Hierarchy For All Packages

Package Hierarchies:

org.expasy.jpl.core.mol, org.expasy.jpl.core.mol.chem, org.expasy.jpl.core.mol.chem.api, org.expasy.jpl.core.mol.chem.impl, org.expasy.jpl.core.mol.modif, org.expasy.jpl.core.mol.monomer.aa, org.expasy.jpl.core.mol.monomer.nuc, org.expasy.jpl.core.mol.polymer, org.expasy.jpl.core.mol.polymer.cutter, org.expasy.jpl.core.mol.polymer.modif, org.expasy.jpl.core.mol.polymer.modif.unimod, org.expasy.jpl.core.mol.polymer.pept, org.expasy.jpl.core.mol.polymer.pept.cutter, org.expasy.jpl.core.mol.polymer.pept.fragmenter, org.expasy.jpl.core.mol.polymer.pept.matcher, org.expasy.jpl.core.mol.polymer.pept.rule, org.expasy.jpl.core.mol.polymer.pept.term, org.expasy.jpl.core.mol.polymer.prot, org.expasy.jpl.core.ms.export, org.expasy.jpl.core.ms.lc, org.expasy.jpl.core.ms.spectrum, org.expasy.jpl.core.ms.spectrum.annot, org.expasy.jpl.core.ms.spectrum.annot.comp, org.expasy.jpl.core.ms.spectrum.cons, org.expasy.jpl.core.ms.spectrum.editor, org.expasy.jpl.core.ms.spectrum.editor.intensity, org.expasy.jpl.core.ms.spectrum.filter, org.expasy.jpl.core.ms.spectrum.peak, org.expasy.jpl.core.ms.spectrum.stat

Class Hierarchy

• java.lang.Object
  • org.expasy.jpl.core.mol.monomer.aa.AAHydropathyManager
  • org.expasy.jpl.core.mol.monomer.aa.AAPKaManager
  • org.expasy.jpl.commons.collection.render.Abstract2DChartRenderer<T> (implements org.expasy.jpl.commons.base.render.ChartRenderer)
    • org.expasy.jpl.core.ms.spectrum.stat.MS1MS2PeaksScatterPlotRenderer (implements org.expasy.jpl.commons.base.render.ChartRenderer)
    • org.expasy.jpl.core.ms.export.MSRenderer (implements org.expasy.jpl.commons.base.render.BarChartRenderer)
  • org.expasy.jpl.core.mol.polymer.AbstractBioPolymer<E> (implements org.expasy.jpl.core.mol.polymer.BioPolymer<E>, java.io.Serializable)
    • org.expasy.jpl.core.mol.polymer.pept.Peptide (implements org.expasy.jpl.core.mol.polymer.pept.AASequence, java.io.Serializable)
  • org.expasy.jpl.core.mol.polymer.AbstractBioPolymer.Builder<E> (implements org.expasy.jpl.core.mol.polymer.BioPolymerBuilder<E>)
    • org.expasy.jpl.core.mol.polymer.pept.Peptide.Builder (implements org.expasy.jpl.core.mol.polymer.pept.NCTermination)
  • org.expasy.jpl.core.mol.polymer.AbstractBioPolymerMerger<T> (implements org.expasy.jpl.core.mol.polymer.BioPolymerMerger<T>)
    • org.expasy.jpl.core.mol.polymer.pept.PeptideMerger
  • org.expasy.jpl.commons.base.AbstractDecorator<T> (implements java.io.Serializable)
    • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationDecorator (implements org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotation)
  • org.expasy.jpl.core.mol.chem.api.AbstractMassCalc<T> (implements java.io.Serializable, org.expasy.jpl.core.mol.chem.api.Weighable)
    • org.expasy.jpl.core.mol.polymer.AbstractBioPolymer.PolymerMassCalc (implements java.io.Serializable)
  • org.expasy.jpl.core.mol.AbstractMolecularSymbolManager<T> (implements org.expasy.jpl.commons.collection.symbol.DataSymbolRegister<T>)
    • org.expasy.jpl.core.mol.monomer.aa.AAManager
    • org.expasy.jpl.core.mol.monomer.aa.AATermManager
    • org.expasy.jpl.core.mol.polymer.pept.term.CTermManager
    • org.expasy.jpl.core.mol.monomer.nuc.DeoxyRiboNucManager
    • org.expasy.jpl.core.mol.polymer.pept.term.NTermManager
    • org.expasy.jpl.core.mol.monomer.nuc.RiboNucManager
  • org.expasy.jpl.core.ms.spectrum.editor.AbstractPeakListEditor (implements org.apache.commons.collections15.Transformer<I,O>)
    • org.expasy.jpl.core.ms.spectrum.editor.IntensityTransformer
    • org.expasy.jpl.core.ms.spectrum.editor.PeakCentroider
    • org.expasy.jpl.core.ms.spectrum.editor.PeakGrouper
  • org.expasy.jpl.core.ms.spectrum.filter.AbstractPeakListFilter (implements org.apache.commons.collections15.Transformer<I,O>)
    • org.expasy.jpl.core.ms.spectrum.filter.AnnotatedNotPrecPeakListFilter
    • org.expasy.jpl.core.ms.spectrum.filter.IntensityThresholdFilter
    • org.expasy.jpl.core.ms.spectrum.filter.NHighestPeaksFilter
    • org.expasy.jpl.core.ms.spectrum.filter.NPeakGroupsPerWindowFilter
    • org.expasy.jpl.core.ms.spectrum.filter.NPeaksPerWindowFilter
    • org.expasy.jpl.core.ms.spectrum.filter.PeakListMzFilter
    • org.expasy.jpl.core.ms.spectrum.filter.PeakTypeFilter
    • org.expasy.jpl.core.ms.spectrum.filter.PrecursorFilter
  • org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner<T> (implements org.expasy.jpl.commons.collection.symbol.seq.SequenceIterable<T>)
    • org.expasy.jpl.core.mol.polymer.pept.matcher.AAMatcher
    • org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher<T>
      • org.expasy.jpl.core.mol.polymer.pept.matcher.AAMotifMatcher (implements org.expasy.jpl.commons.collection.Cachable)
      • org.expasy.jpl.core.mol.polymer.cutter.CuttingSiteMatcher<T>
        • org.expasy.jpl.core.mol.polymer.pept.cutter.CleavageSiteCutter
  • org.expasy.jpl.commons.collection.symbol.AbstractSymbol<T> (implements java.io.Serializable, org.expasy.jpl.commons.collection.symbol.Symbol<T>)
    • org.expasy.jpl.core.mol.monomer.aa.AASymbol
    • org.expasy.jpl.core.mol.monomer.aa.AATermSymbol
    • org.expasy.jpl.core.mol.polymer.pept.term.CTermSymbol
    • org.expasy.jpl.core.mol.monomer.nuc.DeoxyRiboNucSymbol
    • org.expasy.jpl.core.mol.polymer.pept.term.NTermSymbol
    • org.expasy.jpl.core.mol.monomer.nuc.RiboNucSymbol
  • org.expasy.jpl.core.ms.spectrum.peak.AnnotatedPeak (implements org.expasy.jpl.core.ms.spectrum.peak.Peak)
  • org.expasy.jpl.core.ms.spectrum.editor.intensity.BasePeakTransformer (implements org.apache.commons.collections15.Transformer<I,O>)
  • org.antlr.runtime.BaseRecognizer
    • org.antlr.runtime.Lexer (implements org.antlr.runtime.TokenSource)
      • org.expasy.jpl.core.mol.polymer.pept.rule.LossGrammarLexer
    • org.antlr.runtime.Parser
      • org.expasy.jpl.core.mol.polymer.pept.rule.LossGrammarParser
  • org.expasy.jpl.core.ms.spectrum.BinnedPeakListImpl (implements org.expasy.jpl.core.ms.spectrum.BinnedPeakList)
  • org.expasy.jpl.core.ms.spectrum.BinnedPeakListImpl.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.mol.polymer.modif.BioPolymerModifContainer (implements org.expasy.jpl.commons.base.ExplicitlyCloneable, java.io.Serializable)
  • org.expasy.jpl.core.mol.polymer.modif.BioPolymerModifContainer.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>, org.expasy.jpl.commons.base.Resetable)
  • org.expasy.jpl.core.mol.polymer.modif.BioPolymerModifParser
  • org.expasy.jpl.core.mol.polymer.BioPolymerUtils
  • org.expasy.jpl.core.mol.chem.impl.ChargedParticleImpl (implements org.expasy.jpl.core.mol.chem.api.ChargedParticle, org.expasy.jpl.commons.base.Evaluable, org.expasy.jpl.commons.base.Registrable, java.io.Serializable, org.expasy.jpl.core.mol.chem.api.Weighable)
  • org.expasy.jpl.core.mol.chem.ChemicalFacade
  • org.expasy.jpl.core.mol.polymer.pept.cutter.CleavageSiteCutter.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.mol.polymer.pept.cutter.DigestedPeptide (implements org.expasy.jpl.core.mol.polymer.pept.AASequence)
  • org.expasy.jpl.core.mol.polymer.pept.cutter.DigestedPeptide.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.mol.polymer.pept.cutter.Digester (implements org.expasy.jpl.commons.base.cond.ConditionBasedFilterReady<T>)
  • org.expasy.jpl.core.mol.polymer.pept.rule.EditionRule (implements org.expasy.jpl.commons.collection.Cachable)
  • org.expasy.jpl.core.mol.polymer.pept.rule.EditionRule.EditionAction
  • org.expasy.jpl.core.mol.polymer.pept.rule.EditionRule.EditionAction.AtomicAction
  • org.expasy.jpl.core.mol.chem.impl.Element (implements org.expasy.jpl.core.mol.chem.api.Atom)
  • org.expasy.jpl.core.mol.chem.impl.ElementManager
  • org.expasy.jpl.commons.collection.ExtraIterable.AbstractExtraIterator<T> (implements java.util.Iterator<E>)
    • org.expasy.jpl.commons.collection.IndexIterable.Iterator
      • org.expasy.jpl.commons.collection.symbol.seq.AbstractSequencePositioner.Iterator
        • org.expasy.jpl.core.mol.polymer.pept.matcher.AAMatcher.Iterator
        • org.expasy.jpl.commons.collection.symbol.seq.MotifMatcher.Iterator
          • org.expasy.jpl.core.mol.polymer.pept.matcher.AAMotifMatcher.Iterator
          • org.expasy.jpl.core.mol.polymer.cutter.CuttingSiteMatcher.Iterator
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationComparator (implements java.util.Comparator<T>)
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationDoD (implements org.expasy.jpl.commons.base.DomainOfDefinition<T>)
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationDoD.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationGeneric (implements org.expasy.jpl.commons.base.record.DataRecord, org.expasy.jpl.commons.collection.Mappable, org.expasy.jpl.commons.base.Registrable, java.io.Serializable)
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationGeneric.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationImpl (implements org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotation, java.io.Serializable)
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationImpl.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotations (implements java.io.Serializable)
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationsManager
  • org.expasy.jpl.core.mol.polymer.pept.fragmenter.FragmentationConfig
  • org.expasy.jpl.core.mol.polymer.pept.fragmenter.FragmentationConfig.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.ms.spectrum.annot.comp.FragmentChargeComparator (implements java.util.Comparator<T>, org.expasy.jpl.commons.base.builder.StringBasedFactory<T>)
  • org.expasy.jpl.core.ms.spectrum.annot.comp.FragmentModifComparator (implements java.util.Comparator<T>, org.expasy.jpl.commons.base.builder.StringBasedFactory<T>)
  • org.expasy.jpl.core.ms.spectrum.annot.comp.FragmentTypeComparator (implements java.util.Comparator<T>, org.expasy.jpl.commons.base.builder.StringBasedFactory<T>)
  • org.expasy.jpl.core.ms.spectrum.editor.intensity.HomogeneousTransformer (implements org.apache.commons.collections15.Transformer<I,O>)
  • org.expasy.jpl.core.mol.chem.impl.IonizableGroup (implements org.expasy.jpl.core.mol.chem.api.Ionizable, org.expasy.jpl.commons.collection.Mappable)
  • org.expasy.jpl.core.mol.chem.impl.IonizableGroup.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.mol.modif.IonizableModification (implements org.expasy.jpl.core.mol.chem.api.Ionizable, org.expasy.jpl.core.mol.modif.Modification)
  • org.expasy.jpl.core.mol.chem.impl.IonizableMolecule (implements org.expasy.jpl.core.mol.chem.api.Ionizable, org.expasy.jpl.commons.collection.Mappable, org.expasy.jpl.core.mol.chem.api.Molecule)
  • org.expasy.jpl.core.mol.chem.impl.Isotope (implements org.expasy.jpl.core.mol.chem.api.Atom)
  • org.expasy.jpl.core.ms.spectrum.editor.intensity.LogTransformer (implements org.apache.commons.collections15.Transformer<I,O>)
  • org.expasy.jpl.core.mol.polymer.pept.rule.LossGrammarParser.action_scope
  • org.expasy.jpl.core.mol.modif.LossModification (implements org.expasy.jpl.core.mol.modif.Modification)
  • org.expasy.jpl.core.mol.chem.MassCalculator (implements java.io.Serializable)
  • org.expasy.jpl.core.mol.polymer.modif.ModifContainer (implements java.io.Serializable)
  • org.expasy.jpl.core.mol.polymer.modif.ModifContainer.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>, org.expasy.jpl.commons.base.Resetable)
  • org.expasy.jpl.core.mol.polymer.modif.ModifContainerManager (implements java.io.Serializable)
  • org.expasy.jpl.core.mol.modif.ModifFormat (implements java.io.Serializable)
  • org.expasy.jpl.core.mol.modif.ModifFormat.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.mol.modif.ModificationFactory (implements org.expasy.jpl.core.mol.modif.Modification)
  • org.expasy.jpl.core.mol.modif.ModificationUtils
  • org.expasy.jpl.core.mol.chem.impl.ModifiedMolecule (implements org.expasy.jpl.core.mol.chem.api.Molecule)
  • org.expasy.jpl.core.mol.chem.impl.ModifiedMolecule.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.mol.MolecularFormatRegister
  • org.expasy.jpl.core.mol.chem.impl.MoleculeManager
  • org.expasy.jpl.core.mol.chem.MoleculeUtils
  • org.expasy.jpl.core.ms.spectrum.editor.intensity.MovingAvgTransformer (implements org.apache.commons.collections15.Transformer<I,O>)
  • org.expasy.jpl.core.ms.spectrum.stat.MS1MS2PeakDistributions
  • org.expasy.jpl.core.ms.spectrum.stat.MS1MS2PeakDistributions.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.ms.export.MSPeakListDistributionExporter
  • org.expasy.jpl.core.ms.spectrum.editor.intensity.OverExpressedPeakTransformer (implements org.apache.commons.collections15.Transformer<I,O>)
  • org.expasy.jpl.core.ms.spectrum.filter.ParentIonFilter
  • org.expasy.jpl.core.ms.spectrum.peak.PeakChecker
  • org.expasy.jpl.core.ms.spectrum.peak.PeakDoD (implements org.expasy.jpl.commons.base.DomainOfDefinition<T>)
  • org.expasy.jpl.core.ms.spectrum.peak.PeakDoD.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.ms.spectrum.peak.PeakImpl (implements org.expasy.jpl.core.ms.spectrum.peak.Peak)
  • org.expasy.jpl.core.ms.spectrum.peak.PeakImpl.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.ms.spectrum.stat.PeakListDistribution
  • org.expasy.jpl.core.ms.spectrum.stat.PeakListDistribution.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.ms.spectrum.PeakListImpl (implements org.expasy.jpl.core.ms.spectrum.PeakList)
  • org.expasy.jpl.core.ms.spectrum.PeakListImpl.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.ms.spectrum.PeakListImpl.EditorImpl (implements org.expasy.jpl.commons.base.Editor<T>)
  • org.expasy.jpl.core.ms.spectrum.stat.PeakListMZPrecComparator (implements java.util.Comparator<T>)
  • org.expasy.jpl.core.ms.spectrum.PeakListRunStats
  • org.expasy.jpl.core.ms.spectrum.PeakListRunStats.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.ms.spectrum.PeakListSetter
  • org.expasy.jpl.core.ms.spectrum.filter.PeakListsFilter (implements org.apache.commons.collections15.Transformer<I,O>)
  • org.expasy.jpl.core.ms.spectrum.PeakListUtils
  • org.expasy.jpl.core.mol.polymer.pept.cutter.Peptidase (implements org.expasy.jpl.commons.collection.Cachable)
  • org.expasy.jpl.core.mol.polymer.pept.cutter.PeptidaseManager
  • org.expasy.jpl.core.mol.polymer.pept.rule.PeptideEditorFactory (implements org.apache.commons.collections15.Transformer<I,O>)
  • org.expasy.jpl.core.mol.polymer.pept.fragmenter.PeptideFragmenter
  • org.expasy.jpl.core.mol.polymer.pept.fragmenter.PeptideFragmenter.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.mol.polymer.pept.fragmenter.PeptideFragmentProcessorImpl (implements org.expasy.jpl.core.mol.polymer.pept.fragmenter.PeptideFragmentProcessor)
  • org.expasy.jpl.core.mol.polymer.pept.PeptideGenerator
  • org.expasy.jpl.core.mol.polymer.pept.PeptideResidueManager
  • org.expasy.jpl.core.mol.polymer.pept.PeptideTypeComposite (implements org.expasy.jpl.core.mol.polymer.pept.PeptideType, java.util.Set<E>)
  • org.expasy.jpl.core.mol.polymer.pept.PeptideTypeCondition<T>
  • org.expasy.jpl.core.mol.polymer.pept.PeptideTypeCondition.Builder<T> (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>)
  • org.expasy.jpl.core.mol.polymer.pept.PeptideTypeImpl (implements org.expasy.jpl.core.mol.polymer.pept.PeptideType, java.io.Serializable)
  • org.expasy.jpl.core.mol.chem.PhysicalConstants
  • org.expasy.jpl.core.mol.polymer.prot.Protein (implements org.expasy.jpl.commons.base.SerialIdentifiable)
  • org.expasy.jpl.core.ms.spectrum.editor.intensity.RankTransformer (implements org.apache.commons.collections15.Transformer<I,O>)
  • org.expasy.jpl.core.ms.lc.RetentionTime (implements java.lang.Comparable<T>, org.expasy.jpl.commons.base.ExplicitlyCloneable, java.io.Serializable)
  • org.antlr.runtime.RuleReturnScope
    • org.antlr.runtime.ParserRuleReturnScope
      • org.expasy.jpl.core.mol.polymer.pept.rule.LossGrammarParser.range_return
  • org.expasy.jpl.core.ms.spectrum.cons.SpectrumCluster
  • org.expasy.jpl.core.ms.spectrum.cons.SpectrumCluster.Builder (implements org.expasy.jpl.commons.base.builder.InstanceBuilder<T>, org.expasy.jpl.commons.base.Resetable)
  • org.expasy.jpl.core.ms.spectrum.cons.SpectrumCluster.EditorImpl (implements org.expasy.jpl.commons.base.Editor<T>)
  • org.expasy.jpl.core.ms.spectrum.filter.SpectrumProcessorManager (implements org.apache.commons.collections15.Transformer<I,O>)
  • org.expasy.jpl.core.ms.spectrum.editor.intensity.SqrtTransformer (implements org.apache.commons.collections15.Transformer<I,O>)
  • org.expasy.jpl.core.mol.polymer.pept.term.TerminusTypeImpl
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.expasy.jpl.core.ms.lc.IncompatibleRTUnitException
      • org.expasy.jpl.core.ms.spectrum.peak.InvalidPeakException
      • org.expasy.jpl.core.ms.spectrum.InvalidPeakListException
      • org.expasy.jpl.core.mol.polymer.pept.fragmenter.PeptideFragmentationException
      • org.expasy.jpl.core.mol.polymer.pept.PeptideResidueManager.BadPeptideElementException
      • java.lang.RuntimeException
        • org.expasy.jpl.core.ms.spectrum.stat.PeakListMZPrecComparator.MissingPrecursorException
  • org.expasy.jpl.core.mol.polymer.modif.unimod.UnimodManager
  • org.expasy.jpl.core.mol.polymer.modif.unimod.UnimodParser (implements org.expasy.jpl.commons.base.io.Parser<T>)
  • org.expasy.jpl.core.mol.polymer.modif.unimod.UnimodSpecificity (implements org.expasy.jpl.commons.collection.Mappable)

Interface Hierarchy

• org.expasy.jpl.core.ms.spectrum.annot.Annotatable
  • org.expasy.jpl.core.ms.spectrum.BinnedPeakList
  • org.expasy.jpl.core.ms.spectrum.PeakList (also extends org.expasy.jpl.commons.base.ExplicitlyCloneable, java.io.Serializable)
    • org.expasy.jpl.core.ms.spectrum.BinnedPeakList
• org.expasy.jpl.core.mol.polymer.BioPolymerMerger<T>
• org.expasy.jpl.core.mol.chem.api.ChargedParticle
  • org.expasy.jpl.core.mol.chem.api.Molecule (also extends org.expasy.jpl.commons.base.Registrable, java.io.Serializable, org.expasy.jpl.core.mol.chem.api.Weighable)
    • org.expasy.jpl.core.mol.polymer.pept.term.Terminus
  • org.expasy.jpl.core.mol.polymer.pept.term.Terminus
• java.lang.Cloneable
  • org.expasy.jpl.core.ms.spectrum.BinnedPeakList
  • org.expasy.jpl.commons.base.ExplicitlyCloneable
    • org.expasy.jpl.core.ms.spectrum.BinnedPeakList
    • org.expasy.jpl.core.mol.chem.api.Ionizable (also extends java.io.Serializable)
    • org.expasy.jpl.core.mol.modif.Modification (also extends org.expasy.jpl.commons.base.Evaluable, org.expasy.jpl.commons.collection.Mappable, org.expasy.jpl.commons.base.Registrable, java.io.Serializable, org.expasy.jpl.core.mol.chem.api.Weighable)
    • org.expasy.jpl.core.ms.spectrum.peak.Peak (also extends java.lang.Comparable<T>, java.io.Serializable)
    • org.expasy.jpl.core.ms.spectrum.PeakList (also extends org.expasy.jpl.core.ms.spectrum.annot.Annotatable, java.io.Serializable)
      • org.expasy.jpl.core.ms.spectrum.BinnedPeakList
  • org.expasy.jpl.core.mol.chem.api.Ionizable (also extends org.expasy.jpl.commons.base.ExplicitlyCloneable, java.io.Serializable)
  • org.expasy.jpl.core.mol.modif.Modification (also extends org.expasy.jpl.commons.base.Evaluable, org.expasy.jpl.commons.base.ExplicitlyCloneable, org.expasy.jpl.commons.collection.Mappable, org.expasy.jpl.commons.base.Registrable, java.io.Serializable, org.expasy.jpl.core.mol.chem.api.Weighable)
  • org.expasy.jpl.core.ms.spectrum.peak.Peak (also extends java.lang.Comparable<T>, org.expasy.jpl.commons.base.ExplicitlyCloneable, java.io.Serializable)
  • org.expasy.jpl.core.ms.spectrum.PeakList (also extends org.expasy.jpl.core.ms.spectrum.annot.Annotatable, org.expasy.jpl.commons.base.ExplicitlyCloneable, java.io.Serializable)
    • org.expasy.jpl.core.ms.spectrum.BinnedPeakList
• java.lang.Comparable<T>
  • org.expasy.jpl.core.ms.spectrum.peak.Peak (also extends org.expasy.jpl.commons.base.ExplicitlyCloneable, java.io.Serializable)
• org.expasy.jpl.commons.base.Evaluable
  • org.expasy.jpl.core.mol.modif.Modification (also extends org.expasy.jpl.commons.base.ExplicitlyCloneable, org.expasy.jpl.commons.collection.Mappable, org.expasy.jpl.commons.base.Registrable, java.io.Serializable, org.expasy.jpl.core.mol.chem.api.Weighable)
• org.expasy.jpl.commons.base.builder.InstanceBuilder<T>
  • org.expasy.jpl.core.mol.polymer.BioPolymerBuilder<E>
  • org.expasy.jpl.core.mol.chem.api.MolecularExpressionBuilder
• org.expasy.jpl.commons.collection.Mappable
  • org.expasy.jpl.commons.collection.Cachable (also extends org.expasy.jpl.commons.base.Registrable)
    • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotation
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotation
  • org.expasy.jpl.core.mol.modif.Modification (also extends org.expasy.jpl.commons.base.Evaluable, org.expasy.jpl.commons.base.ExplicitlyCloneable, org.expasy.jpl.commons.base.Registrable, java.io.Serializable, org.expasy.jpl.core.mol.chem.api.Weighable)
• org.expasy.jpl.core.mol.polymer.pept.NCTermination
  • org.expasy.jpl.core.mol.polymer.pept.AASequence (also extends org.expasy.jpl.core.mol.polymer.BioPolymer<E>)
• org.expasy.jpl.core.mol.polymer.pept.PeptideType
• org.expasy.jpl.commons.base.process.Processor<T>
  • org.expasy.jpl.core.mol.polymer.pept.fragmenter.Fragmenter
  • org.expasy.jpl.core.mol.polymer.pept.fragmenter.PeptideFragmentProcessor
• org.expasy.jpl.commons.base.Registrable
  • org.expasy.jpl.core.mol.chem.api.Atom (also extends java.io.Serializable, org.expasy.jpl.core.mol.chem.api.Weighable)
  • org.expasy.jpl.commons.collection.Cachable (also extends org.expasy.jpl.commons.collection.Mappable)
    • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotation
  • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotation
  • org.expasy.jpl.core.mol.modif.Modification (also extends org.expasy.jpl.commons.base.Evaluable, org.expasy.jpl.commons.base.ExplicitlyCloneable, org.expasy.jpl.commons.collection.Mappable, java.io.Serializable, org.expasy.jpl.core.mol.chem.api.Weighable)
  • org.expasy.jpl.core.mol.chem.api.Molecule (also extends org.expasy.jpl.core.mol.chem.api.ChargedParticle, java.io.Serializable, org.expasy.jpl.core.mol.chem.api.Weighable)
    • org.expasy.jpl.core.mol.polymer.pept.term.Terminus
  • org.expasy.jpl.core.mol.polymer.pept.term.Terminus
• org.expasy.jpl.commons.collection.symbol.seq.Sequence<T>
  • org.expasy.jpl.core.mol.polymer.pept.AASequence (also extends org.expasy.jpl.core.mol.polymer.BioPolymer<E>, org.expasy.jpl.core.mol.polymer.pept.NCTermination)
  • org.expasy.jpl.core.mol.polymer.BioPolymer<E> (also extends org.expasy.jpl.commons.collection.symbol.seq.SymbolSequence<T>, org.expasy.jpl.core.mol.chem.api.Weighable)
    • org.expasy.jpl.core.mol.polymer.pept.AASequence (also extends org.expasy.jpl.core.mol.polymer.pept.NCTermination)
  • org.expasy.jpl.commons.collection.symbol.seq.SymbolSequence<T>
    • org.expasy.jpl.core.mol.polymer.pept.AASequence (also extends org.expasy.jpl.core.mol.polymer.BioPolymer<E>, org.expasy.jpl.core.mol.polymer.pept.NCTermination)
    • org.expasy.jpl.core.mol.polymer.BioPolymer<E> (also extends org.expasy.jpl.core.mol.chem.api.Weighable)
      • org.expasy.jpl.core.mol.polymer.pept.AASequence (also extends org.expasy.jpl.core.mol.polymer.pept.NCTermination)
• java.io.Serializable
  • org.expasy.jpl.core.mol.chem.api.Atom (also extends org.expasy.jpl.commons.base.Registrable, org.expasy.jpl.core.mol.chem.api.Weighable)
  • org.expasy.jpl.core.ms.spectrum.BinnedPeakList
  • org.expasy.jpl.core.mol.chem.api.Ionizable (also extends org.expasy.jpl.commons.base.ExplicitlyCloneable)
  • org.expasy.jpl.core.mol.modif.Modification (also extends org.expasy.jpl.commons.base.Evaluable, org.expasy.jpl.commons.base.ExplicitlyCloneable, org.expasy.jpl.commons.collection.Mappable, org.expasy.jpl.commons.base.Registrable, org.expasy.jpl.core.mol.chem.api.Weighable)
  • org.expasy.jpl.core.mol.chem.api.Molecule (also extends org.expasy.jpl.core.mol.chem.api.ChargedParticle, org.expasy.jpl.commons.base.Registrable, org.expasy.jpl.core.mol.chem.api.Weighable)
    • org.expasy.jpl.core.mol.polymer.pept.term.Terminus
  • org.expasy.jpl.core.ms.spectrum.peak.Peak (also extends java.lang.Comparable<T>, org.expasy.jpl.commons.base.ExplicitlyCloneable)
  • org.expasy.jpl.core.ms.spectrum.PeakList (also extends org.expasy.jpl.core.ms.spectrum.annot.Annotatable, org.expasy.jpl.commons.base.ExplicitlyCloneable)
    • org.expasy.jpl.core.ms.spectrum.BinnedPeakList
  • org.expasy.jpl.core.mol.polymer.pept.term.Terminus
• org.expasy.jpl.core.mol.polymer.pept.term.TerminusType
• org.expasy.jpl.core.mol.chem.api.Weighable
  • org.expasy.jpl.core.mol.polymer.pept.AASequence (also extends org.expasy.jpl.core.mol.polymer.BioPolymer<E>, org.expasy.jpl.core.mol.polymer.pept.NCTermination)
  • org.expasy.jpl.core.mol.chem.api.Atom (also extends org.expasy.jpl.commons.base.Registrable, java.io.Serializable)
  • org.expasy.jpl.core.mol.polymer.BioPolymer<E> (also extends org.expasy.jpl.commons.collection.symbol.seq.SymbolSequence<T>)
    • org.expasy.jpl.core.mol.polymer.pept.AASequence (also extends org.expasy.jpl.core.mol.polymer.pept.NCTermination)
  • org.expasy.jpl.core.mol.modif.Modification (also extends org.expasy.jpl.commons.base.Evaluable, org.expasy.jpl.commons.base.ExplicitlyCloneable, org.expasy.jpl.commons.collection.Mappable, org.expasy.jpl.commons.base.Registrable, java.io.Serializable)
  • org.expasy.jpl.core.mol.chem.api.Molecule (also extends org.expasy.jpl.core.mol.chem.api.ChargedParticle, org.expasy.jpl.commons.base.Registrable, java.io.Serializable)
    • org.expasy.jpl.core.mol.polymer.pept.term.Terminus
  • org.expasy.jpl.core.mol.polymer.pept.term.Terminus

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.expasy.jpl.core.mol.chem.MassCalculator.Accuracy
    • org.expasy.jpl.core.mol.chem.ChemicalFacade.MonomerType
    • org.expasy.jpl.core.mol.chem.api.Ionizable.NeutralMoleculeType
    • org.expasy.jpl.core.mol.chem.impl.ElementManager.AtomEnclosingToken
    • org.expasy.jpl.core.mol.modif.ModifFormat.Format
    • org.expasy.jpl.core.mol.modif.Modification.ModifType
    • org.expasy.jpl.core.mol.monomer.aa.AminoAcidTerm (implements org.expasy.jpl.core.mol.chem.api.Molecule)
    • org.expasy.jpl.core.mol.monomer.aa.AminoAcid (implements org.expasy.jpl.core.mol.chem.api.Molecule)
    • org.expasy.jpl.core.mol.monomer.nuc.RiboNucleotide (implements org.expasy.jpl.core.mol.chem.api.Molecule)
    • org.expasy.jpl.core.mol.monomer.nuc.DeoxyRiboNucleotide (implements org.expasy.jpl.core.mol.chem.api.Molecule)
    • org.expasy.jpl.core.mol.polymer.modif.unimod.UnimodSpecificity.Type
    • org.expasy.jpl.core.mol.polymer.pept.fragmenter.FragmentationType
    • org.expasy.jpl.core.mol.polymer.pept.rule.EditionRule.MultiActionMode
    • org.expasy.jpl.core.mol.polymer.pept.rule.EditionRule.EditionAction.ActionType
    • org.expasy.jpl.core.mol.polymer.pept.term.TerminusTypeImpl.TypeC (implements org.expasy.jpl.core.mol.polymer.pept.term.TerminusType)
    • org.expasy.jpl.core.mol.polymer.pept.term.TerminusTypeImpl.TypeN (implements org.expasy.jpl.core.mol.polymer.pept.term.TerminusType)
    • org.expasy.jpl.core.mol.polymer.pept.term.NTerminus (implements org.expasy.jpl.core.mol.polymer.pept.term.Terminus)
    • org.expasy.jpl.core.mol.polymer.pept.term.CTerminus (implements org.expasy.jpl.core.mol.polymer.pept.term.Terminus)
    • org.expasy.jpl.core.ms.lc.RetentionTime.RTUnit
    • org.expasy.jpl.core.ms.spectrum.PeakListUtils.IntensityTransformationMethod
    • org.expasy.jpl.core.ms.spectrum.annot.FragmentAnnotationImpl.ModifFormat