@Entity @Indexed public class ComplexImpl extends PhysicalEntityImpl implements Complex
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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ComplexImpl() |
Modifier and Type | Method and Description |
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void |
addComponent(PhysicalEntity component)
Defines the PhysicalEntity subunits of this complex.
|
void |
addComponentStoichiometry(Stoichiometry stoichiometry)
The stoichiometry of components in a complex.
|
protected void |
collectSimpleMembersRecursive(PhysicalEntity pe,
Set<SimplePhysicalEntity> set) |
Set<PhysicalEntity> |
getComponent()
Defines the PhysicalEntity subunits of this complex.
|
Set<Stoichiometry> |
getComponentStoichiometry()
The stoichiometry of components in a complex.
|
Set<EntityReference> |
getMemberReferences()
Gets the
EntityReference s of the member simple physical entities. |
Class<? extends Complex> |
getModelInterface()
Overridden to provide better downcasting
|
Class<? extends PhysicalEntity> |
getPhysicalEntityClass() |
Set<SimplePhysicalEntity> |
getSimpleMembers()
Gets the member physical entities which are not complex.
|
protected Set<SimplePhysicalEntity> |
getSimpleMembers(Set<SimplePhysicalEntity> set) |
void |
removeComponent(PhysicalEntity component)
Defines the PhysicalEntity subunits of this complex.
|
void |
removeComponentStoichiometry(Stoichiometry stoichiometry)
The stoichiometry of components in a complex.
|
protected boolean |
semanticallyEquivalent(BioPAXElement element) |
protected void |
setComponent(Set<PhysicalEntity> component) |
protected void |
setComponentStoichiometry(Set<Stoichiometry> stoichiometry) |
addFeature, addMemberPhysicalEntity, addNotFeature, equivalenceCode, getCellularLocation, getComponentOf, getControllerOf, getFeature, getMemberPhysicalEntity, getMemberPhysicalEntityOf, getNotFeature, hasEquivalentCellularLocation, hasEquivalentFeatures, locationAndFeatureCode, removeFeature, removeMemberPhysicalEntity, removeNotFeature, setCellularLocation, setComponentOf, setControllerOf, setFeature, setMemberPhysicalEntity, setMemberPhysicalEntityOf, setNotFeature
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
addFeature, addMemberPhysicalEntity, addNotFeature, getCellularLocation, getComponentOf, getFeature, getMemberPhysicalEntity, getMemberPhysicalEntityOf, getNotFeature, hasEquivalentCellularLocation, hasEquivalentFeatures, removeFeature, removeMemberPhysicalEntity, removeNotFeature, setCellularLocation
getControllerOf
addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource
addEvidence, getEvidence, removeEvidence
addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName
addXref, getXref, removeXref
addComment, getComment, removeComment
equivalenceCode, getAnnotations, getRDFId, isEquivalent
public ComplexImpl()
public Class<? extends Complex> getModelInterface()
PhysicalEntity
getModelInterface
in interface BioPAXElement
getModelInterface
in interface PhysicalEntity
getModelInterface
in class PhysicalEntityImpl
org.biopax.paxtools.model
package
corresponding to a BioPAX class.public Set<PhysicalEntity> getComponent()
Complex
getComponent
in interface Complex
public void addComponent(PhysicalEntity component)
Complex
addComponent
in interface Complex
component
- to be added as a new memberpublic void removeComponent(PhysicalEntity component)
Complex
removeComponent
in interface Complex
component
- to be removed from members.protected void setComponent(Set<PhysicalEntity> component)
public Set<Stoichiometry> getComponentStoichiometry()
Complex
getComponentStoichiometry
in interface Complex
public void addComponentStoichiometry(Stoichiometry stoichiometry)
Complex
addComponentStoichiometry
in interface Complex
stoichiometry
- add a stoichiometry for the member.public void removeComponentStoichiometry(Stoichiometry stoichiometry)
Complex
removeComponentStoichiometry
in interface Complex
stoichiometry
- remove a stoichiometry for the member.protected void setComponentStoichiometry(Set<Stoichiometry> stoichiometry)
public Set<SimplePhysicalEntity> getSimpleMembers()
Complex
getSimpleMembers
in interface Complex
protected Set<SimplePhysicalEntity> getSimpleMembers(Set<SimplePhysicalEntity> set)
protected void collectSimpleMembersRecursive(PhysicalEntity pe, Set<SimplePhysicalEntity> set)
public Set<EntityReference> getMemberReferences()
Complex
EntityReference
s of the member simple physical entities. When the complex is nested,
contents of the member complexes are retrieved recursively.getMemberReferences
in interface Complex
public Class<? extends PhysicalEntity> getPhysicalEntityClass()
protected boolean semanticallyEquivalent(BioPAXElement element)
semanticallyEquivalent
in class PhysicalEntityImpl
Copyright © 2015 BioPAX. All rights reserved.