org.biopax.paxtools.model.level3
Interface SimplePhysicalEntity

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Controller, Entity, Level3Element, Named, Observable, PhysicalEntity, java.io.Serializable, XReferrable

All Known Subinterfaces:

Dna, DnaRegion, NucleicAcid, Protein, Rna, RnaRegion, SmallMolecule

All Known Implementing Classes:

DnaImpl, DnaRegionImpl, NucleicAcidImpl, ProteinImpl, RnaImpl, RnaRegionImpl, SimplePhysicalEntityImpl, SmallMoleculeImpl

public interface SimplePhysicalEntity
extends PhysicalEntity

Tagger interface for non-complex physical entities

Method Summary

EntityReference	getEntityReference() Reference entity for this physical entity.
java.util.Set<EntityReference>	getGenericEntityReferences() This method returns: The entity reference of this PhysicalEntity plus If this PhysicalEntity has member PhysicalEntities their generic EntityReferences iteratively plus If the EntityReference of this PhysicalEntity has member EntityReferences their members iteratively
void	setEntityReference(EntityReference entityReference) Reference entity for this physical entity.

Methods inherited from interface org.biopax.paxtools.model.level3.PhysicalEntity

addFeature, addMemberPhysicalEntity, addNotFeature, getCellularLocation, getComponentOf, getFeature, getMemberPhysicalEntity, getMemberPhysicalEntityOf, getModelInterface, getNotFeature, hasEquivalentCellularLocation, hasEquivalentFeatures, removeFeature, removeMemberPhysicalEntity, removeNotFeature, setCellularLocation

Methods inherited from interface org.biopax.paxtools.model.level3.Controller

getControllerOf

Methods inherited from interface org.biopax.paxtools.model.level3.Entity

addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Method Detail

getEntityReference

EntityReference getEntityReference()

Reference entity for this physical entity.

setEntityReference

void setEntityReference(EntityReference entityReference)

Reference entity for this physical entity.

getGenericEntityReferences

java.util.Set<EntityReference> getGenericEntityReferences()

This method returns:

The entity reference of this PhysicalEntity plus

If this PhysicalEntity has member PhysicalEntities their generic EntityReferences iteratively plus

If the EntityReference of this PhysicalEntity has member EntityReferences their members iteratively