Package org.biopax.paxtools.impl.level3

Class PhysicalEntityImpl

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

All Implemented Interfaces:

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

Direct Known Subclasses:

ComplexImpl, SimplePhysicalEntityImpl

public class PhysicalEntityImpl
extends EntityImpl
implements PhysicalEntity

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
PhysicalEntityImpl()

Method Summary

Modifier and Type	Method	Description
void	addFeature(EntityFeature feature)
void	addMemberPhysicalEntity(PhysicalEntity mpe)
void	addNotFeature(EntityFeature feature)
int	equivalenceCode()	If two elements are equivalent, then their equivalence code should be the same.
CellularLocationVocabulary	getCellularLocation()	A cellular location, e.g.
Set<Complex>	getComponentOf()
Set<Control>	getControllerOf()	This method returns the list of Control interactions that this entity controls.
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)
protected int	locationAndFeatureCode()
void	removeFeature(EntityFeature feature)
void	removeMemberPhysicalEntity(PhysicalEntity oldMember)
void	removeNotFeature(EntityFeature feature)
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setCellularLocation(CellularLocationVocabulary location)	A cellular location, e.g.

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.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.XReferrable

addXref, getXref, removeXref

Constructor Details

PhysicalEntityImpl

public PhysicalEntityImpl()

Method Details

getModelInterface

public Class<? extends PhysicalEntity> getModelInterface()

Description copied from interface: PhysicalEntity

Overridden to provide better downcasting

Specified by:

getModelInterface in interface BioPAXElement

Specified by:

getModelInterface in interface PhysicalEntity

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getComponentOf

public Set<Complex> getComponentOf()

Specified by:

getComponentOf in interface PhysicalEntity

getCellularLocation

public CellularLocationVocabulary getCellularLocation()

Description copied from interface: PhysicalEntity

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.

Specified by:

getCellularLocation in interface PhysicalEntity

Returns:

cellular location of this physical entity

setCellularLocation

public void setCellularLocation(CellularLocationVocabulary location)

Description copied from interface: PhysicalEntity

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.

Specified by:

setCellularLocation in interface PhysicalEntity

Parameters:

location - for this physical entity

getFeature

public Set<EntityFeature> getFeature()

Specified by:

getFeature in interface PhysicalEntity

addFeature

public void addFeature(EntityFeature feature)

Specified by:

addFeature in interface PhysicalEntity

removeFeature

public void removeFeature(EntityFeature feature)

Specified by:

removeFeature in interface PhysicalEntity

getNotFeature

public Set<EntityFeature> getNotFeature()

Specified by:

getNotFeature in interface PhysicalEntity

addNotFeature

public void addNotFeature(EntityFeature feature)

Specified by:

addNotFeature in interface PhysicalEntity

removeNotFeature

public void removeNotFeature(EntityFeature feature)

Specified by:

removeNotFeature in interface PhysicalEntity

getMemberPhysicalEntity

public Set<PhysicalEntity> getMemberPhysicalEntity()

Description copied from interface: PhysicalEntity

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...

Specified by:

getMemberPhysicalEntity in interface PhysicalEntity

Returns:

member physical entities

addMemberPhysicalEntity

public void addMemberPhysicalEntity(PhysicalEntity mpe)

Specified by:

addMemberPhysicalEntity in interface PhysicalEntity

removeMemberPhysicalEntity

public void removeMemberPhysicalEntity(PhysicalEntity oldMember)

Specified by:

removeMemberPhysicalEntity in interface PhysicalEntity

getMemberPhysicalEntityOf

public Set<PhysicalEntity> getMemberPhysicalEntityOf()

Specified by:

getMemberPhysicalEntityOf in interface PhysicalEntity

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class EntityImpl

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 XReferrableImpl

Returns:

an integer that is same across all equivalent entities.

hasEquivalentCellularLocation

public boolean hasEquivalentCellularLocation(PhysicalEntity that)

Specified by:

hasEquivalentCellularLocation in interface PhysicalEntity

hasEquivalentFeatures

public boolean hasEquivalentFeatures(PhysicalEntity that)

Specified by:

hasEquivalentFeatures in interface PhysicalEntity

locationAndFeatureCode

protected int locationAndFeatureCode()

getControllerOf

public Set<Control> getControllerOf()

Description copied from interface: Controller

This method returns the list of Control interactions that this entity controls. Reverse method of Control.getController(). Contents of this set is automatically maintained and should not be modified.

Specified by:

getControllerOf in interface Controller

Returns:

list of Control interactions that this entity controls.