| OpenMS 2.5.0

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

### - g -

- g : IDBoostGraph
- GAMMA : SVMWrapper
- gamma_ : MessagePasserFactory< Label >
- 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
- gene_name : LightCompound
- GeneName : TransitionTSVFile::TSVTransition
- generateCandidates() : DeNovoAlgorithm
- generateDecoyAssays_() : MRMAssay
- generateDecoyInSilicoMap_() : MRMAssay
- generateDecoys() : MRMDecoy
- generateDecoySequences_() : MRMAssay
- generateDescriptorSet_() : SvmTheoreticalSpectrumGenerator
- generateDistributionImage_() : IDDecoyProbability
- generateKnockoutDeltaMasses() : MultiplexDeltaMassesGenerator
- generateLFQInput_() : NucleicAcidSearchEngine
- generateMapsCentroided_() : FeatureFinderMultiplexAlgorithm
- generateMapsProfile_() : FeatureFinderMultiplexAlgorithm
- generateMSESpectra_() : RawTandemMSSignalSimulation
- generateMzTabMetaDataSection_() : MzTabFile
- generateMzTabNucleicAcidHeader_() : MzTabFile
- generateMzTabOligonucleotideHeader_() : MzTabFile
- generateMzTabOSMHeader_() : MzTabFile
- generateMzTabPeptideHeader_() : MzTabFile
- generateMzTabProteinHeader_() : MzTabFile
- generateMzTabPSMHeader_() : MzTabFile
- generateMzTabSection_() : MzTabFile
- generateMzTabSectionRow_() : MzTabFile
- generateMzTabSmallMoleculeHeader_() : MzTabFile
- generateMzTabStringFromFixedModifications() : MzTab
- generateMzTabStringFromModifications() : MzTab
- generateMzTabStringFromVariableModifications() : MzTab
- 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
- generateTheoreticalPeptidoforms_() : MRMAssay
- generateTheoreticalPeptidoformsDecoy_() : MRMAssay
- 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 , NASequence , 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
- getAAByMass_() : Tagger
- getAAFrequencies() : AASequence
- getAbsolute() : FineIsotopePatternGenerator
- getAbsoluteMZTolerance_() : IDMapper
- getAbundance() : IMSIsotopeDistribution
- getAbundances() : IMSIsotopeDistribution
- getACAndACType() : InspectOutfile , SequestOutfile
- getAcceptableAbsolute() : FuzzyStringComparator
- getAcceptableRelative() : FuzzyStringComparator
- getAccession() : CVMappingTerm , CVTerm , MzTabParameter , ProteinHit
- getAccession_() : PeptideAndProteinQuant
- getAccessionToGroupMap_() : MSstatsFile
- 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 >
- 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 , NASequence , Residue
- getAveragine() : IsotopeWavelet
- getAvgDistance() : ClusterProxyKD
- getAvgMass() : Ribonucleotide
- 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_() : SimpleTSGXLMS , TheoreticalSpectrumGeneratorXLMS
- getBackwardVariable_() : HiddenMarkovModel
- getBase_() : UniqueIdIndexer< RandomAccessContainer >
- getBaseDir() : FIAMSScheduler
- getBaselossFormula() : Ribonucleotide
- getBaseName() : PeptideIdentification
- getBasePeak() : MSSpectrum
- getBest_() : PeptideAndProteinQuant
- getBestFeature() : MRMTransitionGroup< ChromatogramType, TransitionType >
- getBestHit() : IDFilter
- getBestHitSequence_() : StablePairFinder
- getBestMatchPerQuery() : IdentificationData
- getBestModificationByDiffMonoMass() : ModificationsDB
- getBinIndex() : BinnedSpectrum
- getBinIntensity() : BinnedSpectrum
- getBinLowerMZ() : BinnedSpectrum
- getBins() : BinnedSpectrum
- getBinSize() : BinnedSpectrum
- getBinSizes() : FIAMSDataProcessor
- getBinSpread() : BinnedSpectrum
- getBiologicalRng() : SimRandomNumberGenerator
- getBlacklist() : FeatureFinderMultiplexAlgorithm , MultiplexFiltering
- getBlind() : InspectInfile
- getBothGnuplotFormula() : PosteriorErrorProbabilityModel
- getBoundary() : MascotInfile
- getBoundingBox() : ConvexHull2D , GridBasedCluster
- getBPI_() : Ms2SpectrumStats
- getBranch() : VersionInfo
- getC() : QuadraticRegression
- getC13MassError() : DeconvPeak
- getCalculatedMassToCharge() : IdentificationHit
- getCalculatedMZ() : AccurateMassSearchResult
- getCalibrationPoints() : InternalCalibration
- getCandidates() : SiriusAdapterAlgorithm
- 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
- getCentroidedExperiment() : MultiplexFiltering
- getCentroidMZ() : FeatureHypothesis , MassTrace
- getCentroidRT() : FeatureHypothesis , MassTrace
- getCentroidSD() : MassTrace
- getCentroidWindowWidth() : SuperHirnParameters
- getChannelInformation() : IsobaricQuantitationMethod , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
- getChannelIntensityName() : BaseLabeler
- getCharge() : AccurateMassSearchResult , Adduct , AdductInfo , BaseFeature , ChargePair , DeconvPeak , EmpiricalFormula , ExtendedIsotopeModel , FeatureHandle , FeatureHypothesis , IdentificationHit , IsotopeModel , MultiplexIsotopicPeakPattern , OptimizePeakDeconvolution , PeptideHit , Precursor
- getChargeConsensus() : MSSim
- getChargeContribution_() : RTSimulation
- getChargeDistribution() : SwathQC
- getChargeRange() : ProteinIdentification::SearchParameters
- getCharges() : MascotInfile
- getChargeState() : PeptideCompound , TraMLProduct , LightCompound , Peptide
- getChargeStateIntensities() : ProtonDistributionModel
- getChargeValue_() : ProteinIdentification::SearchParameters
- 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
- getCode() : Ribonucleotide
- 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 , IDBoostGraph
- getComponentFeatureConcentrations() : AbsoluteQuantitationStandards
- getComponentName() : AbsoluteQuantitationMethod
- getCompoundByRef() : TargetedExperiment , LightTargetedExperiment
- getCompoundRef() : IncludeExcludeTarget , ReactionMonitoringTransition , LightTransition
- getCompounds() : TargetedExperiment , LightTargetedExperiment
- getCompression() : PeakFileOptions
- getCompressionTerm_() : MzMLHandlerHelper
- getConcentration() : Sample
- getConcentrationUnits() : AbsoluteQuantitationMethod
- getConditionalFragmentIsotopeDist() : EmpiricalFormula
- getConditionToPathLabelVector() : ExperimentalDesign
- getConditionToSampleMapping() : ExperimentalDesign
- getConf() : IsoSpecGeneratorWrapper , IsoSpecOrderedGeneratorWrapper , IsoSpecThresholdGeneratorWrapper , IsoSpecTotalProbGeneratorWrapper
- 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
- getCurrentProcessingStep() : IdentificationData
- getCurrentSpectrum() : LayerData
- getCurrentSpectrumIndex() : LayerData
- getCustomizations() : Instrument
- getCutOff() : BaseModel< D >
- getCutsAfterRegEx() : DigestionEnzymeRNA
- getCutsBeforeRegEx() : DigestionEnzymeRNA
- 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
- getDataProcessingSoftwares() : IdentificationData
- getDataProcessingSteps() : IdentificationData
- getDataQueries() : IdentificationData
- getDataRange() : MSExperiment , SpectrumCanvas
- getDate() : DateTime
- getDateTime() : ExperimentalSettings , ProteinIdentification
- getDb() : InspectInfile
- getDB() : MascotInfile , SqliteConnector
- getDBSearchParams() : IdentificationData
- getDBSearchSteps() : IdentificationData
- 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 , MRMFeatureFilter , 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
- getDiffAbsolute() : DaTrait , PpmTrait , ValueTrait
- getDiffAverageMass() : ResidueModification
- getDiffFormula() : ResidueModification
- getDiffMonoMass() : ResidueModification
- getDigestionTime() : Digestion
- getDirectory() : TOPPASOutputFilesDialog
- getDistance_() : QTClusterFinder
- getDocumentationURL() : TOPPBase
- getDoubleList_() : TOPPBase
- getDoubleOption_() : TOPPBase
- getDoubleParameter() : SVMWrapper
- getDownstreamNodes() : IDBoostGraph
- getDrawMode() : Spectrum1DCanvas
- getDriftTime() : MSSpectrum , Precursor , PeptideCompound , LightCompound
- getDriftTimeArray() : OSSpectrum
- getDriftTimeUnit() : MSSpectrum , Precursor
- 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
- getEmpiricalFormula() : AdductInfo
- 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_() : CompNovoIdentificationBase
- getExcludeTargets() : TargetedExperiment
- getExecutablePath() : File
- getExperiment() : InspectOutfile , MSSim
- getExperimentalMassToCharge() : IdentificationHit
- getExperimentalSettings() : MSExperiment , OnDiscMSExperiment
- getExperimentLabel() : PeptideIdentification
- getExperimentType() : ConsensusMap
- getExpSettingsFunc() : SwathQC
- getExpTableMaxIndex() : IsotopeWavelet
- getExternalToolConfigFiles_() : ToolHandler
- getExternalTools_() : ToolHandler
- getExternalToolsPath() : ToolHandler
- getExtraPeakInfo() : CentroidPeak , MSPeak
- getFactor_() : ZhangSimilarityScore
- getFactorColIdx() : ExperimentalDesign::SampleSection
- getFactors() : ExperimentalDesign::SampleSection
- getFactorValue() : ExperimentalDesign::SampleSection
- getFactory() : SingletonRegistry
- getFAUJ880111() : AAIndex
- 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
- getFeatureOnly() : SiriusAdapterAlgorithm
- 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
- getFivePrimeMod() : NASequence
- getFixedModificationNames() : ModificationDefinitionsSet
- getFixedModifications() : ModificationDefinitionsSet , PrecursorIonSelectionPreprocessing
- getFlag_() : TOPPBase
- getFlags() : Annotation1DTextItem
- getFloatDataArrayByName() : ProteinIdentification::ProteinGroup
- getFloatDataArrays() : MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
- getFlux() : HPLC
- getForceMQCompatability() : PeakFileOptions
- getForceTPPCompatability() : PeakFileOptions
- getFormat() : SaveImageDialog
- getFormula() : AASequence , Adduct , IsotopeModel , NASequence , Residue , ResidueModification , Ribonucleotide
- getFormulaString() : AccurateMassSearchResult
- getFormVersion() : MascotInfile
- getForwardLosses_() : SimpleTSGXLMS , 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
- getFragmentPositions_() : RNaseDigestion
- 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
- getHTMLCode() : Ribonucleotide
- getHTTPPeakListEnclosure() : MascotGenericFile
- getHullPoints() : ConvexHull2D
- getID() : Compomer , GridFeature
- getId() : IdentificationHit
- getID() : MS2Feature
- getId() : ResidueModification
- getID_() : DocumentIDTagger
- getId_() : XFDRAlgorithm
- getIDDetails_() : IDMapper
- getIdentification() : CompNovoIdentification , CompNovoIdentificationCID , DeNovoIdentification
- getIdentificationMZ_() : SpectrumCanvas
- getIdentifications() : CompNovoIdentification , CompNovoIdentificationBase , CompNovoIdentificationCID , DeNovoIdentification , MSSim
- getIdentifiedCompoundRef() : MoleculeQueryMatch
- getIdentifiedCompounds() : IdentificationData
- getIdentifiedOligoRef() : MoleculeQueryMatch
- getIdentifiedOligos() : IdentificationData
- getIdentifiedPeptideRef() : MoleculeQueryMatch
- getIdentifiedPeptides() : IdentificationData
- getIdentifier() : Acquisition , CVMappingRule , CVReference , DocumentIdentifier , PeptideIdentification , ProteinIdentification
- getInchiString() : SpectralMatch
- getIncludeTargets() : TargetedExperiment
- getIncorrectlyAssignedFitResult() : PosteriorErrorProbabilityModel
- getIncorrectlyAssignedGumbelFitResult() : PosteriorErrorProbabilityModel
- getIndex() : ClusteringGrid , FidHandler , IsotopicDist , KDTreeFeatureNode , ListUtils , MetaInfoRegistry
- getIndistinguishableProteins() : ProteinIdentification
- getIndividualIntensities() : AccurateMassSearchResult
- getInferenceEngine() : ProteinIdentification
- getInferenceEngineVersion() : ProteinIdentification
- getIniLocation_() : TOPPBase
- getInitialTrTolerance() : SuperHirnParameters
- getInletType() : IonSource
- getInput() : ToolsDialog
- getInputFilename() : XTandemInfile
- getInputFiles() : IdentificationData
- 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 , RibonucleotideDB
- getInstance_() : UniqueIdGenerator
- getInstitution() : ContactPerson
- getInstrument() : ExperimentalSettings , HPLC , InspectInfile , MascotInfile
- getInstruments() : TargetedExperiment
- getInstrumentSettings() : ChromatogramSettings , SpectrumSettings
- getIntegerDataArrayByName() : ProteinIdentification::ProteinGroup
- getIntegerDataArrays() : MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
- getIntensity() : BaseModel< D > , CalibrationData , CentroidPeak , ChromatogramPeak , FeatureOpenMS , FidHandler , InterpolationModel , IsoSpecGeneratorWrapper , IsoSpecOrderedGeneratorWrapper , IsoSpecThresholdGeneratorWrapper , IsoSpecTotalProbGeneratorWrapper , 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 , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
- getIsotopeDistances() : FeatureHypothesis
- getIsotopeDistribution() : Element , EmpiricalFormula , IMSElement , IsotopeDistributionCache , IsotopeModel
- getIsotopeDistribution_() : FeatureFinderAlgorithmPicked
- getIsotopeMatrixAsStringList() : ItraqConstants
- getIsotopePatternIterations() : SiriusAdapterAlgorithm
- 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
- getLabelAsUInt() : ConsensusMap::ColumnHeader
- 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 , TextFile
- getLinearInterpolation() : IsotopeWaveletTransform< PeakType >
- getLinearIonSpectrum() : SimpleTSGXLMS , 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
- getLogIntensity() : IsoSpecGeneratorWrapper , IsoSpecOrderedGeneratorWrapper , IsoSpecThresholdGeneratorWrapper , IsoSpecTotalProbGeneratorWrapper
- 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 , IsoSpecGeneratorWrapper , IsoSpecOrderedGeneratorWrapper , IsoSpecThresholdGeneratorWrapper , IsoSpecTotalProbGeneratorWrapper , 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
- getMethodName() : IsobaricQuantitationMethod , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , TMTTenPlexQuantitationMethod
- getMethodOfCombination() : AcquisitionInfo
- getMIContrastMatrix() : MRMScoring
- getMIMatrix() : MRMScoring
- getMin() : IsotopeDistribution , RangeManager< D > , Spectrum1DGoToDialog
- getMinElementCoordinates() : DistanceMatrix< Value >
- getMinFeatureChrg() : SuperHirnParameters
- getMinFeatureMZ() : SuperHirnParameters
- getMinimalIntensityLevel() : ProcessData
- getMinInt() : RangeManager< D >
- getMinIntensity() : SpectrumCanvas , SuperHirnParameters
- getMinIonsMatched_() : XFDRAlgorithm
- getMinMZ() : MSExperiment , Spectrum2DGoToDialog
- getMinNbClusterMembers() : SuperHirnParameters
- getMinPeakGroupSize() : Deisotoper
- getMinRoundingError() : Weights
- getMinRT() : MSExperiment , Spectrum2DGoToDialog
- getMinScore() : XQuestResultXMLHandler , XQuestResultXMLFile
- getMinSpacing() : IsotopeWaveletTransform< PeakType >
- getMinTR() : SuperHirnParameters
- getMIPrecursorCombinedMatrix() : MRMScoring
- getMIPrecursorContrastMatrix() : MRMScoring
- 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 , ModifiedPeptideGenerator , PepNovoInfile , ProteinHit , SequestInfile , XTandemInfile
- getModifications_() : NucleicAcidSearchEngine
- getModificationsPerPeptide() : InspectInfile
- getModifiedAASequence_() : CompNovoIdentificationBase
- getModifiedResidue() : ResidueDB
- getModifiedStringFromAASequence_() : CompNovoIdentificationBase
- getModifString_() : IBSpectraFile
- getModOrSubstIdentifier() : MzTabModification
- getMoleculeQueryMatches() : IdentificationData
- getMoleculeType() : MoleculeQueryMatch
- getMonoisotopicFeatureIntensity() : FeatureHypothesis
- getMonoisotopicPeaks_() : TOFCalibration
- getMonoMass() : ResidueModification , Ribonucleotide
- getMonoWeight() : AASequence , Element , EmpiricalFormula , NASequence , 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
- getMultipleSpectra() : NucleicAcidSpectrumGenerator
- 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
- getMzPeakCutOffAtMonoPos() : IsotopeWavelet
- getMZRange() : FeatureFileOptions , PeakFileOptions
- getMZs() : FIAMSDataProcessor
- getMZShiftAt() : MultiplexIsotopicPeakPattern
- getMZShiftCount() : MultiplexIsotopicPeakPattern
- getMZTolerance() : TwoDOptimization
- getMzTolPpm() : SuperHirnParameters
- getNADH010106() : AAIndex
- getNADH010107() : AAIndex
- getName() : AdductInfo , Contaminants , CVReference , CVTerm , DefaultParamHandler , DigestionEnzyme , Element , BaseException , FragmentMassError , HMMState , IdentificationHit , IMSAlphabet , IMSElement , IncludeExcludeTarget , Instrument , MetaInfoDescription , MetaInfoRegistry , MissedCleavages , ModelDescription< D > , Ms2IdentificationRate , Ms2SpectrumStats , MSChromatogram , MSSpectrum , MzCalibration , MzTabParameter , Param::ParamIterator , QCBase , ReactionMonitoringTransition , Residue , ResidueModification , Ribonucleotide , RTAlignment , Sample , Software , TIC , 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() : SplineInterpolatedPeaks
- 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
- getNewCode() : Ribonucleotide
- getNewIdentifier_() : IDMergerAlgorithm
- getNewToolName() : INIUpdater
- getNextLogCounter_() : LogStreamBuf
- getNextPeakGroup() : CentroidData
- getNextPos() : SplineInterpolatedPeaks::Navigator
- getNextPrecursors() : PrecursorIonSelection
- getNextPrecursorsSeq() : PrecursorIonSelection
- getNextSpectrum_() : MascotGenericFile , MascotInfile
- getNoise() : CentroidData
- getNoiseSuppression() : XTandemInfile
- getNoMasstraceInfoIsotopePattern() : SiriusAdapterAlgorithm
- 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
- getNrCombos() : GridSearch< TupleTypes >
- getNrConnectedComponents() : IDBoostGraph
- 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
- getNucleicAcidOptionalColumnNames() : MzTab
- getNucleicAcidSectionRows() : MzTab
- getNucleotideReadingFrame() : SequestInfile
- getNumber() : Sample
- getNumberIterations() : OptimizePick
- getNumberOf() : EmpiricalFormula
- getNumberOfAtoms() : EmpiricalFormula
- getNumberOfChannels() : IsobaricQuantitationMethod , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , 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
- getNumpressConfigurationFloatDataArray() : PeakFileOptions
- 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 >
- getOligonucleotideOptionalColumnNames() : MzTab
- getOligonucleotideSectionRows() : MzTab
- getOMSSAID() : DigestionEnzymeProtein
- getOnDiscPeakData() : LayerData
- getOneLetterCode() : Residue
- getOOBM850104() : AAIndex
- getOpenMSDataPath() : File
- getOpenMSHomePath() : File
- getOptimizedParameters_() : EGHTraceFitter , GaussTraceFitter , TraceFitter
- getOptionalColumnNames_() : MzTab
- getOptions() : ConsensusXMLFile , DTA2DFile , FeatureXMLFile , FileHandler , IndexedMzMLFileLoader , MzMLHandler , MzDataFile , MzMLFile , MzXMLFile
- getOrder() : IonDetector , IonSource , MassAnalyzer
- getOrganism() : Sample
- getOrgIntensity() : CentroidPeak
- getOrigin() : ResidueModification , Ribonucleotide
- getOSAsString() : OpenMSOSInfo
- getOSMOptionalColumnNames() : MzTab
- getOSMSectionRows() : MzTab
- 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
- getParentMoleculeGroupings() : IdentificationData
- getParentMolecules() : IdentificationData
- getParsingSuccess() : IndexedMzMLHandler
- getPartialSequence() : SequestInfile
- getPassThreshold() : IdentificationHit
- getPath_() : MzMLValidator , SemanticValidator
- getPathLabelToConditionMapping() : ExperimentalDesign
- getPathLabelToFractionGroupMapping() : ExperimentalDesign
- getPathLabelToFractionMapping() : ExperimentalDesign
- getPathLabelToPrefractionationMapping() : ExperimentalDesign
- getPathLabelToSampleMapping() : ExperimentalDesign
- getPathLocations() : File
- getPathToFile() : SourceFile
- getPeak() : MultiplexFilteredMSExperiment , PeakIndex
- getPeakAnnotations() : PeptideHit
- getPeakArea_() : PeakPickerCWT
- getPeakBoundaries() : MultiplexFilteringProfile
- 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
- getPeptideOccurrence_() : UTILProteomicsLFQ
- getPeptideOptionalColumnNames() : MzTab
- getPeptideProbabilityThreshold() : SuperHirnParameters
- getPeptideProteinCounter() : PrecursorIonSelection
- getPeptideRef() : IncludeExcludeTarget , ReactionMonitoringTransition , LightTransition
- getPeptideResults() : PeptideAndProteinQuant
- getPeptides() : TargetedExperiment
- getPeptideScoresFromMap_() : IDScoreGetterSetter
- 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
- getPosMax() : SplineInterpolatedPeaks , SplinePackage
- getPosMin() : SplineInterpolatedPeaks , SplinePackage
- getPossibleChargeStates() : Precursor
- getPosStepWidth() : SplinePackage
- getPow_() : QCBase::Status
- 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
- getPrecursorMZSelectedIon() : PeakFileOptions
- getPrecursorRTandMZ() : InspectOutfile
- getPrecursors() : BinnedSpectrum , PrecursorCorrection , SpectrumSettings
- getPrecursorSpectrum() : MSExperiment
- getPredecessorStates() : HMMState
- getPrediction() : IncludeExcludeTarget , ReactionMonitoringTransition
- getPrefix() : AASequence , NASequence
- 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
- getProteinIDs() : IDBoostGraph
- 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
- getQueryMatchGroups() : IdentificationData
- getRandomSample_() : FeatureFinderIdentificationAlgorithm
- getRandomSequence_() : MRMAssay
- getRank() : IdentificationHit , PeptideHit , ProteinHit
- getRatios() : ConsensusFeature
- getReagentName() : Modification
- getReference_() : MapAlignmentAlgorithmIdentification
- getReferenceChannel() : IsobaricQuantitationMethod , ItraqEightPlexQuantitationMethod , ItraqFourPlexQuantitationMethod , TMTElevenPlexQuantitationMethod , TMTSixPlexQuantitationMethod , TMTSixteenPlexQuantitationMethod , 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() : Contaminants , FragmentMassError , GridBasedClustering< Metric > , MascotRemoteQuery , MissedCleavages , Ms2IdentificationRate , ProteinResolver , TIC
- getRetentionTime() : CentroidPeak , IncludeExcludeTarget , MS2Info , ReactionMonitoringTransition , PeptideCompound
- getRetentionTimes_() : MapAlignmentAlgorithmIdentification
- getRetentionTimeType() : PeptideCompound
- getRetentionTimeUnit() : PeptideCompound
- getRevision() : VersionInfo
- getRIAClusterCenter() : MetaProSIPClustering
- getRibonucleotide() : RibonucleotideDB
- getRibonucleotideAlternatives() : RibonucleotideDB
- getRibonucleotidePrefix() : RibonucleotideDB
- 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 , FIAMSScheduler , InterpolationModel , ProductModel< 2 >
- getSampleSection() : ExperimentalDesign
- getSamplesLabelsList() : MultiplexDeltaMassesGenerator
- getSampleToConditionMapping() : ExperimentalDesign
- getSampleToPrefractionationMapping() : ExperimentalDesign
- 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 , ScoredProcessingResult , OpenSwathOSWWriter , PeptideHit , ProteinHit
- getScoreAndStep() : ScoredProcessingResult
- getScores() : MRMFeature
- getScores_() : IDScoreGetterSetter
- getScoresInOrder() : AppliedProcessingStep
- getScoreType() : PeptideIdentification , PercolatorOutfile , ProteinIdentification
- getScoreTypes() : IdentificationData
- 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
- getSeparateScore() : OpenSwathOSWWriter
- getSeparator_() : QuantitativeExperimentalDesign
- getSequence() : IMSElement , NASequence , 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
- getSpectraProcessingFunc() : SwathQC
- getSpectraScanNumberEnd() : ClusteredMS2ConsensusSpectrum
- getSpectraScanNumberStart() : ClusteredMS2ConsensusSpectrum
- getSpectrum() : CachedmzML , LayerData , MSExperiment , NucleicAcidSpectrumGenerator , OnDiscMSExperiment , PeakIndex , TheoreticalSpectrumGenerator
- getSpectrumAccessOpenMSPtr() : SimpleOpenMSSpectraFactory
- getSpectrumAlignment() : SpectrumAlignment
- getSpectrumAlignmentFastCharge() : OPXLSpectrumProcessingAlgorithms
- getSpectrumAlignmentSimple() : 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 , TransformationDescription
- getStatus() : LPWrapper , TOPPASToolVertex
- getStepsAndScoresByStep() : ScoredProcessingResult
- getStream() : LogConfigHandler , StreamHandler
- getStreamTypeByName_() : LogConfigHandler
- getString() : RNPxlReportRow , RNPxlReportRowHeader , StringView
- getStringDataArrayByName() : ProteinIdentification::ProteinGroup
- getStringDataArrays() : MSChromatogram , MSSpectrum , ProteinIdentification::ProteinGroup
- getStringList_() : TOPPBase
- getStringOption_() : TOPPBase
- getSubordinates() : Feature
- getSubsamples() : Sample
- getSubsection_() : TOPPBase
- getSubsectionDefaults_() : Epifany , TOPPBase
- getSubsections() : DefaultParamHandler
- getSubsequence() : AASequence , NASequence
- getSubtreeStatus() : TOPPASVertex
- getSuccessorStates() : HMMState
- getSuffix() : AASequence , NASequence
- getSuffixCounts() : TOPPASVertex::TOPPASFilenames
- 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
- getTag() : Tagger
- getTag_() : Tagger
- getTagCount() : InspectInfile
- getTags() : Param
- getTargetCVTerms() : TargetedExperiment
- getTargetInParam() : TOPPASEdge
- getTargetInParamName() : TOPPASEdge
- getTargetVertex() : TOPPASEdge
- getTau() : EGHTraceFitter
- getTaxon() : XTandemInfile
- getTaxonomy() : MascotInfile
- getTaxonomyFilename() : XTandemInfile
- getTDLabel_() : IDScoreGetterSetter
- getTechnicalRng() : SimRandomNumberGenerator
- getTempDir() : TOPPASScene
- getTempDirectory() : File
- getTemperature() : Digestion , HPLC
- getTemporaryFile() : File
- getTerm() : ControlledVocabulary
- getTermByName() : ControlledVocabulary
- getTermName() : CVMappingTerm
- getTerms() : ControlledVocabulary
- getTermSpecificity() : ResidueModification , Ribonucleotide
- getTermSpecificityName() : ResidueModification
- getText() : Annotation1DItem
- getTheoreticalmaxPosition() : FeatureFinderAlgorithmPickedHelperStructs::MassTraces
- getTheoreticIsotopicMassWindow_() : FeatureFindingMetabo
- getTheta() : Deisotoper
- getThreeLetterCode() : Residue
- getThreePrimeGain() : DigestionEnzymeRNA
- getThreePrimeMod() : NASequence
- getThreshold() : ClusterHierarchical , FineIsotopePatternGenerator
- getTIC() : MSExperiment , MSSpectrum
- getTime() : DateTime , VersionInfo
- getTimeArray() : Chromatogram , OSChromatogram
- getTimepoints() : Gradient
- getTmpDir() : SiriusAdapterAlgorithm::SiriusTemporaryFileSystemObjects
- getTmpMsFile() : SiriusAdapterAlgorithm::SiriusTemporaryFileSystemObjects
- getTmpOutDir() : SiriusAdapterAlgorithm::SiriusTemporaryFileSystemObjects
- getTOFTotalPathLength() : MassAnalyzer
- getTolerance() : SpectrumAlignmentDialog
- getToleranceMZ() : SuperHirnParameters
- getTool() : ToolsDialog
- getToolDescriptions() : ToolDescriptionHandler
- getToolNamesFromINI() : INIUpdater
- getToolToolStatus_() : TOPPASEdge
- getToolUserDefaults_() : TOPPBase
- getTopNHits() : SiriusAdapterAlgorithm
- getTopoNr() : TOPPASVertex
- getTOPPToolList() : ToolHandler
- getTotalProbability() : FineIsotopePatternGenerator
- 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 , MSSpectrum , OPXLDataStructs::ProteinProteinCrossLink , SampleTreatment , SpectrumSettings , TOPPASToolVertex
- getTypeByContent() : FileHandler
- getTypeByFileName() : FileHandler
- getTypes() : ToolHandler
- getULOD() : AbsoluteQuantitationMethod
- getULOQ() : AbsoluteQuantitationMethod
- getUnassignedPeptideIdentifications() : ConsensusMap , FeatureMap
- getUnassignedPeptideIdentifications_() : Ms2SpectrumStats
- getUnbiasedSample_() : FeatureFinderIdentificationAlgorithm
- getUnchargedMass() : Precursor
- getUnchargedSpectrum_() : NucleicAcidSpectrumGenerator
- getUniModAccession() : ResidueModification
- getUniModRecordId() : ResidueModification
- getUniqueId() : UniqueIdGenerator , UniqueIdInterface
- getUniqueName() : File
- getUniqueSampleRowToSampleMapping() : ExperimentalDesign
- getUniqueSorted() : MRMFeatureFilter
- getUnit() : CVTerm , DataValue , MetaInfoRegistry
- getUnitType() : DataValue
- getUnmodifiedAASequence_() : ICPLLabeler
- getUnmodifiedSequence_() : SILACLabeler
- getUpper() : LinearRegression
- getUpperRTBound() : EGHTraceFitter , GaussTraceFitter , TraceFitter
- getUpstreamNodes() : IDBoostGraph
- getUpstreamNodesNonRecursive() : IDBoostGraph
- 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
- getXCorrContrastMatrix() : MRMScoring
- getXCorrMatrix() : MRMScoring
- getXCorrPrecursorCombinedMatrix() : MRMScoring
- getXCorrPrecursorContrastMatrix() : MRMScoring
- getXIC_() : PSLPFormulation
- getXIntercept() : LinearRegression
- getXLinkIonSpectrum() : SimpleTSGXLMS , 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 : MzTabNucleicAcidSectionRow , 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
- Graph : IDBoostGraph
- GraphConst : IDBoostGraph
- Graphs : IDBoostGraph
- GREATER_EQUAL : DataFilters
- Grid : HashGrid< Cluster > , QTClusterFinder
- grid_ : GridBasedClustering< Metric > , GridSearch< TupleTypes > , 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
- GridSearch() : GridSearch< TupleTypes >
- GridVector : AxisPainter , AxisTickCalculator , AxisWidget
- ground_ : Spectrum3DOpenGLCanvas
- group() : FeatureGroupingAlgorithm , FeatureGroupingAlgorithmKD , FeatureGroupingAlgorithmLabeled , FeatureGroupingAlgorithmQT , FeatureGroupingAlgorithmUnlabeled
- group_() : FeatureGroupingAlgorithmKD , FeatureGroupingAlgorithmQT
- group_id : TransitionTSVFile::TSVTransition
- group_label_2d_ : TOPPViewBase
- group_type_stack_ : XTandemXMLFile
- group_unassigned_2d_ : TOPPViewBase
- groups : ParentMoleculeGrouping
- groups_ : CalibrationData
- GroupType : XTandemXMLFile
- gs : IDBoostGraph::dfs_ccsplit_visitor
- guessExperimentType_() : IBSpectraFile
- GUI : ProgressLogger
- gui_ : TOPPASScene
- GUIHelpers() : GUIHelpers
- GUIProgressLoggerImpl() : GUIProgressLoggerImpl
- GumbelDistributionFitResult() : GumbelDistributionFitter::GumbelDistributionFitResult , GumbelMaxLikelihoodFitter::GumbelDistributionFitResult
- GumbelDistributionFitter() : GumbelDistributionFitter
- GumbelDistributionFunctor() : GumbelMaxLikelihoodFitter::GumbelDistributionFunctor
- GumbelMaxLikelihoodFitter() : GumbelMaxLikelihoodFitter
- gzerror_ : GzipIfstream
- gzfile_ : GzipIfstream
- gzip_ : GzipInputStream
- GzipIfstream() : GzipIfstream
- GzipInputStream() : GzipInputStream