public interface EntityFeature extends UtilityClass, Observable
PhysicalEntity
). Pools are defined by a set of
Entity Features in the sense that a single molecule must have all of the features in the set in order to be
considered a member of the pool. Since it is impossible to list and experimentally test all potential features for
an entity, features that are not listed in the selection criteria is neglected Pools can also be defined by the
converse by specifying features that are known to NOT exist in a specific context. As DNA,
RNA and Proteins can be hierarchically organized into families based on sequence homology so can entity features.
The memberFeature property allows capturing such hierarchical classifications among entity features.
Usage: Subclasses of entity feature describe most common biological instances and should be preferred whenever
possible. One common use case for instantiating entity feature is, for describing active/inactive states of
proteins where more specific feature information is not available.
Examples: Open/close conformational state of channel proteins, "active"/"inactive" states,
excited states of photoreactive groups.UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT
Modifier and Type | Method and Description |
---|---|
void |
addMemberFeature(EntityFeature entityFeature)
An entity feature that belongs to this homology grouping.
|
boolean |
atEquivalentLocation(EntityFeature that) |
EntityReference |
getEntityFeatureOf()
Inverse of
EntityReference.getEntityFeature() |
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
getMemberFeature() |
Set<PhysicalEntity> |
getNotFeatureOf()
Inverse of
PhysicalEntity.getNotFeature()
Contents of this set is generated automatically and should not be modified. |
void |
removeMemberFeature(EntityFeature entityFeature)
An entity feature that belongs to this homology grouping.
|
void |
setFeatureLocation(SequenceLocation sequenceLocation)
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.
|
addEvidence, getEvidence, removeEvidence
addComment, getComment, removeComment
equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent
EntityReference getEntityFeatureOf()
EntityReference.getEntityFeature()
Set<PhysicalEntity> getFeatureOf()
PhysicalEntity.getFeature()
Contents of this set is generated automatically and should not be modified.Set<PhysicalEntity> getNotFeatureOf()
PhysicalEntity.getNotFeature()
Contents of this set is generated automatically and should not be modified.SequenceLocation getFeatureLocation()
void setFeatureLocation(SequenceLocation sequenceLocation)
sequenceLocation
- of the featureSequenceRegionVocabulary getFeatureLocationType()
void setFeatureLocationType(SequenceRegionVocabulary regionVocabulary)
regionVocabulary
- A CV term describing the location of the featureSet<EntityFeature> getMemberFeature()
void addMemberFeature(EntityFeature entityFeature)
entityFeature
- An entity feature that belongs to this homology grouping.void removeMemberFeature(EntityFeature entityFeature)
entityFeature
- An entity feature that belongs to this homology grouping.boolean atEquivalentLocation(EntityFeature that)
that
- EntityFeature to be comparedSet<EntityFeature> getMemberFeatureOf()
getMemberFeature()
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