@Entity public abstract class EntityReferenceImpl extends NamedImpl implements EntityReference
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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EntityReferenceImpl()
Constructor.
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Modifier and Type | Method and Description |
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void |
addEntityFeature(EntityFeature entityFeature)
Variable features that are observed for the entities of this entityReference - such as known PTM
or methylation sites and non-covalent bonds.
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void |
addEntityReferenceType(EntityReferenceTypeVocabulary entityReferenceType)
Adds the given cv to the list of types
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void |
addEvidence(Evidence evidence) |
void |
addMemberEntityReference(EntityReference memberEntity)
Adds the given entityReference to the member list
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Set<EntityFeature> |
getEntityFeature()
The contents of this set should NOT be modified.
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Set<SimplePhysicalEntity> |
getEntityReferenceOf()
Inverse of
SimplePhysicalEntity.getEntityReference() |
Set<EntityReferenceTypeVocabulary> |
getEntityReferenceType() |
Set<Evidence> |
getEvidence() |
Set<EntityReference> |
getMemberEntityReference() |
Set<EntityReference> |
getMemberEntityReferenceOf()
Reverse of
EntityReference.getMemberEntityReference() |
Class<? extends EntityReference> |
getModelInterface()
This method returns the actual model interface that a class implements.
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void |
removeEntityFeature(EntityFeature entityFeature)
Variable features that are observed for the entities of this entityReference - such as known PTM
or methylation sites and non-covalent bonds.
|
void |
removeEntityReferenceType(EntityReferenceTypeVocabulary entityReferenceType)
Removes the given cv from the list of types
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void |
removeEvidence(Evidence evidence) |
void |
removeMemberEntityReference(EntityReference memberEntity)
Removes the given entityReference from the member list
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protected void |
setEntityFeature(Set<EntityFeature> entityFeature) |
protected void |
setEntityReferenceOf(Set<SimplePhysicalEntity> entityReferenceOf) |
protected void |
setEntityReferenceType(Set<EntityReferenceTypeVocabulary> entityReferenceType) |
void |
setEvidence(Set<Evidence> evidence) |
protected void |
setMemberEntity(Set<EntityReference> memberEntity) |
void |
setMemberEntityReference(Set<EntityReference> memberEntity) |
protected void |
setMemberEntityReferenceOf(Set<EntityReference> newOwnerEntityReferenceSet) |
addName, getDisplayName, getDisplayNameX, getName, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setStandardName, setStandardNameX
addXref, equivalenceCode, getXref, removeXref, setXref
addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment
equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, semanticallyEquivalent, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName
addXref, getXref, removeXref
addComment, getComment, removeComment
equivalenceCode, getAnnotations, getRDFId, isEquivalent
public EntityReferenceImpl()
public Class<? extends EntityReference> getModelInterface()
BioPAXElement
getModelInterface
in interface BioPAXElement
org.biopax.paxtools.model
package
corresponding to a BioPAX class.public Set<EntityFeature> getEntityFeature()
getEntityFeature
in interface EntityReference
public void addEntityFeature(EntityFeature entityFeature)
EntityReference
addEntityFeature
in interface EntityReference
entityFeature
- to be added.public void removeEntityFeature(EntityFeature entityFeature)
EntityReference
removeEntityFeature
in interface EntityReference
entityFeature
- to be removed.protected void setEntityFeature(Set<EntityFeature> entityFeature)
public Set<SimplePhysicalEntity> getEntityReferenceOf()
EntityReference
SimplePhysicalEntity.getEntityReference()
getEntityReferenceOf
in interface EntityReference
SimplePhysicalEntity
that has this EntityReferencepublic Set<EntityReferenceTypeVocabulary> getEntityReferenceType()
getEntityReferenceType
in interface EntityReference
public void addEntityReferenceType(EntityReferenceTypeVocabulary entityReferenceType)
EntityReference
addEntityReferenceType
in interface EntityReference
entityReferenceType
- A controlled vocabulary term that is used to describe the type of grouping such as
homology or functional group.public void removeEntityReferenceType(EntityReferenceTypeVocabulary entityReferenceType)
EntityReference
removeEntityReferenceType
in interface EntityReference
entityReferenceType
- A controlled vocabulary term that is used to describe the type of grouping such as
homology or functional group.protected void setEntityReferenceType(Set<EntityReferenceTypeVocabulary> entityReferenceType)
public Set<EntityReference> getMemberEntityReference()
getMemberEntityReference
in interface EntityReference
public void addMemberEntityReference(EntityReference memberEntity)
EntityReference
addMemberEntityReference
in interface EntityReference
memberEntity
- An entity reference that qualifies for the definition of this group. For
example a member of a PFAM protein family.public void removeMemberEntityReference(EntityReference memberEntity)
EntityReference
removeMemberEntityReference
in interface EntityReference
memberEntity
- An entity reference that qualifies for the definition of this group. For
example a member of a PFAM protein family.public void setMemberEntityReference(Set<EntityReference> memberEntity)
public Set<EntityReference> getMemberEntityReferenceOf()
EntityReference
EntityReference.getMemberEntityReference()
getMemberEntityReferenceOf
in interface EntityReference
protected void setMemberEntityReferenceOf(Set<EntityReference> newOwnerEntityReferenceSet)
public Set<Evidence> getEvidence()
getEvidence
in interface Observable
public void addEvidence(Evidence evidence)
addEvidence
in interface Observable
public void removeEvidence(Evidence evidence)
removeEvidence
in interface Observable
public void setEvidence(Set<Evidence> evidence)
protected void setEntityReferenceOf(Set<SimplePhysicalEntity> entityReferenceOf)
protected void setMemberEntity(Set<EntityReference> memberEntity)
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