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

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
void	addFeature(EntityFeature feature)
void	addMemberPhysicalEntity(PhysicalEntity memberPhysicalEntity)
void	addNotFeature(EntityFeature feature)
CellularLocationVocabulary	getCellularLocation() A cellular location, e.g.
Set<Complex>	getComponentOf()
Set<EntityFeature>	getFeature()
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.
Set<PhysicalEntity>	getMemberPhysicalEntityOf()
Class<? extends PhysicalEntity>	getModelInterface() Overridden to provide better downcasting
Set<EntityFeature>	getNotFeature()
boolean	hasEquivalentCellularLocation(PhysicalEntity that)
boolean	hasEquivalentFeatures(PhysicalEntity that)
void	removeFeature(EntityFeature feature)
void	removeMemberPhysicalEntity(PhysicalEntity memberPhysicalEntity)
void	removeNotFeature(EntityFeature feature)
void	setCellularLocation(CellularLocationVocabulary newCellularLocation) A cellular location, e.g.

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, getRDFId, isEquivalent

Method Detail

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.