@Entity @Indexed public class EntityFeatureImpl extends L3ElementImpl implements EntityFeature
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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EntityFeatureImpl() |
Modifier and Type | Method and Description |
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void |
addEvidence(Evidence evidence) |
void |
addMemberFeature(EntityFeature feature)
An entity feature that belongs to this homology grouping.
|
boolean |
atEquivalentLocation(EntityFeature that) |
int |
equivalenceCode()
If two elements are equivalent, then their equivalence code should be the
same.
|
EntityReference |
getEntityFeatureOf()
Inverse of
EntityReference.getEntityFeature() |
Set<Evidence> |
getEvidence() |
SequenceLocation |
getFeatureLocation()
Location of the feature on the sequence of the interactor.
|
SequenceRegionVocabulary |
getFeatureLocationType()
A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain.
|
Set<PhysicalEntity> |
getFeatureOf()
Inverse of
PhysicalEntity.getFeature()
Contents of this set is generated automatically and should not be modified. |
Set<EntityFeature> |
getMemberFeature()
An entity feature that belongs to this homology grouping.
|
Set<EntityFeature> |
getMemberFeatureOf()
Reverse of
EntityFeature.getMemberFeature() |
Class<? extends EntityFeature> |
getModelInterface()
This method returns the actual model interface that a class implements.
|
Set<PhysicalEntity> |
getNotFeatureOf()
Inverse of
PhysicalEntity.getNotFeature()
Contents of this set is generated automatically and should not be modified. |
protected int |
locationCode() |
void |
removeEvidence(Evidence evidence) |
void |
removeMemberFeature(EntityFeature feature)
An entity feature that belongs to this homology grouping.
|
protected boolean |
semanticallyEquivalent(BioPAXElement element) |
void |
setEntityFeatureOf(EntityReference entityReference) |
protected void |
setEvidence(Set<Evidence> evidence) |
void |
setFeatureLocation(SequenceLocation featureLocation)
Location of the feature on the sequence of the interactor.
|
void |
setFeatureLocationType(SequenceRegionVocabulary regionVocabulary)
A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain.
|
protected void |
setFeatureOf(Set<PhysicalEntity> featureOf) |
protected void |
setMemberFeature(Set<EntityFeature> memberFeature) |
protected void |
setMemberFeatureOf(Set<EntityFeature> memberFeatureOf) |
protected void |
setNotFeatureOf(Set<PhysicalEntity> notFeatureOf) |
addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment
equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
addComment, getComment, removeComment
getAnnotations, getRDFId, isEquivalent
public EntityFeatureImpl()
public Class<? extends EntityFeature> getModelInterface()
BioPAXElement
getModelInterface
in interface BioPAXElement
org.biopax.paxtools.model
package
corresponding to a BioPAX class.public EntityReference getEntityFeatureOf()
EntityFeature
EntityReference.getEntityFeature()
getEntityFeatureOf
in interface EntityFeature
public void setEntityFeatureOf(EntityReference entityReference)
public Set<PhysicalEntity> getFeatureOf()
EntityFeature
PhysicalEntity.getFeature()
Contents of this set is generated automatically and should not be modified.getFeatureOf
in interface EntityFeature
public Set<PhysicalEntity> getNotFeatureOf()
EntityFeature
PhysicalEntity.getNotFeature()
Contents of this set is generated automatically and should not be modified.getNotFeatureOf
in interface EntityFeature
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
protected void setEvidence(Set<Evidence> evidence)
public SequenceLocation getFeatureLocation()
EntityFeature
getFeatureLocation
in interface EntityFeature
public void setFeatureLocation(SequenceLocation featureLocation)
EntityFeature
setFeatureLocation
in interface EntityFeature
featureLocation
- of the featurepublic SequenceRegionVocabulary getFeatureLocationType()
EntityFeature
getFeatureLocationType
in interface EntityFeature
public void setFeatureLocationType(SequenceRegionVocabulary regionVocabulary)
EntityFeature
setFeatureLocationType
in interface EntityFeature
regionVocabulary
- A CV term describing the location of the featurepublic Set<EntityFeature> getMemberFeature()
EntityFeature
getMemberFeature
in interface EntityFeature
protected void setMemberFeature(Set<EntityFeature> memberFeature)
public void addMemberFeature(EntityFeature feature)
EntityFeature
addMemberFeature
in interface EntityFeature
feature
- An entity feature that belongs to this homology grouping.public void removeMemberFeature(EntityFeature feature)
EntityFeature
removeMemberFeature
in interface EntityFeature
feature
- An entity feature that belongs to this homology grouping.public Set<EntityFeature> getMemberFeatureOf()
EntityFeature
EntityFeature.getMemberFeature()
getMemberFeatureOf
in interface EntityFeature
protected void setMemberFeatureOf(Set<EntityFeature> memberFeatureOf)
public boolean atEquivalentLocation(EntityFeature that)
atEquivalentLocation
in interface EntityFeature
that
- EntityFeature to be comparedprotected int locationCode()
protected boolean semanticallyEquivalent(BioPAXElement element)
semanticallyEquivalent
in class BioPAXElementImpl
public int equivalenceCode()
BioPAXElement
equivalenceCode
in interface BioPAXElement
equivalenceCode
in class BioPAXElementImpl
protected void setFeatureOf(Set<PhysicalEntity> featureOf)
protected void setNotFeatureOf(Set<PhysicalEntity> notFeatureOf)
Copyright © 2015 BioPAX. All rights reserved.