : FeatureGroupingAlgorithmKD , FeatureGroupingAlgorithmQT
• group_id : TransitionTSVFile::TSVTransition
• group_label_2d_ : TOPPViewBase
• group_unassigned_2d_ : TOPPViewBase
• groups_ : CalibrationData
• guessExperimentType_() : IBSpectraFile
• GUI : ProgressLogger
• gui_ : TOPPASScene
• GUIHelpers() : GUIHelpers
• GUIProgressLoggerImpl() : GUIProgressLoggerImpl
• GumbelDistributionFitResult() : GumbelDistributionFitter::GumbelDistributionFitResult
• GumbelDistributionFitter() : GumbelDistributionFitter
• gzerror_ : GzipIfstream
• gzfile_ : GzipIfstream
• gzip_ : GzipInputStream
• GzipIfstream() : GzipIfstream
• GzipInputStream() : GzipInputStream