@Entity @Indexed @Boost(value=1.2999999523162842f) @FullTextFilterDef(name="organism",impl=OrganismFilterFactory.class) @FullTextFilterDef(name="datasource",impl=DataSourceFilterFactory.class) public class PhysicalEntityImpl extends EntityImpl implements PhysicalEntity
FIELD_AVAILABILITY, FIELD_COMMENT, FIELD_DATASOURCE, FIELD_ECNUMBER, FIELD_KEYWORD, FIELD_NAME, FIELD_ORGANISM, FIELD_PATHWAY, FIELD_SEQUENCE, FIELD_TERM, FIELD_XREFDB, FIELD_XREFID, FILTER_BY_DATASOURCE, FILTER_BY_ORGANISM
UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT
Constructor and Description |
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PhysicalEntityImpl() |
Modifier and Type | Method and Description |
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void |
addFeature(EntityFeature feature) |
void |
addMemberPhysicalEntity(PhysicalEntity newMember) |
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.
|
protected void |
setComponentOf(Set<Complex> componentOf) |
protected void |
setControllerOf(Set<Control> controllerOf) |
protected void |
setFeature(Set<EntityFeature> feature) |
protected void |
setMemberPhysicalEntity(Set<PhysicalEntity> memberPhysicalEntity) |
protected void |
setMemberPhysicalEntityOf(Set<PhysicalEntity> memberPhysicalEntityOf) |
protected void |
setNotFeature(Set<EntityFeature> featureSet) |
addAvailability, addDataSource, addEvidence, getAvailability, getDataSource, getEvidence, getParticipantOf, removeAvailability, removeDataSource, removeEvidence, setAvailability, setDataSource, setEvidence, setParticipantOf
addName, getDisplayName, getDisplayNameX, getName, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setStandardName, setStandardNameX
addXref, getXref, removeXref, setXref
addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment
equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource
addEvidence, getEvidence, removeEvidence
addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName
addXref, getXref, removeXref
addComment, getComment, removeComment
getAnnotations, getRDFId, isEquivalent
public PhysicalEntityImpl()
public Class<? extends PhysicalEntity> getModelInterface()
PhysicalEntity
getModelInterface
in interface BioPAXElement
getModelInterface
in interface PhysicalEntity
org.biopax.paxtools.model
package
corresponding to a BioPAX class.public Set<Complex> getComponentOf()
getComponentOf
in interface PhysicalEntity
public CellularLocationVocabulary getCellularLocation()
PhysicalEntity
getCellularLocation
in interface PhysicalEntity
public void setCellularLocation(CellularLocationVocabulary location)
PhysicalEntity
setCellularLocation
in interface PhysicalEntity
location
- for this physical entitypublic Set<EntityFeature> getFeature()
getFeature
in interface PhysicalEntity
public void addFeature(EntityFeature feature)
addFeature
in interface PhysicalEntity
public void removeFeature(EntityFeature feature)
removeFeature
in interface PhysicalEntity
protected void setFeature(Set<EntityFeature> feature)
public Set<EntityFeature> getNotFeature()
getNotFeature
in interface PhysicalEntity
public void addNotFeature(EntityFeature feature)
addNotFeature
in interface PhysicalEntity
public void removeNotFeature(EntityFeature feature)
removeNotFeature
in interface PhysicalEntity
protected void setNotFeature(Set<EntityFeature> featureSet)
public Set<PhysicalEntity> getMemberPhysicalEntity()
PhysicalEntity
getMemberPhysicalEntity
in interface PhysicalEntity
public void addMemberPhysicalEntity(PhysicalEntity newMember)
addMemberPhysicalEntity
in interface PhysicalEntity
public void removeMemberPhysicalEntity(PhysicalEntity oldMember)
removeMemberPhysicalEntity
in interface PhysicalEntity
protected void setMemberPhysicalEntity(Set<PhysicalEntity> memberPhysicalEntity)
public Set<PhysicalEntity> getMemberPhysicalEntityOf()
getMemberPhysicalEntityOf
in interface PhysicalEntity
protected boolean semanticallyEquivalent(BioPAXElement element)
semanticallyEquivalent
in class EntityImpl
public int equivalenceCode()
BioPAXElement
equivalenceCode
in interface BioPAXElement
equivalenceCode
in class XReferrableImpl
public boolean hasEquivalentCellularLocation(PhysicalEntity that)
hasEquivalentCellularLocation
in interface PhysicalEntity
public boolean hasEquivalentFeatures(PhysicalEntity that)
hasEquivalentFeatures
in interface PhysicalEntity
protected int locationAndFeatureCode()
public Set<Control> getControllerOf()
Controller
Control
interactions that this entity controls. Reverse method of
Control.getController()
. Contents of this set is automatically maintained and should not be modified.getControllerOf
in interface Controller
Control
interactions that this entity controls.protected void setControllerOf(Set<Control> controllerOf)
protected void setMemberPhysicalEntityOf(Set<PhysicalEntity> memberPhysicalEntityOf)
protected void setComponentOf(Set<Complex> componentOf)
Copyright © 2015 BioPAX. All rights reserved.