Package org.biojava.bio.seq
Interface RemoteFeature
- All Superinterfaces:
Annotatable
,Changeable
,Feature
,FeatureHolder
,StrandedFeature
- All Known Implementing Classes:
SimpleRemoteFeature
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:
-
Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic final class
A tuple of Location and sequence ID.static interface
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
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
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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
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Method Summary
Modifier and TypeMethodDescriptionRetrieve the list of Regions that locate this feature both localy and remotely.Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.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
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Method Details
-
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
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
-