Package org.biopax.paxtools.model.level3

Interface Named

All Superinterfaces:
BioPAXElement, Cloneable, Level3Element, Serializable, XReferrable
All Known Subinterfaces:
BiochemicalReaction, BioSource, Catalysis, Complex, ComplexAssembly, Control, Controller, Conversion, Degradation, Dna, DnaReference, DnaRegion, DnaRegionReference, Entity, EntityReference, Gene, GeneticInteraction, Interaction, Modulation, MolecularInteraction, NucleicAcid, NucleicAcidReference, NucleicAcidRegionReference, Pathway, PhysicalEntity, Process, Protein, ProteinReference, Provenance, Rna, RnaReference, RnaRegion, RnaRegionReference, SequenceEntity, SequenceEntityReference, SimplePhysicalEntity, SmallMolecule, SmallMoleculeReference, TemplateReaction, TemplateReactionRegulation, Transport, TransportWithBiochemicalReaction
All Known Implementing Classes:
BiochemicalReactionImpl, BioSourceImpl, CatalysisImpl, ComplexAssemblyImpl, ComplexImpl, ControlImpl, ConversionImpl, DegradationImpl, DnaImpl, DnaReferenceImpl, DnaRegionImpl, DnaRegionReferenceImpl, EntityImpl, EntityReferenceImpl, GeneImpl, GeneticInteractionImpl, InteractionImpl, ModulationImpl, MolecularInteractionImpl, NamedImpl, NucleicAcidImpl, NucleicAcidReferenceImpl, NucleicAcidRegionReferenceImpl, PathwayImpl, PhysicalEntityImpl, ProcessImpl, ProteinImpl, ProteinReferenceImpl, ProvenanceImpl, RnaImpl, RnaReferenceImpl, RnaRegionImpl, RnaRegionReferenceImpl, SequenceEntityReferenceImpl, SimplePhysicalEntityImpl, SmallMoleculeImpl, SmallMoleculeReferenceImpl, TemplateReactionImpl, TemplateReactionRegulationImpl, TransportImpl, TransportWithBiochemicalReactionImpl
public interface Named extends XReferrable
Interface for all classes that can have names in BioPAX. All named BioPAX elements can have multiple names, and exactly one standardName and exactly one shortName. standardName and shortName are OWL subproperties of name in BioPAX, so these are automatically considered as a name if defined. Paxtools refle Warning: There is a potential OWL-JAVA semantic mismatch when manipulating names. If a user decides to assign a different name to standardName or shortName, what happens to the old name is not well defined - they can be "demoted" to a regular name or removed from the names list altogether. Paxtools currently does the latter. If this is not the desired behaviour, the old name should be added manually back to the names list.

  • Method Details

    • getName

      Set<String> getName()
      Names for this entity, including standardName and shortName if defined. The contents of this set can be modified directly but semantic consistency is not guaranteed. Using addName(java.lang.String) and removeName(java.lang.String) is recommended.
      Returns:
      Names for this entity, including standardName and shortName if defined.

    • setName

      void setName(Set<String> names)
      This method is reserved for batch operations and should not be used for normal use. Use add/remove name methods to manipulate the names instead.
      Parameters:
      names - new names to set (or replace all existing ones)

    • addName

      void addName(String name)
      This method adds the given value to the name set.
      Parameters:
      name - a new name to be added

    • removeName

      void removeName(String name)
      This method removes the given value from the name set.
      Parameters:
      name - a new name to be removed

    • getDisplayName

      String getDisplayName()
      An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.
      Returns:
      An abbreviated name for this entity

    • setDisplayName

      void setDisplayName(String displayName)
      An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.
      Parameters:
      displayName - new display name (preferably a short one)

    • getStandardName

      String getStandardName()
      The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.
      Returns:
      standard name for this entity

    • setStandardName

      void setStandardName(String standardName)
      The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.
      Parameters:
      standardName - standard name for this entity