Package org.biopax.paxtools.model.level3

Interface PhysicalEntity

All Superinterfaces:
BioPAXElement, Cloneable, Controller, Entity, Level3Element, Named, Observable, Serializable, XReferrable
All Known Subinterfaces:
Complex, Dna, DnaRegion, NucleicAcid, Protein, Rna, RnaRegion, SequenceEntity, SimplePhysicalEntity, SmallMolecule
All Known Implementing Classes:
ComplexImpl, DnaImpl, DnaRegionImpl, NucleicAcidImpl, PhysicalEntityImpl, ProteinImpl, RnaImpl, RnaRegionImpl, SimplePhysicalEntityImpl, SmallMoleculeImpl
public interface PhysicalEntity extends Entity, Controller

  • Method Details

    • getComponentOf

      Set<Complex> getComponentOf()

    • getCellularLocation

      CellularLocationVocabulary getCellularLocation()
      A cellular location, e.g. 'cytoplasm'. This should reference a term in the Gene Ontology Cellular Component ontology. The location referred to by this property should be as specific as is known. If an interaction is known to occur in multiple locations, separate interactions (and physicalEntities) must be created for each different location. If the location of a participant in a complex is unspecified, it may be assumed to be the same location as that of the complex. A molecule in two different cellular locations are considered two different physical entities.
      Returns:
      cellular location of this physical entity

    • setCellularLocation

      void setCellularLocation(CellularLocationVocabulary newCellularLocation)
      A cellular location, e.g. 'cytoplasm'. This should reference a term in the Gene Ontology Cellular Component ontology. The location referred to by this property should be as specific as is known. If an interaction is known to occur in multiple locations, separate interactions (and physicalEntities) must be created for each different location. If the location of a participant in a complex is unspecified, it may be assumed to be the same location as that of the complex. A molecule in two different cellular locations are considered two different physical entities.
      Parameters:
      newCellularLocation - for this physical entity

    • hasEquivalentFeatures

      boolean hasEquivalentFeatures(PhysicalEntity that)

    • hasEquivalentCellularLocation

      boolean hasEquivalentCellularLocation(PhysicalEntity that)

    • getFeature

      Set<EntityFeature> getFeature()

    • addFeature

      void addFeature(EntityFeature feature)

    • removeFeature

      void removeFeature(EntityFeature feature)

    • getNotFeature

      Set<EntityFeature> getNotFeature()

    • addNotFeature

      void addNotFeature(EntityFeature feature)

    • removeNotFeature

      void removeNotFeature(EntityFeature feature)

    • getMemberPhysicalEntity

      Set<PhysicalEntity> getMemberPhysicalEntity()
      Please avoid using this property in your BioPAX L3 models unless absolutely sure/required, for there is an alternative way (using PhysicalEntity/entityReference/memberEntityReference), and this will probably be deprecated in the future BioPAX releases. It's usually hard to say what this relationship (grouping) means...
      Returns:
      member physical entities

    • addMemberPhysicalEntity

      void addMemberPhysicalEntity(PhysicalEntity memberPhysicalEntity)

    • removeMemberPhysicalEntity

      void removeMemberPhysicalEntity(PhysicalEntity memberPhysicalEntity)

    • getMemberPhysicalEntityOf

      Set<PhysicalEntity> getMemberPhysicalEntityOf()

    • getModelInterface

      Class<? extends PhysicalEntity> getModelInterface()
      Overridden to provide better downcasting
      Specified by:
      getModelInterface in interface BioPAXElement
      Returns:
      an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.