Hierarchy For All Packages

Package Hierarchies:

• org.biopax.paxtools.command,
• org.biopax.paxtools.controller,
• org.biopax.paxtools.converter,
• org.biopax.paxtools.impl,
• org.biopax.paxtools.impl.level2,
• org.biopax.paxtools.impl.level3,
• org.biopax.paxtools.io,
• org.biopax.paxtools.model,
• org.biopax.paxtools.model.level2,
• org.biopax.paxtools.model.level3,
• org.biopax.paxtools.util

Class Hierarchy

• java.lang.Object
  • org.biopax.paxtools.command.AbstractAddRemoveCommand (implements org.biopax.paxtools.command.Command)
    • org.biopax.paxtools.command.AddCommand
    • org.biopax.paxtools.command.RemoveCommand
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractSet<E> (implements java.util.Set<E>)
      • org.biopax.paxtools.util.AbstractFilterSet<F,E> (implements org.biopax.paxtools.util.Filter<T>)
        • org.biopax.paxtools.util.ClassFilterSet<E,F>
      • org.biopax.paxtools.util.BiopaxSafeSet<E>
      • java.util.HashSet<E> (implements java.lang.Cloneable, java.io.Serializable, java.util.Set<E>)
        • org.biopax.paxtools.util.AccessibleSet<E>
  • org.biopax.paxtools.command.AbstractPropertyCommand<D,R> (implements org.biopax.paxtools.command.Command)
    • org.biopax.paxtools.command.PropertyAddCommand
    • org.biopax.paxtools.command.PropertyRemoveCommand
    • org.biopax.paxtools.command.PropertySetCommand<D,R>
  • org.biopax.paxtools.impl.BioPAXElementImpl (implements org.biopax.paxtools.model.BioPAXElement)
    • org.biopax.paxtools.impl.level3.L3ElementImpl (implements org.biopax.paxtools.model.level3.Level3Element)
      • org.biopax.paxtools.impl.level3.ChemicalConstantImpl (implements org.biopax.paxtools.model.level3.ChemicalConstant)
        • org.biopax.paxtools.impl.level3.DeltaGImpl (implements org.biopax.paxtools.model.level3.DeltaG)
        • org.biopax.paxtools.impl.level3.KPrimeImpl (implements org.biopax.paxtools.model.level3.KPrime)
      • org.biopax.paxtools.impl.level3.ChemicalStructureImpl (implements org.biopax.paxtools.model.level3.ChemicalStructure)
      • org.biopax.paxtools.impl.level3.EntityFeatureImpl (implements org.biopax.paxtools.model.level3.EntityFeature)
        • org.biopax.paxtools.impl.level3.BindingFeatureImpl (implements org.biopax.paxtools.model.level3.BindingFeature)
          • org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl (implements org.biopax.paxtools.model.level3.CovalentBindingFeature)
        • org.biopax.paxtools.impl.level3.FragmentFeatureImpl (implements org.biopax.paxtools.model.level3.FragmentFeature)
        • org.biopax.paxtools.impl.level3.ModificationFeatureImpl (implements org.biopax.paxtools.model.level3.ModificationFeature)
      • org.biopax.paxtools.impl.level3.ExperimentalFormImpl (implements org.biopax.paxtools.model.level3.ExperimentalForm)
      • org.biopax.paxtools.impl.level3.PathwayStepImpl (implements org.biopax.paxtools.model.level3.PathwayStep)
        • org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl (implements org.biopax.paxtools.model.level3.BiochemicalPathwayStep)
      • org.biopax.paxtools.impl.level3.SequenceLocationImpl (implements org.biopax.paxtools.model.level3.SequenceLocation)
        • org.biopax.paxtools.impl.level3.SequenceIntervalImpl (implements org.biopax.paxtools.model.level3.SequenceInterval)
        • org.biopax.paxtools.impl.level3.SequenceSiteImpl (implements org.biopax.paxtools.model.level3.SequenceSite)
      • org.biopax.paxtools.impl.level3.StoichiometryImpl (implements org.biopax.paxtools.model.level3.Stoichiometry)
      • org.biopax.paxtools.impl.level3.XReferrableImpl (implements org.biopax.paxtools.model.level3.XReferrable)
        • org.biopax.paxtools.impl.level3.ControlledVocabularyImpl (implements org.biopax.paxtools.model.level3.ControlledVocabulary)
          • org.biopax.paxtools.impl.level3.CellularLocationVocabularyImpl (implements org.biopax.paxtools.model.level3.CellularLocationVocabulary)
          • org.biopax.paxtools.impl.level3.CellVocabularyImpl (implements org.biopax.paxtools.model.level3.CellVocabulary)
          • org.biopax.paxtools.impl.level3.EntityReferenceTypeVocabularyImpl (implements org.biopax.paxtools.model.level3.EntityReferenceTypeVocabulary)
          • org.biopax.paxtools.impl.level3.EvidenceCodeVocabularyImpl (implements org.biopax.paxtools.model.level3.EvidenceCodeVocabulary)
          • org.biopax.paxtools.impl.level3.ExperimentalFormVocabularyImpl (implements org.biopax.paxtools.model.level3.ExperimentalFormVocabulary)
          • org.biopax.paxtools.impl.level3.InteractionVocabularyImpl (implements org.biopax.paxtools.model.level3.InteractionVocabulary)
          • org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl (implements org.biopax.paxtools.model.level3.PhenotypeVocabulary)
          • org.biopax.paxtools.impl.level3.RelationshipTypeVocabularyImpl (implements org.biopax.paxtools.model.level3.RelationshipTypeVocabulary)
          • org.biopax.paxtools.impl.level3.SequenceModificationVocabularyImpl (implements org.biopax.paxtools.model.level3.SequenceModificationVocabulary)
          • org.biopax.paxtools.impl.level3.SequenceRegionVocabularyImpl (implements org.biopax.paxtools.model.level3.SequenceRegionVocabulary)
          • org.biopax.paxtools.impl.level3.TissueVocabularyImpl (implements org.biopax.paxtools.model.level3.TissueVocabulary)
        • org.biopax.paxtools.impl.level3.EvidenceImpl (implements org.biopax.paxtools.model.level3.Evidence)
        • org.biopax.paxtools.impl.level3.NamedImpl (implements org.biopax.paxtools.model.level3.Named)
          • org.biopax.paxtools.impl.level3.BioSourceImpl (implements org.biopax.paxtools.model.level3.BioSource)
          • org.biopax.paxtools.impl.level3.EntityImpl (implements org.biopax.paxtools.model.level3.Entity)
            • org.biopax.paxtools.impl.level3.GeneImpl (implements org.biopax.paxtools.model.level3.Gene)
            • org.biopax.paxtools.impl.level3.PhysicalEntityImpl (implements org.biopax.paxtools.model.level3.PhysicalEntity)
              • org.biopax.paxtools.impl.level3.ComplexImpl (implements org.biopax.paxtools.model.level3.Complex)
              • org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl (implements org.biopax.paxtools.model.level3.SimplePhysicalEntity)
                • org.biopax.paxtools.impl.level3.NucleicAcidImpl (implements org.biopax.paxtools.model.level3.NucleicAcid)
                  • org.biopax.paxtools.impl.level3.DnaImpl (implements org.biopax.paxtools.model.level3.Dna)
                  • org.biopax.paxtools.impl.level3.DnaRegionImpl (implements org.biopax.paxtools.model.level3.DnaRegion)
                  • org.biopax.paxtools.impl.level3.RnaImpl (implements org.biopax.paxtools.model.level3.Rna)
                  • org.biopax.paxtools.impl.level3.RnaRegionImpl (implements org.biopax.paxtools.model.level3.RnaRegion)
                • org.biopax.paxtools.impl.level3.ProteinImpl (implements org.biopax.paxtools.model.level3.Protein)
                • org.biopax.paxtools.impl.level3.SmallMoleculeImpl (implements org.biopax.paxtools.model.level3.SmallMolecule)
            • org.biopax.paxtools.impl.level3.ProcessImpl (implements org.biopax.paxtools.model.level3.Process)
              • org.biopax.paxtools.impl.level3.InteractionImpl (implements org.biopax.paxtools.model.level3.Interaction)
                • org.biopax.paxtools.impl.level3.ControlImpl (implements org.biopax.paxtools.model.level3.Control)
                  • org.biopax.paxtools.impl.level3.CatalysisImpl (implements org.biopax.paxtools.model.level3.Catalysis)
                  • org.biopax.paxtools.impl.level3.ModulationImpl (implements org.biopax.paxtools.model.level3.Modulation)
                  • org.biopax.paxtools.impl.level3.TemplateReactionRegulationImpl (implements org.biopax.paxtools.model.level3.TemplateReactionRegulation)
                • org.biopax.paxtools.impl.level3.ConversionImpl (implements org.biopax.paxtools.model.level3.Conversion)
                  • org.biopax.paxtools.impl.level3.BiochemicalReactionImpl (implements org.biopax.paxtools.model.level3.BiochemicalReaction)
                    • org.biopax.paxtools.impl.level3.TransportWithBiochemicalReactionImpl (implements org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction)
                  • org.biopax.paxtools.impl.level3.ComplexAssemblyImpl (implements org.biopax.paxtools.model.level3.ComplexAssembly)
                  • org.biopax.paxtools.impl.level3.DegradationImpl (implements org.biopax.paxtools.model.level3.Degradation)
                  • org.biopax.paxtools.impl.level3.TransportImpl (implements org.biopax.paxtools.model.level3.Transport)
                • org.biopax.paxtools.impl.level3.GeneticInteractionImpl (implements org.biopax.paxtools.model.level3.GeneticInteraction)
                • org.biopax.paxtools.impl.level3.MolecularInteractionImpl (implements org.biopax.paxtools.model.level3.MolecularInteraction)
                • org.biopax.paxtools.impl.level3.TemplateReactionImpl (implements org.biopax.paxtools.model.level3.TemplateReaction)
              • org.biopax.paxtools.impl.level3.PathwayImpl (implements org.biopax.paxtools.model.level3.Pathway)
          • org.biopax.paxtools.impl.level3.EntityReferenceImpl (implements org.biopax.paxtools.model.level3.EntityReference)
            • org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl (implements org.biopax.paxtools.model.level3.SequenceEntityReference)
              • org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl (implements org.biopax.paxtools.model.level3.NucleicAcidReference)
                • org.biopax.paxtools.impl.level3.DnaReferenceImpl (implements org.biopax.paxtools.model.level3.DnaReference)
                • org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl (implements org.biopax.paxtools.model.level3.NucleicAcidRegionReference)
                  • org.biopax.paxtools.impl.level3.DnaRegionReferenceImpl (implements org.biopax.paxtools.model.level3.DnaRegionReference)
                  • org.biopax.paxtools.impl.level3.RnaRegionReferenceImpl (implements org.biopax.paxtools.model.level3.RnaRegionReference)
                • org.biopax.paxtools.impl.level3.RnaReferenceImpl (implements org.biopax.paxtools.model.level3.RnaReference)
              • org.biopax.paxtools.impl.level3.ProteinReferenceImpl (implements org.biopax.paxtools.model.level3.ProteinReference)
            • org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl (implements org.biopax.paxtools.model.level3.SmallMoleculeReference)
          • org.biopax.paxtools.impl.level3.ProvenanceImpl (implements org.biopax.paxtools.model.level3.Provenance)
        • org.biopax.paxtools.impl.level3.ScoreImpl (implements org.biopax.paxtools.model.level3.Score)
      • org.biopax.paxtools.impl.level3.XrefImpl (implements org.biopax.paxtools.model.level3.Xref)
        • org.biopax.paxtools.impl.level3.PublicationXrefImpl (implements org.biopax.paxtools.model.level3.PublicationXref)
        • org.biopax.paxtools.impl.level3.RelationshipXrefImpl (implements org.biopax.paxtools.model.level3.RelationshipXref)
        • org.biopax.paxtools.impl.level3.UnificationXrefImpl (implements org.biopax.paxtools.model.level3.UnificationXref)
  • org.biopax.paxtools.model.BioPAXFactory
    • org.biopax.paxtools.impl.MockFactory
  • org.biopax.paxtools.io.BioPAXIOHandlerAdapter (implements org.biopax.paxtools.io.BioPAXIOHandler)
    • org.biopax.paxtools.io.SimpleIOHandler
  • org.biopax.paxtools.controller.Cloner (implements org.biopax.paxtools.controller.Visitor)
  • org.biopax.paxtools.command.CommandManager
  • org.biopax.paxtools.controller.Completer (implements org.biopax.paxtools.controller.Visitor)
  • org.biopax.paxtools.util.CompositeIterator<T> (implements java.util.Iterator<E>)
  • org.biopax.paxtools.controller.ConversionScore (implements java.lang.Comparable<T>)
  • org.biopax.paxtools.controller.EditorMapImpl (implements org.biopax.paxtools.controller.EditorMap)
  • org.biopax.paxtools.util.EquivalenceGrouper<T>
  • org.biopax.paxtools.controller.Fetcher
  • org.biopax.paxtools.controller.IdFetcher
  • org.biopax.paxtools.controller.Integrator
  • org.biopax.paxtools.controller.Merger (implements org.biopax.paxtools.controller.Visitor)
  • org.biopax.paxtools.impl.ModelImpl (implements org.biopax.paxtools.model.Model)
  • org.biopax.paxtools.controller.ModelUtils
  • org.biopax.paxtools.controller.PropertyAccessorAdapter<D,R> (implements org.biopax.paxtools.controller.PropertyAccessor<D,R>)
    • org.biopax.paxtools.controller.DecoratingPropertyAccessor<D,R>
      • org.biopax.paxtools.controller.FilteredByDomainPropertyAccessor<D,R>
      • org.biopax.paxtools.controller.FilteredPropertyAccessor<D,R>
      • org.biopax.paxtools.controller.TransitivePropertyAccessor<R,D>
    • org.biopax.paxtools.controller.PathAccessor
    • org.biopax.paxtools.controller.SimplePropertyAccessor<D,R>
      • org.biopax.paxtools.controller.AbstractPropertyEditor<D,R> (implements org.biopax.paxtools.controller.PropertyEditor<D,R>)
        • org.biopax.paxtools.controller.EnumeratedPropertyEditor<D,R> (implements org.biopax.paxtools.controller.DataPropertyEditor<D,R>)
        • org.biopax.paxtools.controller.ObjectPropertyEditor<D,R>
        • org.biopax.paxtools.controller.PrimitivePropertyEditor<D,R> (implements org.biopax.paxtools.controller.DataPropertyEditor<D,R>)
        • org.biopax.paxtools.controller.StringPropertyEditor<D> (implements org.biopax.paxtools.controller.DataPropertyEditor<D,R>)
    • org.biopax.paxtools.controller.UnionPropertyAccessor<D,R>
  • org.biopax.paxtools.controller.ReusedPEPHelper
  • org.biopax.paxtools.util.SetEquivalenceChecker
  • org.biopax.paxtools.controller.ShallowCopy (implements org.biopax.paxtools.controller.Visitor)
  • org.biopax.paxtools.io.SimpleIOHandler.Triple
  • org.biopax.paxtools.controller.SimpleMerger
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • org.biopax.paxtools.util.BioPaxIOException
        • java.lang.IllegalArgumentException
          • org.biopax.paxtools.util.IllegalBioPAXArgumentException
  • org.biopax.paxtools.controller.Traverser
    • org.biopax.paxtools.controller.AbstractTraverser (implements org.biopax.paxtools.controller.Visitor)
      • org.biopax.paxtools.converter.LevelUpgrader (implements org.biopax.paxtools.controller.ModelFilter)
    • org.biopax.paxtools.controller.TraverserBilinked

Interface Hierarchy

• org.biopax.paxtools.io.BioPAXIOHandler
• org.biopax.paxtools.util.BPCollections.CollectionProvider
• java.lang.Cloneable
  • org.biopax.paxtools.model.BioPAXElement (also extends java.io.Serializable)
    • org.biopax.paxtools.model.level2.Level2Element
      • org.biopax.paxtools.model.level2.entity (also extends org.biopax.paxtools.model.level2.InteractionParticipant, org.biopax.paxtools.model.level2.XReferrable)
        • org.biopax.paxtools.model.level2.physicalEntity
          • org.biopax.paxtools.model.level2.complex
          • org.biopax.paxtools.model.level2.sequenceEntity
            • org.biopax.paxtools.model.level2.dna
            • org.biopax.paxtools.model.level2.protein
            • org.biopax.paxtools.model.level2.rna
          • org.biopax.paxtools.model.level2.smallMolecule
        • org.biopax.paxtools.model.level2.process (also extends org.biopax.paxtools.model.level2.pathwayComponent)
          • org.biopax.paxtools.model.level2.interaction
            • org.biopax.paxtools.model.level2.physicalInteraction
              • org.biopax.paxtools.model.level2.control
                • org.biopax.paxtools.model.level2.catalysis
                • org.biopax.paxtools.model.level2.modulation
              • org.biopax.paxtools.model.level2.conversion
                • org.biopax.paxtools.model.level2.biochemicalReaction
                  • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.transport)
                • org.biopax.paxtools.model.level2.complexAssembly
                • org.biopax.paxtools.model.level2.transport
                  • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.biochemicalReaction)
          • org.biopax.paxtools.model.level2.pathway
      • org.biopax.paxtools.model.level2.InteractionParticipant
        • org.biopax.paxtools.model.level2.entity (also extends org.biopax.paxtools.model.level2.Level2Element, org.biopax.paxtools.model.level2.XReferrable)
          • org.biopax.paxtools.model.level2.physicalEntity
            • org.biopax.paxtools.model.level2.complex
            • org.biopax.paxtools.model.level2.sequenceEntity
              • org.biopax.paxtools.model.level2.dna
              • org.biopax.paxtools.model.level2.protein
              • org.biopax.paxtools.model.level2.rna
            • org.biopax.paxtools.model.level2.smallMolecule
          • org.biopax.paxtools.model.level2.process (also extends org.biopax.paxtools.model.level2.pathwayComponent)
            • org.biopax.paxtools.model.level2.interaction
              • org.biopax.paxtools.model.level2.physicalInteraction
                • org.biopax.paxtools.model.level2.control
                  • org.biopax.paxtools.model.level2.catalysis
                  • org.biopax.paxtools.model.level2.modulation
                • org.biopax.paxtools.model.level2.conversion
                  • org.biopax.paxtools.model.level2.biochemicalReaction
                    • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.transport)
                  • org.biopax.paxtools.model.level2.complexAssembly
                  • org.biopax.paxtools.model.level2.transport
                    • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.biochemicalReaction)
            • org.biopax.paxtools.model.level2.pathway
        • org.biopax.paxtools.model.level2.physicalEntityParticipant (also extends org.biopax.paxtools.model.level2.utilityClass)
          • org.biopax.paxtools.model.level2.sequenceParticipant
      • org.biopax.paxtools.model.level2.pathwayComponent
        • org.biopax.paxtools.model.level2.pathwayStep (also extends org.biopax.paxtools.model.level2.utilityClass)
        • org.biopax.paxtools.model.level2.process (also extends org.biopax.paxtools.model.level2.entity)
          • org.biopax.paxtools.model.level2.interaction
            • org.biopax.paxtools.model.level2.physicalInteraction
              • org.biopax.paxtools.model.level2.control
                • org.biopax.paxtools.model.level2.catalysis
                • org.biopax.paxtools.model.level2.modulation
              • org.biopax.paxtools.model.level2.conversion
                • org.biopax.paxtools.model.level2.biochemicalReaction
                  • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.transport)
                • org.biopax.paxtools.model.level2.complexAssembly
                • org.biopax.paxtools.model.level2.transport
                  • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.biochemicalReaction)
          • org.biopax.paxtools.model.level2.pathway
      • org.biopax.paxtools.model.level2.utilityClass
        • org.biopax.paxtools.model.level2.chemicalStructure
        • org.biopax.paxtools.model.level2.confidence (also extends org.biopax.paxtools.model.level2.XReferrable)
        • org.biopax.paxtools.model.level2.deltaGprimeO
        • org.biopax.paxtools.model.level2.evidence (also extends org.biopax.paxtools.model.level2.XReferrable)
        • org.biopax.paxtools.model.level2.experimentalForm
        • org.biopax.paxtools.model.level2.externalReferenceUtilityClass
          • org.biopax.paxtools.model.level2.bioSource
          • org.biopax.paxtools.model.level2.dataSource (also extends org.biopax.paxtools.model.level2.XReferrable)
          • org.biopax.paxtools.model.level2.openControlledVocabulary (also extends org.biopax.paxtools.model.level2.XReferrable)
          • org.biopax.paxtools.model.level2.xref
            • org.biopax.paxtools.model.level2.publicationXref
            • org.biopax.paxtools.model.level2.relationshipXref
            • org.biopax.paxtools.model.level2.unificationXref
        • org.biopax.paxtools.model.level2.kPrime
        • org.biopax.paxtools.model.level2.pathwayStep (also extends org.biopax.paxtools.model.level2.pathwayComponent)
        • org.biopax.paxtools.model.level2.physicalEntityParticipant (also extends org.biopax.paxtools.model.level2.InteractionParticipant)
          • org.biopax.paxtools.model.level2.sequenceParticipant
        • org.biopax.paxtools.model.level2.sequenceFeature (also extends org.biopax.paxtools.model.level2.XReferrable)
        • org.biopax.paxtools.model.level2.sequenceLocation
          • org.biopax.paxtools.model.level2.sequenceInterval
          • org.biopax.paxtools.model.level2.sequenceSite
      • org.biopax.paxtools.model.level2.XReferrable
        • org.biopax.paxtools.model.level2.confidence (also extends org.biopax.paxtools.model.level2.utilityClass)
        • org.biopax.paxtools.model.level2.dataSource (also extends org.biopax.paxtools.model.level2.externalReferenceUtilityClass)
        • org.biopax.paxtools.model.level2.entity (also extends org.biopax.paxtools.model.level2.InteractionParticipant, org.biopax.paxtools.model.level2.Level2Element)
          • org.biopax.paxtools.model.level2.physicalEntity
            • org.biopax.paxtools.model.level2.complex
            • org.biopax.paxtools.model.level2.sequenceEntity
              • org.biopax.paxtools.model.level2.dna
              • org.biopax.paxtools.model.level2.protein
              • org.biopax.paxtools.model.level2.rna
            • org.biopax.paxtools.model.level2.smallMolecule
          • org.biopax.paxtools.model.level2.process (also extends org.biopax.paxtools.model.level2.pathwayComponent)
            • org.biopax.paxtools.model.level2.interaction
              • org.biopax.paxtools.model.level2.physicalInteraction
                • org.biopax.paxtools.model.level2.control
                  • org.biopax.paxtools.model.level2.catalysis
                  • org.biopax.paxtools.model.level2.modulation
                • org.biopax.paxtools.model.level2.conversion
                  • org.biopax.paxtools.model.level2.biochemicalReaction
                    • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.transport)
                  • org.biopax.paxtools.model.level2.complexAssembly
                  • org.biopax.paxtools.model.level2.transport
                    • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.biochemicalReaction)
            • org.biopax.paxtools.model.level2.pathway
        • org.biopax.paxtools.model.level2.evidence (also extends org.biopax.paxtools.model.level2.utilityClass)
        • org.biopax.paxtools.model.level2.openControlledVocabulary (also extends org.biopax.paxtools.model.level2.externalReferenceUtilityClass)
        • org.biopax.paxtools.model.level2.sequenceFeature (also extends org.biopax.paxtools.model.level2.utilityClass)
    • org.biopax.paxtools.model.level3.Level3Element
      • org.biopax.paxtools.model.level3.Entity (also extends org.biopax.paxtools.model.level3.Named, org.biopax.paxtools.model.level3.Observable)
        • org.biopax.paxtools.model.level3.Controller
          • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Process)
          • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Entity)
            • org.biopax.paxtools.model.level3.Complex
            • org.biopax.paxtools.model.level3.SimplePhysicalEntity
              • org.biopax.paxtools.model.level3.SequenceEntity
                • org.biopax.paxtools.model.level3.NucleicAcid
                  • org.biopax.paxtools.model.level3.Dna
                  • org.biopax.paxtools.model.level3.DnaRegion
                  • org.biopax.paxtools.model.level3.Rna
                  • org.biopax.paxtools.model.level3.RnaRegion
                • org.biopax.paxtools.model.level3.Protein
              • org.biopax.paxtools.model.level3.SmallMolecule
        • org.biopax.paxtools.model.level3.Gene
        • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Controller)
          • org.biopax.paxtools.model.level3.Complex
          • org.biopax.paxtools.model.level3.SimplePhysicalEntity
            • org.biopax.paxtools.model.level3.SequenceEntity
              • org.biopax.paxtools.model.level3.NucleicAcid
                • org.biopax.paxtools.model.level3.Dna
                • org.biopax.paxtools.model.level3.DnaRegion
                • org.biopax.paxtools.model.level3.Rna
                • org.biopax.paxtools.model.level3.RnaRegion
              • org.biopax.paxtools.model.level3.Protein
            • org.biopax.paxtools.model.level3.SmallMolecule
        • org.biopax.paxtools.model.level3.Process
          • org.biopax.paxtools.model.level3.Interaction
            • org.biopax.paxtools.model.level3.Control
              • org.biopax.paxtools.model.level3.Catalysis
              • org.biopax.paxtools.model.level3.Modulation
              • org.biopax.paxtools.model.level3.TemplateReactionRegulation
            • org.biopax.paxtools.model.level3.Conversion
              • org.biopax.paxtools.model.level3.BiochemicalReaction
                • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.Transport)
              • org.biopax.paxtools.model.level3.ComplexAssembly
              • org.biopax.paxtools.model.level3.Degradation
              • org.biopax.paxtools.model.level3.Transport
                • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.BiochemicalReaction)
            • org.biopax.paxtools.model.level3.GeneticInteraction
            • org.biopax.paxtools.model.level3.MolecularInteraction
            • org.biopax.paxtools.model.level3.TemplateReaction
          • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Controller)
      • org.biopax.paxtools.model.level3.Observable
        • org.biopax.paxtools.model.level3.Entity (also extends org.biopax.paxtools.model.level3.Level3Element, org.biopax.paxtools.model.level3.Named)
          • org.biopax.paxtools.model.level3.Controller
            • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Process)
            • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Entity)
              • org.biopax.paxtools.model.level3.Complex
              • org.biopax.paxtools.model.level3.SimplePhysicalEntity
                • org.biopax.paxtools.model.level3.SequenceEntity
                  • org.biopax.paxtools.model.level3.NucleicAcid
                    • org.biopax.paxtools.model.level3.Dna
                    • org.biopax.paxtools.model.level3.DnaRegion
                    • org.biopax.paxtools.model.level3.Rna
                    • org.biopax.paxtools.model.level3.RnaRegion
                  • org.biopax.paxtools.model.level3.Protein
                • org.biopax.paxtools.model.level3.SmallMolecule
          • org.biopax.paxtools.model.level3.Gene
          • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Controller)
            • org.biopax.paxtools.model.level3.Complex
            • org.biopax.paxtools.model.level3.SimplePhysicalEntity
              • org.biopax.paxtools.model.level3.SequenceEntity
                • org.biopax.paxtools.model.level3.NucleicAcid
                  • org.biopax.paxtools.model.level3.Dna
                  • org.biopax.paxtools.model.level3.DnaRegion
                  • org.biopax.paxtools.model.level3.Rna
                  • org.biopax.paxtools.model.level3.RnaRegion
                • org.biopax.paxtools.model.level3.Protein
              • org.biopax.paxtools.model.level3.SmallMolecule
          • org.biopax.paxtools.model.level3.Process
            • org.biopax.paxtools.model.level3.Interaction
              • org.biopax.paxtools.model.level3.Control
                • org.biopax.paxtools.model.level3.Catalysis
                • org.biopax.paxtools.model.level3.Modulation
                • org.biopax.paxtools.model.level3.TemplateReactionRegulation
              • org.biopax.paxtools.model.level3.Conversion
                • org.biopax.paxtools.model.level3.BiochemicalReaction
                  • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.Transport)
                • org.biopax.paxtools.model.level3.ComplexAssembly
                • org.biopax.paxtools.model.level3.Degradation
                • org.biopax.paxtools.model.level3.Transport
                  • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.BiochemicalReaction)
              • org.biopax.paxtools.model.level3.GeneticInteraction
              • org.biopax.paxtools.model.level3.MolecularInteraction
              • org.biopax.paxtools.model.level3.TemplateReaction
            • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Controller)
        • org.biopax.paxtools.model.level3.EntityFeature (also extends org.biopax.paxtools.model.level3.UtilityClass)
          • org.biopax.paxtools.model.level3.BindingFeature
            • org.biopax.paxtools.model.level3.CovalentBindingFeature (also extends org.biopax.paxtools.model.level3.ModificationFeature)
          • org.biopax.paxtools.model.level3.FragmentFeature
          • org.biopax.paxtools.model.level3.ModificationFeature
            • org.biopax.paxtools.model.level3.CovalentBindingFeature (also extends org.biopax.paxtools.model.level3.BindingFeature)
        • org.biopax.paxtools.model.level3.EntityReference (also extends org.biopax.paxtools.model.level3.Named, org.biopax.paxtools.model.level3.UtilityClass)
          • org.biopax.paxtools.model.level3.SequenceEntityReference
            • org.biopax.paxtools.model.level3.NucleicAcidReference
              • org.biopax.paxtools.model.level3.DnaReference
              • org.biopax.paxtools.model.level3.NucleicAcidRegionReference
                • org.biopax.paxtools.model.level3.DnaRegionReference
                • org.biopax.paxtools.model.level3.RnaRegionReference
              • org.biopax.paxtools.model.level3.RnaReference
            • org.biopax.paxtools.model.level3.ProteinReference
          • org.biopax.paxtools.model.level3.SmallMoleculeReference
        • org.biopax.paxtools.model.level3.PathwayStep (also extends org.biopax.paxtools.model.level3.UtilityClass)
          • org.biopax.paxtools.model.level3.BiochemicalPathwayStep
      • org.biopax.paxtools.model.level3.UtilityClass
        • org.biopax.paxtools.model.level3.BioSource (also extends org.biopax.paxtools.model.level3.Named)
        • org.biopax.paxtools.model.level3.ChemicalConstant
          • org.biopax.paxtools.model.level3.DeltaG
          • org.biopax.paxtools.model.level3.KPrime
        • org.biopax.paxtools.model.level3.ChemicalStructure
        • org.biopax.paxtools.model.level3.ControlledVocabulary (also extends org.biopax.paxtools.model.level3.XReferrable)
          • org.biopax.paxtools.model.level3.CellularLocationVocabulary
          • org.biopax.paxtools.model.level3.CellVocabulary
          • org.biopax.paxtools.model.level3.EntityReferenceTypeVocabulary
          • org.biopax.paxtools.model.level3.EvidenceCodeVocabulary
          • org.biopax.paxtools.model.level3.ExperimentalFormVocabulary
          • org.biopax.paxtools.model.level3.InteractionVocabulary
          • org.biopax.paxtools.model.level3.PhenotypeVocabulary
          • org.biopax.paxtools.model.level3.RelationshipTypeVocabulary
          • org.biopax.paxtools.model.level3.SequenceModificationVocabulary
          • org.biopax.paxtools.model.level3.SequenceRegionVocabulary
          • org.biopax.paxtools.model.level3.TissueVocabulary
        • org.biopax.paxtools.model.level3.EntityFeature (also extends org.biopax.paxtools.model.level3.Observable)
          • org.biopax.paxtools.model.level3.BindingFeature
            • org.biopax.paxtools.model.level3.CovalentBindingFeature (also extends org.biopax.paxtools.model.level3.ModificationFeature)
          • org.biopax.paxtools.model.level3.FragmentFeature
          • org.biopax.paxtools.model.level3.ModificationFeature
            • org.biopax.paxtools.model.level3.CovalentBindingFeature (also extends org.biopax.paxtools.model.level3.BindingFeature)
        • org.biopax.paxtools.model.level3.EntityReference (also extends org.biopax.paxtools.model.level3.Named, org.biopax.paxtools.model.level3.Observable)
          • org.biopax.paxtools.model.level3.SequenceEntityReference
            • org.biopax.paxtools.model.level3.NucleicAcidReference
              • org.biopax.paxtools.model.level3.DnaReference
              • org.biopax.paxtools.model.level3.NucleicAcidRegionReference
                • org.biopax.paxtools.model.level3.DnaRegionReference
                • org.biopax.paxtools.model.level3.RnaRegionReference
              • org.biopax.paxtools.model.level3.RnaReference
            • org.biopax.paxtools.model.level3.ProteinReference
          • org.biopax.paxtools.model.level3.SmallMoleculeReference
        • org.biopax.paxtools.model.level3.Evidence (also extends org.biopax.paxtools.model.level3.XReferrable)
        • org.biopax.paxtools.model.level3.ExperimentalForm
        • org.biopax.paxtools.model.level3.PathwayStep (also extends org.biopax.paxtools.model.level3.Observable)
          • org.biopax.paxtools.model.level3.BiochemicalPathwayStep
        • org.biopax.paxtools.model.level3.Provenance (also extends org.biopax.paxtools.model.level3.Named, org.biopax.paxtools.model.level3.XReferrable)
        • org.biopax.paxtools.model.level3.Score (also extends org.biopax.paxtools.model.level3.XReferrable)
        • org.biopax.paxtools.model.level3.SequenceLocation
          • org.biopax.paxtools.model.level3.SequenceInterval
          • org.biopax.paxtools.model.level3.SequenceSite
        • org.biopax.paxtools.model.level3.Stoichiometry
        • org.biopax.paxtools.model.level3.Xref
          • org.biopax.paxtools.model.level3.PublicationXref
          • org.biopax.paxtools.model.level3.RelationshipXref
          • org.biopax.paxtools.model.level3.UnificationXref
      • org.biopax.paxtools.model.level3.XReferrable
        • org.biopax.paxtools.model.level3.ControlledVocabulary (also extends org.biopax.paxtools.model.level3.UtilityClass)
          • org.biopax.paxtools.model.level3.CellularLocationVocabulary
          • org.biopax.paxtools.model.level3.CellVocabulary
          • org.biopax.paxtools.model.level3.EntityReferenceTypeVocabulary
          • org.biopax.paxtools.model.level3.EvidenceCodeVocabulary
          • org.biopax.paxtools.model.level3.ExperimentalFormVocabulary
          • org.biopax.paxtools.model.level3.InteractionVocabulary
          • org.biopax.paxtools.model.level3.PhenotypeVocabulary
          • org.biopax.paxtools.model.level3.RelationshipTypeVocabulary
          • org.biopax.paxtools.model.level3.SequenceModificationVocabulary
          • org.biopax.paxtools.model.level3.SequenceRegionVocabulary
          • org.biopax.paxtools.model.level3.TissueVocabulary
        • org.biopax.paxtools.model.level3.Evidence (also extends org.biopax.paxtools.model.level3.UtilityClass)
        • org.biopax.paxtools.model.level3.Named
          • org.biopax.paxtools.model.level3.BioSource (also extends org.biopax.paxtools.model.level3.UtilityClass)
          • org.biopax.paxtools.model.level3.Entity (also extends org.biopax.paxtools.model.level3.Level3Element, org.biopax.paxtools.model.level3.Observable)
            • org.biopax.paxtools.model.level3.Controller
              • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Process)
              • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Entity)
                • org.biopax.paxtools.model.level3.Complex
                • org.biopax.paxtools.model.level3.SimplePhysicalEntity
                  • org.biopax.paxtools.model.level3.SequenceEntity
                    • org.biopax.paxtools.model.level3.NucleicAcid
                      • org.biopax.paxtools.model.level3.Dna
                      • org.biopax.paxtools.model.level3.DnaRegion
                      • org.biopax.paxtools.model.level3.Rna
                      • org.biopax.paxtools.model.level3.RnaRegion
                    • org.biopax.paxtools.model.level3.Protein
                  • org.biopax.paxtools.model.level3.SmallMolecule
            • org.biopax.paxtools.model.level3.Gene
            • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Controller)
              • org.biopax.paxtools.model.level3.Complex
              • org.biopax.paxtools.model.level3.SimplePhysicalEntity
                • org.biopax.paxtools.model.level3.SequenceEntity
                  • org.biopax.paxtools.model.level3.NucleicAcid
                    • org.biopax.paxtools.model.level3.Dna
                    • org.biopax.paxtools.model.level3.DnaRegion
                    • org.biopax.paxtools.model.level3.Rna
                    • org.biopax.paxtools.model.level3.RnaRegion
                  • org.biopax.paxtools.model.level3.Protein
                • org.biopax.paxtools.model.level3.SmallMolecule
            • org.biopax.paxtools.model.level3.Process
              • org.biopax.paxtools.model.level3.Interaction
                • org.biopax.paxtools.model.level3.Control
                  • org.biopax.paxtools.model.level3.Catalysis
                  • org.biopax.paxtools.model.level3.Modulation
                  • org.biopax.paxtools.model.level3.TemplateReactionRegulation
                • org.biopax.paxtools.model.level3.Conversion
                  • org.biopax.paxtools.model.level3.BiochemicalReaction
                    • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.Transport)
                  • org.biopax.paxtools.model.level3.ComplexAssembly
                  • org.biopax.paxtools.model.level3.Degradation
                  • org.biopax.paxtools.model.level3.Transport
                    • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.BiochemicalReaction)
                • org.biopax.paxtools.model.level3.GeneticInteraction
                • org.biopax.paxtools.model.level3.MolecularInteraction
                • org.biopax.paxtools.model.level3.TemplateReaction
              • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Controller)
          • org.biopax.paxtools.model.level3.EntityReference (also extends org.biopax.paxtools.model.level3.Observable, org.biopax.paxtools.model.level3.UtilityClass)
            • org.biopax.paxtools.model.level3.SequenceEntityReference
              • org.biopax.paxtools.model.level3.NucleicAcidReference
                • org.biopax.paxtools.model.level3.DnaReference
                • org.biopax.paxtools.model.level3.NucleicAcidRegionReference
                  • org.biopax.paxtools.model.level3.DnaRegionReference
                  • org.biopax.paxtools.model.level3.RnaRegionReference
                • org.biopax.paxtools.model.level3.RnaReference
              • org.biopax.paxtools.model.level3.ProteinReference
            • org.biopax.paxtools.model.level3.SmallMoleculeReference
          • org.biopax.paxtools.model.level3.Provenance (also extends org.biopax.paxtools.model.level3.UtilityClass, org.biopax.paxtools.model.level3.XReferrable)
        • org.biopax.paxtools.model.level3.Provenance (also extends org.biopax.paxtools.model.level3.Named, org.biopax.paxtools.model.level3.UtilityClass)
        • org.biopax.paxtools.model.level3.Score (also extends org.biopax.paxtools.model.level3.UtilityClass)
• org.biopax.paxtools.command.Command
• org.biopax.paxtools.controller.EditorMap
• org.biopax.paxtools.util.Filter<T>
  • org.biopax.paxtools.controller.PropertyFilterBilinked
• org.biopax.paxtools.controller.ModelFilter
• org.biopax.paxtools.controller.PropertyAccessor<D,R>
  • org.biopax.paxtools.controller.PropertyEditor<D,R>
    • org.biopax.paxtools.controller.DataPropertyEditor<D,R>
• java.io.Serializable
  • org.biopax.paxtools.model.BioPAXElement (also extends java.lang.Cloneable)
    • org.biopax.paxtools.model.level2.Level2Element
      • org.biopax.paxtools.model.level2.entity (also extends org.biopax.paxtools.model.level2.InteractionParticipant, org.biopax.paxtools.model.level2.XReferrable)
        • org.biopax.paxtools.model.level2.physicalEntity
          • org.biopax.paxtools.model.level2.complex
          • org.biopax.paxtools.model.level2.sequenceEntity
            • org.biopax.paxtools.model.level2.dna
            • org.biopax.paxtools.model.level2.protein
            • org.biopax.paxtools.model.level2.rna
          • org.biopax.paxtools.model.level2.smallMolecule
        • org.biopax.paxtools.model.level2.process (also extends org.biopax.paxtools.model.level2.pathwayComponent)
          • org.biopax.paxtools.model.level2.interaction
            • org.biopax.paxtools.model.level2.physicalInteraction
              • org.biopax.paxtools.model.level2.control
                • org.biopax.paxtools.model.level2.catalysis
                • org.biopax.paxtools.model.level2.modulation
              • org.biopax.paxtools.model.level2.conversion
                • org.biopax.paxtools.model.level2.biochemicalReaction
                  • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.transport)
                • org.biopax.paxtools.model.level2.complexAssembly
                • org.biopax.paxtools.model.level2.transport
                  • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.biochemicalReaction)
          • org.biopax.paxtools.model.level2.pathway
      • org.biopax.paxtools.model.level2.InteractionParticipant
        • org.biopax.paxtools.model.level2.entity (also extends org.biopax.paxtools.model.level2.Level2Element, org.biopax.paxtools.model.level2.XReferrable)
          • org.biopax.paxtools.model.level2.physicalEntity
            • org.biopax.paxtools.model.level2.complex
            • org.biopax.paxtools.model.level2.sequenceEntity
              • org.biopax.paxtools.model.level2.dna
              • org.biopax.paxtools.model.level2.protein
              • org.biopax.paxtools.model.level2.rna
            • org.biopax.paxtools.model.level2.smallMolecule
          • org.biopax.paxtools.model.level2.process (also extends org.biopax.paxtools.model.level2.pathwayComponent)
            • org.biopax.paxtools.model.level2.interaction
              • org.biopax.paxtools.model.level2.physicalInteraction
                • org.biopax.paxtools.model.level2.control
                  • org.biopax.paxtools.model.level2.catalysis
                  • org.biopax.paxtools.model.level2.modulation
                • org.biopax.paxtools.model.level2.conversion
                  • org.biopax.paxtools.model.level2.biochemicalReaction
                    • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.transport)
                  • org.biopax.paxtools.model.level2.complexAssembly
                  • org.biopax.paxtools.model.level2.transport
                    • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.biochemicalReaction)
            • org.biopax.paxtools.model.level2.pathway
        • org.biopax.paxtools.model.level2.physicalEntityParticipant (also extends org.biopax.paxtools.model.level2.utilityClass)
          • org.biopax.paxtools.model.level2.sequenceParticipant
      • org.biopax.paxtools.model.level2.pathwayComponent
        • org.biopax.paxtools.model.level2.pathwayStep (also extends org.biopax.paxtools.model.level2.utilityClass)
        • org.biopax.paxtools.model.level2.process (also extends org.biopax.paxtools.model.level2.entity)
          • org.biopax.paxtools.model.level2.interaction
            • org.biopax.paxtools.model.level2.physicalInteraction
              • org.biopax.paxtools.model.level2.control
                • org.biopax.paxtools.model.level2.catalysis
                • org.biopax.paxtools.model.level2.modulation
              • org.biopax.paxtools.model.level2.conversion
                • org.biopax.paxtools.model.level2.biochemicalReaction
                  • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.transport)
                • org.biopax.paxtools.model.level2.complexAssembly
                • org.biopax.paxtools.model.level2.transport
                  • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.biochemicalReaction)
          • org.biopax.paxtools.model.level2.pathway
      • org.biopax.paxtools.model.level2.utilityClass
        • org.biopax.paxtools.model.level2.chemicalStructure
        • org.biopax.paxtools.model.level2.confidence (also extends org.biopax.paxtools.model.level2.XReferrable)
        • org.biopax.paxtools.model.level2.deltaGprimeO
        • org.biopax.paxtools.model.level2.evidence (also extends org.biopax.paxtools.model.level2.XReferrable)
        • org.biopax.paxtools.model.level2.experimentalForm
        • org.biopax.paxtools.model.level2.externalReferenceUtilityClass
          • org.biopax.paxtools.model.level2.bioSource
          • org.biopax.paxtools.model.level2.dataSource (also extends org.biopax.paxtools.model.level2.XReferrable)
          • org.biopax.paxtools.model.level2.openControlledVocabulary (also extends org.biopax.paxtools.model.level2.XReferrable)
          • org.biopax.paxtools.model.level2.xref
            • org.biopax.paxtools.model.level2.publicationXref
            • org.biopax.paxtools.model.level2.relationshipXref
            • org.biopax.paxtools.model.level2.unificationXref
        • org.biopax.paxtools.model.level2.kPrime
        • org.biopax.paxtools.model.level2.pathwayStep (also extends org.biopax.paxtools.model.level2.pathwayComponent)
        • org.biopax.paxtools.model.level2.physicalEntityParticipant (also extends org.biopax.paxtools.model.level2.InteractionParticipant)
          • org.biopax.paxtools.model.level2.sequenceParticipant
        • org.biopax.paxtools.model.level2.sequenceFeature (also extends org.biopax.paxtools.model.level2.XReferrable)
        • org.biopax.paxtools.model.level2.sequenceLocation
          • org.biopax.paxtools.model.level2.sequenceInterval
          • org.biopax.paxtools.model.level2.sequenceSite
      • org.biopax.paxtools.model.level2.XReferrable
        • org.biopax.paxtools.model.level2.confidence (also extends org.biopax.paxtools.model.level2.utilityClass)
        • org.biopax.paxtools.model.level2.dataSource (also extends org.biopax.paxtools.model.level2.externalReferenceUtilityClass)
        • org.biopax.paxtools.model.level2.entity (also extends org.biopax.paxtools.model.level2.InteractionParticipant, org.biopax.paxtools.model.level2.Level2Element)
          • org.biopax.paxtools.model.level2.physicalEntity
            • org.biopax.paxtools.model.level2.complex
            • org.biopax.paxtools.model.level2.sequenceEntity
              • org.biopax.paxtools.model.level2.dna
              • org.biopax.paxtools.model.level2.protein
              • org.biopax.paxtools.model.level2.rna
            • org.biopax.paxtools.model.level2.smallMolecule
          • org.biopax.paxtools.model.level2.process (also extends org.biopax.paxtools.model.level2.pathwayComponent)
            • org.biopax.paxtools.model.level2.interaction
              • org.biopax.paxtools.model.level2.physicalInteraction
                • org.biopax.paxtools.model.level2.control
                  • org.biopax.paxtools.model.level2.catalysis
                  • org.biopax.paxtools.model.level2.modulation
                • org.biopax.paxtools.model.level2.conversion
                  • org.biopax.paxtools.model.level2.biochemicalReaction
                    • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.transport)
                  • org.biopax.paxtools.model.level2.complexAssembly
                  • org.biopax.paxtools.model.level2.transport
                    • org.biopax.paxtools.model.level2.transportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level2.biochemicalReaction)
            • org.biopax.paxtools.model.level2.pathway
        • org.biopax.paxtools.model.level2.evidence (also extends org.biopax.paxtools.model.level2.utilityClass)
        • org.biopax.paxtools.model.level2.openControlledVocabulary (also extends org.biopax.paxtools.model.level2.externalReferenceUtilityClass)
        • org.biopax.paxtools.model.level2.sequenceFeature (also extends org.biopax.paxtools.model.level2.utilityClass)
    • org.biopax.paxtools.model.level3.Level3Element
      • org.biopax.paxtools.model.level3.Entity (also extends org.biopax.paxtools.model.level3.Named, org.biopax.paxtools.model.level3.Observable)
        • org.biopax.paxtools.model.level3.Controller
          • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Process)
          • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Entity)
            • org.biopax.paxtools.model.level3.Complex
            • org.biopax.paxtools.model.level3.SimplePhysicalEntity
              • org.biopax.paxtools.model.level3.SequenceEntity
                • org.biopax.paxtools.model.level3.NucleicAcid
                  • org.biopax.paxtools.model.level3.Dna
                  • org.biopax.paxtools.model.level3.DnaRegion
                  • org.biopax.paxtools.model.level3.Rna
                  • org.biopax.paxtools.model.level3.RnaRegion
                • org.biopax.paxtools.model.level3.Protein
              • org.biopax.paxtools.model.level3.SmallMolecule
        • org.biopax.paxtools.model.level3.Gene
        • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Controller)
          • org.biopax.paxtools.model.level3.Complex
          • org.biopax.paxtools.model.level3.SimplePhysicalEntity
            • org.biopax.paxtools.model.level3.SequenceEntity
              • org.biopax.paxtools.model.level3.NucleicAcid
                • org.biopax.paxtools.model.level3.Dna
                • org.biopax.paxtools.model.level3.DnaRegion
                • org.biopax.paxtools.model.level3.Rna
                • org.biopax.paxtools.model.level3.RnaRegion
              • org.biopax.paxtools.model.level3.Protein
            • org.biopax.paxtools.model.level3.SmallMolecule
        • org.biopax.paxtools.model.level3.Process
          • org.biopax.paxtools.model.level3.Interaction
            • org.biopax.paxtools.model.level3.Control
              • org.biopax.paxtools.model.level3.Catalysis
              • org.biopax.paxtools.model.level3.Modulation
              • org.biopax.paxtools.model.level3.TemplateReactionRegulation
            • org.biopax.paxtools.model.level3.Conversion
              • org.biopax.paxtools.model.level3.BiochemicalReaction
                • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.Transport)
              • org.biopax.paxtools.model.level3.ComplexAssembly
              • org.biopax.paxtools.model.level3.Degradation
              • org.biopax.paxtools.model.level3.Transport
                • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.BiochemicalReaction)
            • org.biopax.paxtools.model.level3.GeneticInteraction
            • org.biopax.paxtools.model.level3.MolecularInteraction
            • org.biopax.paxtools.model.level3.TemplateReaction
          • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Controller)
      • org.biopax.paxtools.model.level3.Observable
        • org.biopax.paxtools.model.level3.Entity (also extends org.biopax.paxtools.model.level3.Level3Element, org.biopax.paxtools.model.level3.Named)
          • org.biopax.paxtools.model.level3.Controller
            • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Process)
            • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Entity)
              • org.biopax.paxtools.model.level3.Complex
              • org.biopax.paxtools.model.level3.SimplePhysicalEntity
                • org.biopax.paxtools.model.level3.SequenceEntity
                  • org.biopax.paxtools.model.level3.NucleicAcid
                    • org.biopax.paxtools.model.level3.Dna
                    • org.biopax.paxtools.model.level3.DnaRegion
                    • org.biopax.paxtools.model.level3.Rna
                    • org.biopax.paxtools.model.level3.RnaRegion
                  • org.biopax.paxtools.model.level3.Protein
                • org.biopax.paxtools.model.level3.SmallMolecule
          • org.biopax.paxtools.model.level3.Gene
          • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Controller)
            • org.biopax.paxtools.model.level3.Complex
            • org.biopax.paxtools.model.level3.SimplePhysicalEntity
              • org.biopax.paxtools.model.level3.SequenceEntity
                • org.biopax.paxtools.model.level3.NucleicAcid
                  • org.biopax.paxtools.model.level3.Dna
                  • org.biopax.paxtools.model.level3.DnaRegion
                  • org.biopax.paxtools.model.level3.Rna
                  • org.biopax.paxtools.model.level3.RnaRegion
                • org.biopax.paxtools.model.level3.Protein
              • org.biopax.paxtools.model.level3.SmallMolecule
          • org.biopax.paxtools.model.level3.Process
            • org.biopax.paxtools.model.level3.Interaction
              • org.biopax.paxtools.model.level3.Control
                • org.biopax.paxtools.model.level3.Catalysis
                • org.biopax.paxtools.model.level3.Modulation
                • org.biopax.paxtools.model.level3.TemplateReactionRegulation
              • org.biopax.paxtools.model.level3.Conversion
                • org.biopax.paxtools.model.level3.BiochemicalReaction
                  • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.Transport)
                • org.biopax.paxtools.model.level3.ComplexAssembly
                • org.biopax.paxtools.model.level3.Degradation
                • org.biopax.paxtools.model.level3.Transport
                  • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.BiochemicalReaction)
              • org.biopax.paxtools.model.level3.GeneticInteraction
              • org.biopax.paxtools.model.level3.MolecularInteraction
              • org.biopax.paxtools.model.level3.TemplateReaction
            • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Controller)
        • org.biopax.paxtools.model.level3.EntityFeature (also extends org.biopax.paxtools.model.level3.UtilityClass)
          • org.biopax.paxtools.model.level3.BindingFeature
            • org.biopax.paxtools.model.level3.CovalentBindingFeature (also extends org.biopax.paxtools.model.level3.ModificationFeature)
          • org.biopax.paxtools.model.level3.FragmentFeature
          • org.biopax.paxtools.model.level3.ModificationFeature
            • org.biopax.paxtools.model.level3.CovalentBindingFeature (also extends org.biopax.paxtools.model.level3.BindingFeature)
        • org.biopax.paxtools.model.level3.EntityReference (also extends org.biopax.paxtools.model.level3.Named, org.biopax.paxtools.model.level3.UtilityClass)
          • org.biopax.paxtools.model.level3.SequenceEntityReference
            • org.biopax.paxtools.model.level3.NucleicAcidReference
              • org.biopax.paxtools.model.level3.DnaReference
              • org.biopax.paxtools.model.level3.NucleicAcidRegionReference
                • org.biopax.paxtools.model.level3.DnaRegionReference
                • org.biopax.paxtools.model.level3.RnaRegionReference
              • org.biopax.paxtools.model.level3.RnaReference
            • org.biopax.paxtools.model.level3.ProteinReference
          • org.biopax.paxtools.model.level3.SmallMoleculeReference
        • org.biopax.paxtools.model.level3.PathwayStep (also extends org.biopax.paxtools.model.level3.UtilityClass)
          • org.biopax.paxtools.model.level3.BiochemicalPathwayStep
      • org.biopax.paxtools.model.level3.UtilityClass
        • org.biopax.paxtools.model.level3.BioSource (also extends org.biopax.paxtools.model.level3.Named)
        • org.biopax.paxtools.model.level3.ChemicalConstant
          • org.biopax.paxtools.model.level3.DeltaG
          • org.biopax.paxtools.model.level3.KPrime
        • org.biopax.paxtools.model.level3.ChemicalStructure
        • org.biopax.paxtools.model.level3.ControlledVocabulary (also extends org.biopax.paxtools.model.level3.XReferrable)
          • org.biopax.paxtools.model.level3.CellularLocationVocabulary
          • org.biopax.paxtools.model.level3.CellVocabulary
          • org.biopax.paxtools.model.level3.EntityReferenceTypeVocabulary
          • org.biopax.paxtools.model.level3.EvidenceCodeVocabulary
          • org.biopax.paxtools.model.level3.ExperimentalFormVocabulary
          • org.biopax.paxtools.model.level3.InteractionVocabulary
          • org.biopax.paxtools.model.level3.PhenotypeVocabulary
          • org.biopax.paxtools.model.level3.RelationshipTypeVocabulary
          • org.biopax.paxtools.model.level3.SequenceModificationVocabulary
          • org.biopax.paxtools.model.level3.SequenceRegionVocabulary
          • org.biopax.paxtools.model.level3.TissueVocabulary
        • org.biopax.paxtools.model.level3.EntityFeature (also extends org.biopax.paxtools.model.level3.Observable)
          • org.biopax.paxtools.model.level3.BindingFeature
            • org.biopax.paxtools.model.level3.CovalentBindingFeature (also extends org.biopax.paxtools.model.level3.ModificationFeature)
          • org.biopax.paxtools.model.level3.FragmentFeature
          • org.biopax.paxtools.model.level3.ModificationFeature
            • org.biopax.paxtools.model.level3.CovalentBindingFeature (also extends org.biopax.paxtools.model.level3.BindingFeature)
        • org.biopax.paxtools.model.level3.EntityReference (also extends org.biopax.paxtools.model.level3.Named, org.biopax.paxtools.model.level3.Observable)
          • org.biopax.paxtools.model.level3.SequenceEntityReference
            • org.biopax.paxtools.model.level3.NucleicAcidReference
              • org.biopax.paxtools.model.level3.DnaReference
              • org.biopax.paxtools.model.level3.NucleicAcidRegionReference
                • org.biopax.paxtools.model.level3.DnaRegionReference
                • org.biopax.paxtools.model.level3.RnaRegionReference
              • org.biopax.paxtools.model.level3.RnaReference
            • org.biopax.paxtools.model.level3.ProteinReference
          • org.biopax.paxtools.model.level3.SmallMoleculeReference
        • org.biopax.paxtools.model.level3.Evidence (also extends org.biopax.paxtools.model.level3.XReferrable)
        • org.biopax.paxtools.model.level3.ExperimentalForm
        • org.biopax.paxtools.model.level3.PathwayStep (also extends org.biopax.paxtools.model.level3.Observable)
          • org.biopax.paxtools.model.level3.BiochemicalPathwayStep
        • org.biopax.paxtools.model.level3.Provenance (also extends org.biopax.paxtools.model.level3.Named, org.biopax.paxtools.model.level3.XReferrable)
        • org.biopax.paxtools.model.level3.Score (also extends org.biopax.paxtools.model.level3.XReferrable)
        • org.biopax.paxtools.model.level3.SequenceLocation
          • org.biopax.paxtools.model.level3.SequenceInterval
          • org.biopax.paxtools.model.level3.SequenceSite
        • org.biopax.paxtools.model.level3.Stoichiometry
        • org.biopax.paxtools.model.level3.Xref
          • org.biopax.paxtools.model.level3.PublicationXref
          • org.biopax.paxtools.model.level3.RelationshipXref
          • org.biopax.paxtools.model.level3.UnificationXref
      • org.biopax.paxtools.model.level3.XReferrable
        • org.biopax.paxtools.model.level3.ControlledVocabulary (also extends org.biopax.paxtools.model.level3.UtilityClass)
          • org.biopax.paxtools.model.level3.CellularLocationVocabulary
          • org.biopax.paxtools.model.level3.CellVocabulary
          • org.biopax.paxtools.model.level3.EntityReferenceTypeVocabulary
          • org.biopax.paxtools.model.level3.EvidenceCodeVocabulary
          • org.biopax.paxtools.model.level3.ExperimentalFormVocabulary
          • org.biopax.paxtools.model.level3.InteractionVocabulary
          • org.biopax.paxtools.model.level3.PhenotypeVocabulary
          • org.biopax.paxtools.model.level3.RelationshipTypeVocabulary
          • org.biopax.paxtools.model.level3.SequenceModificationVocabulary
          • org.biopax.paxtools.model.level3.SequenceRegionVocabulary
          • org.biopax.paxtools.model.level3.TissueVocabulary
        • org.biopax.paxtools.model.level3.Evidence (also extends org.biopax.paxtools.model.level3.UtilityClass)
        • org.biopax.paxtools.model.level3.Named
          • org.biopax.paxtools.model.level3.BioSource (also extends org.biopax.paxtools.model.level3.UtilityClass)
          • org.biopax.paxtools.model.level3.Entity (also extends org.biopax.paxtools.model.level3.Level3Element, org.biopax.paxtools.model.level3.Observable)
            • org.biopax.paxtools.model.level3.Controller
              • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Process)
              • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Entity)
                • org.biopax.paxtools.model.level3.Complex
                • org.biopax.paxtools.model.level3.SimplePhysicalEntity
                  • org.biopax.paxtools.model.level3.SequenceEntity
                    • org.biopax.paxtools.model.level3.NucleicAcid
                      • org.biopax.paxtools.model.level3.Dna
                      • org.biopax.paxtools.model.level3.DnaRegion
                      • org.biopax.paxtools.model.level3.Rna
                      • org.biopax.paxtools.model.level3.RnaRegion
                    • org.biopax.paxtools.model.level3.Protein
                  • org.biopax.paxtools.model.level3.SmallMolecule
            • org.biopax.paxtools.model.level3.Gene
            • org.biopax.paxtools.model.level3.PhysicalEntity (also extends org.biopax.paxtools.model.level3.Controller)
              • org.biopax.paxtools.model.level3.Complex
              • org.biopax.paxtools.model.level3.SimplePhysicalEntity
                • org.biopax.paxtools.model.level3.SequenceEntity
                  • org.biopax.paxtools.model.level3.NucleicAcid
                    • org.biopax.paxtools.model.level3.Dna
                    • org.biopax.paxtools.model.level3.DnaRegion
                    • org.biopax.paxtools.model.level3.Rna
                    • org.biopax.paxtools.model.level3.RnaRegion
                  • org.biopax.paxtools.model.level3.Protein
                • org.biopax.paxtools.model.level3.SmallMolecule
            • org.biopax.paxtools.model.level3.Process
              • org.biopax.paxtools.model.level3.Interaction
                • org.biopax.paxtools.model.level3.Control
                  • org.biopax.paxtools.model.level3.Catalysis
                  • org.biopax.paxtools.model.level3.Modulation
                  • org.biopax.paxtools.model.level3.TemplateReactionRegulation
                • org.biopax.paxtools.model.level3.Conversion
                  • org.biopax.paxtools.model.level3.BiochemicalReaction
                    • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.Transport)
                  • org.biopax.paxtools.model.level3.ComplexAssembly
                  • org.biopax.paxtools.model.level3.Degradation
                  • org.biopax.paxtools.model.level3.Transport
                    • org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction (also extends org.biopax.paxtools.model.level3.BiochemicalReaction)
                • org.biopax.paxtools.model.level3.GeneticInteraction
                • org.biopax.paxtools.model.level3.MolecularInteraction
                • org.biopax.paxtools.model.level3.TemplateReaction
              • org.biopax.paxtools.model.level3.Pathway (also extends org.biopax.paxtools.model.level3.Controller)
          • org.biopax.paxtools.model.level3.EntityReference (also extends org.biopax.paxtools.model.level3.Observable, org.biopax.paxtools.model.level3.UtilityClass)
            • org.biopax.paxtools.model.level3.SequenceEntityReference
              • org.biopax.paxtools.model.level3.NucleicAcidReference
                • org.biopax.paxtools.model.level3.DnaReference
                • org.biopax.paxtools.model.level3.NucleicAcidRegionReference
                  • org.biopax.paxtools.model.level3.DnaRegionReference
                  • org.biopax.paxtools.model.level3.RnaRegionReference
                • org.biopax.paxtools.model.level3.RnaReference
              • org.biopax.paxtools.model.level3.ProteinReference
            • org.biopax.paxtools.model.level3.SmallMoleculeReference
          • org.biopax.paxtools.model.level3.Provenance (also extends org.biopax.paxtools.model.level3.UtilityClass, org.biopax.paxtools.model.level3.XReferrable)
        • org.biopax.paxtools.model.level3.Provenance (also extends org.biopax.paxtools.model.level3.Named, org.biopax.paxtools.model.level3.UtilityClass)
        • org.biopax.paxtools.model.level3.Score (also extends org.biopax.paxtools.model.level3.UtilityClass)
  • org.biopax.paxtools.model.Model
• org.biopax.paxtools.controller.Visitor

Annotation Interface Hierarchy

• org.biopax.paxtools.util.AutoComplete (implements java.lang.annotation.Annotation)

Enum Class Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    • org.biopax.paxtools.model.BioPAXLevel
    • org.biopax.paxtools.util.BPCollections
    • org.biopax.paxtools.model.level3.CatalysisDirectionType
    • org.biopax.paxtools.model.level2.ControlType
    • org.biopax.paxtools.model.level3.ControlType
    • org.biopax.paxtools.model.level3.ConversionDirectionType
    • org.biopax.paxtools.model.level2.Direction
    • org.biopax.paxtools.model.level2.PositionStatusType
    • org.biopax.paxtools.model.level3.PositionStatusType
    • org.biopax.paxtools.controller.SimpleEditorMap (implements org.biopax.paxtools.controller.EditorMap)
    • org.biopax.paxtools.model.level2.SpontaneousType
    • org.biopax.paxtools.model.level3.StepDirection
    • org.biopax.paxtools.model.level3.StructureFormatType
    • org.biopax.paxtools.model.level3.TemplateDirectionType