All Classes

AAHydropathyManager AAManager AAMatcher AAMotifMatcher AAPKaManager AASequence AASymbol AATermManager AATermSymbol AbstractBioPolymer AbstractBioPolymer.Builder AbstractBioPolymerMerger AbstractMassCalc AbstractMolecularSymbolManager AbstractPeakListEditor AbstractPeakListFilter AminoAcid AminoAcidTerm Annotatable AnnotatedNotPrecPeakListFilter AnnotatedPeak Atom BasePeakTransformer BinnedPeakList BinnedPeakListImpl BinnedPeakListImpl.Builder BioPolymer BioPolymerBuilder BioPolymerMerger BioPolymerModifContainer BioPolymerModifContainer.Builder BioPolymerModifParser BioPolymerUtils ChargedParticle ChargedParticleImpl ChemicalFacade ChemicalFacade.MonomerType CleavageSiteCutter CleavageSiteCutter.Builder CTerminus CTermManager CTermSymbol CuttingSiteMatcher DeoxyRiboNucleotide DeoxyRiboNucManager DeoxyRiboNucSymbol DigestedPeptide DigestedPeptide.Builder Digester EditionRule EditionRule.EditionAction EditionRule.EditionAction.ActionType EditionRule.EditionAction.AtomicAction EditionRule.MultiActionMode Element ElementManager ElementManager.AtomEnclosingToken FragmentAnnotation FragmentAnnotationComparator FragmentAnnotationDecorator FragmentAnnotationDoD FragmentAnnotationDoD.Builder FragmentAnnotationGeneric FragmentAnnotationGeneric.Builder FragmentAnnotationImpl FragmentAnnotationImpl.Builder FragmentAnnotationImpl.ModifFormat FragmentAnnotations FragmentAnnotationsManager FragmentationConfig FragmentationConfig.Builder FragmentationType FragmentChargeComparator Fragmenter FragmentModifComparator FragmentTypeComparator HomogeneousTransformer IncompatibleRTUnitException IntensityThresholdFilter IntensityTransformer InvalidPeakException InvalidPeakListException Ionizable Ionizable.NeutralMoleculeType IonizableGroup IonizableGroup.Builder IonizableModification IonizableMolecule Isotope LogTransformer LossGrammarLexer LossGrammarParser LossGrammarParser.action_scope LossGrammarParser.range_return LossModification MassCalculator MassCalculator.Accuracy ModifContainer ModifContainer.Builder ModifContainerManager ModifFormat ModifFormat.Builder ModifFormat.Format Modification Modification.ModifType ModificationFactory ModificationUtils ModifiedMolecule ModifiedMolecule.Builder MolecularExpressionBuilder MolecularFormatRegister Molecule MoleculeManager MoleculeUtils MovingAvgTransformer MS1MS2PeakDistributions MS1MS2PeakDistributions.Builder MS1MS2PeaksScatterPlotRenderer MSPeakListDistributionExporter MSRenderer NCTermination NHighestPeaksFilter NPeakGroupsPerWindowFilter NPeaksPerWindowFilter NTerminus NTermManager NTermSymbol OverExpressedPeakTransformer ParentIonFilter Peak PeakCentroider PeakChecker PeakDoD PeakDoD.Builder PeakGrouper PeakImpl PeakImpl.Builder PeakList PeakListDistribution PeakListDistribution.Builder PeakListImpl PeakListImpl.Builder PeakListImpl.EditorImpl PeakListMzFilter PeakListMZPrecComparator PeakListMZPrecComparator.MissingPrecursorException PeakListRunStats PeakListRunStats.Builder PeakListSetter PeakListsFilter PeakListUtils PeakListUtils.IntensityTransformationMethod PeakTypeFilter Peptidase PeptidaseManager Peptide Peptide.Builder PeptideEditorFactory PeptideFragmentationException PeptideFragmenter PeptideFragmenter.Builder PeptideFragmentProcessor PeptideFragmentProcessorImpl PeptideGenerator PeptideMerger PeptideResidueManager PeptideResidueManager.BadPeptideElementException PeptideType PeptideTypeComposite PeptideTypeCondition PeptideTypeCondition.Builder PeptideTypeImpl PhysicalConstants PrecursorFilter Protein RankTransformer RetentionTime RetentionTime.RTUnit RiboNucleotide RiboNucManager RiboNucSymbol SpectrumCluster SpectrumCluster.Builder SpectrumCluster.EditorImpl SpectrumProcessorManager SqrtTransformer Terminus TerminusType TerminusTypeImpl TerminusTypeImpl.TypeC TerminusTypeImpl.TypeN UnimodManager UnimodParser UnimodSpecificity UnimodSpecificity.Type Weighable