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public interface RemoteFeature
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.
RichFeature
Nested Class Summary | |
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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
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature |
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StrandedFeature.Strand |
Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature |
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Feature.ByLocationComparator |
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder |
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FeatureHolder.EmptyFeatureHolder |
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
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Annotatable.AnnotationForwarder |
Field Summary |
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Fields inherited from interface org.biojava.bio.seq.StrandedFeature |
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NEGATIVE, POSITIVE, STRAND, UNKNOWN |
Fields inherited from interface org.biojava.bio.seq.Feature |
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byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
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EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA |
Fields inherited from interface org.biojava.bio.Annotatable |
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ANNOTATION |
Method Summary | |
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java.util.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()
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Methods inherited from interface org.biojava.bio.seq.StrandedFeature |
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getStrand, getSymbols, setStrand |
Methods inherited from interface org.biojava.bio.seq.Feature |
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features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm |
Methods inherited from interface org.biojava.bio.seq.FeatureHolder |
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containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from interface org.biojava.bio.Annotatable |
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getAnnotation |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Method Detail |
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java.util.List getRegions()
Feature getRemoteFeature() throws BioException
This method should be equivalent to calling
getResolver().resolve(this)
.
BioException
- if for any reason the remote Feature could not be
constructedRemoteFeature.Resolver getResolver()
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