Package org.biopax.paxtools.impl.level3

Class SimplePhysicalEntityImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.XReferrableImpl

org.biopax.paxtools.impl.level3.NamedImpl

org.biopax.paxtools.impl.level3.EntityImpl

org.biopax.paxtools.impl.level3.PhysicalEntityImpl

org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl

All Implemented Interfaces:

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

Direct Known Subclasses:

NucleicAcidImpl, ProteinImpl, SmallMoleculeImpl

public abstract class SimplePhysicalEntityImpl
extends PhysicalEntityImpl
implements SimplePhysicalEntity

See Also:

• Serialized Form

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor	Description
SimplePhysicalEntityImpl()

Method Summary

Modifier and Type	Method	Description
int	equivalenceCode()	If two elements are equivalent, then their equivalence code should be the same.
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
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setEntityReference(EntityReference entityReference)	Reference entity for this physical entity.

Methods inherited from class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

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

Methods inherited from class org.biopax.paxtools.impl.level3.EntityImpl

addAvailability, addDataSource, addEvidence, getAvailability, getDataSource, getEvidence, getParticipantOf, removeAvailability, removeDataSource, removeEvidence, setDataSource

Methods inherited from class org.biopax.paxtools.impl.level3.NamedImpl

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

Methods inherited from class org.biopax.paxtools.impl.level3.XReferrableImpl

addXref, getXref, removeXref, setXref

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, getAnnotations, getUri, hashCode, isEquivalent, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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

getAnnotations, getUri, isEquivalent

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.Level3Element

addComment, getComment, removeComment

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.Observable

addEvidence, getEvidence, removeEvidence

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.XReferrable

addXref, getXref, removeXref

Constructor Details

SimplePhysicalEntityImpl

public SimplePhysicalEntityImpl()

Method Details

getGenericEntityReferences

public Set<EntityReference> getGenericEntityReferences()

Description copied from interface: SimplePhysicalEntity

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

Specified by:

getGenericEntityReferences in interface SimplePhysicalEntity

Returns:

this and members' entity references (see above)

getEntityReference

public EntityReference getEntityReference()

Description copied from interface: SimplePhysicalEntity

Reference entity for this physical entity.

Specified by:

getEntityReference in interface SimplePhysicalEntity

Returns:

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

setEntityReference

public void setEntityReference(EntityReference entityReference)

Description copied from interface: SimplePhysicalEntity

Reference entity for this physical entity.

Specified by:

setEntityReference in interface SimplePhysicalEntity

Parameters:

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

equivalenceCode

public int equivalenceCode()

Description copied from interface: BioPAXElement

If two elements are equivalent, then their equivalence code should be the same.

Specified by:

equivalenceCode in interface BioPAXElement

Overrides:

equivalenceCode in class PhysicalEntityImpl

Returns:

an integer that is same across all equivalent entities.

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class PhysicalEntityImpl