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:

RichFeature

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	RemoteFeature.Region	A tuple of Location and sequence ID.
static interface	RemoteFeature.Resolver	The interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature.
static class	RemoteFeature.Template

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature

Feature.ByLocationComparator

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

FeatureHolder.EmptyFeatureHolder

Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature

StrandedFeature.Strand

Field Summary

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojava.bio.seq.Feature

byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Fields inherited from interface org.biojava.bio.seq.StrandedFeature

NEGATIVE, POSITIVE, STRAND, UNKNOWN

Method Summary

Modifier and Type	Method	Description
List	getRegions()	Retrieve the list of Regions that locate this feature both localy and remotely.
Feature	getRemoteFeature()	Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.
RemoteFeature.Resolver	getResolver()

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.seq.Feature

features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm

Methods inherited from interface org.biojava.bio.seq.FeatureHolder

containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature

Methods inherited from interface org.biojava.bio.seq.StrandedFeature

getStrand, getSymbols, setStrand

Method Detail

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()