org.biojava.bio.seq
Interface RemoteFeature
- All Superinterfaces:
- Annotatable, Changeable, Feature, FeatureHolder, StrandedFeature
- All Known Implementing Classes:
- SimpleRemoteFeature
public interface RemoteFeature
- extends StrandedFeature
A feature that indicates that there is some remote feature that can't be
represented entirely on a single Sequence.
These are the sort of features that represent things like the horible Embl
remote feature spans (such as AL24199:100..200). The method getRemoteFeature
should return a Feature on another Sequence that properly represents the
Location. This Seqeunce will often be an Assembly of the parent Sequence to
this Feature, and the Sequence associated with the remote Location sequence
ID. Thse Features are also applicable to the case when a portion of a
Sequence is projected but some Feature overlaps the boundary of the projected
portion.
- Since:
- 1.2
- Author:
- Matthew Pocock, Greg Cox
- See Also:
RichFeature
Methods inherited from interface org.biojava.bio.seq.Feature |
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm |
getRegions
java.util.List getRegions()
- Retrieve the list of Regions that locate this feature both localy and
remotely. Local Regions have a null sequence ID.
- Returns:
- an immutable List of Regions
getRemoteFeature
Feature getRemoteFeature()
throws BioException
- Retrieve the Feature on some assembly Sequence that can represent this
RemoteFeature properly.
This method should be equivalent to calling
getResolver().resolve(this)
.
- Returns:
- the Feature on another Sequence that this is projected onto
- Throws:
BioException
- if for any reason the remote Feature could not be
constructed
getResolver
RemoteFeature.Resolver getResolver()