org.biopax.paxtools.model.level3

Interface SimplePhysicalEntity

All Superinterfaces:

BioPAXElement, Cloneable, Controller, Entity, Level3Element, Named, Observable, PhysicalEntity, Serializable, XReferrable

All Known Subinterfaces:

Dna, DnaRegion, NucleicAcid, Protein, Rna, RnaRegion, SequenceEntity, 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

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Modifier and Type	Method and Description
EntityReference	getEntityReference() Reference entity for this physical entity.
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, setName, setStandardName

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

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getUri, isEquivalent

Method Detail

getEntityReference

EntityReference getEntityReference()

Reference entity for this physical entity.

Returns:

entity reference; i.e., that of a stateless canonical identifiable entity

setEntityReference

void setEntityReference(EntityReference entityReference)

Reference entity for this physical entity.

Parameters:

entityReference - a BioPAX EntityReference object (usually a more specific subclass of)

getGenericEntityReferences

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

Returns:

this and members' entity references (see above)