Package 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:

  • Method Details

    • getRegions

      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()