Package org.biojava.bio.seq.impl
Class SimpleRemoteFeature
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.impl.SimpleFeature
org.biojava.bio.seq.impl.SimpleStrandedFeature
org.biojava.bio.seq.impl.SimpleRemoteFeature
- All Implemented Interfaces:
Serializable,Annotatable,Feature,FeatureHolder,RealizingFeatureHolder,RemoteFeature,StrandedFeature,Changeable
public class SimpleRemoteFeature
extends SimpleStrandedFeature
implements RemoteFeature, Serializable
A no-frills implementation of a remote feature.
- Since:
- 1.2
- Author:
- Matthew Pocock, Greg Cox
- See Also:
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Nested Class Summary
Nested ClassesNested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarderNested classes/interfaces inherited from interface org.biojava.bio.seq.Feature
Feature.ByLocationComparator, Feature.TemplateNested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolderNested classes/interfaces inherited from interface org.biojava.bio.seq.RemoteFeature
RemoteFeature.Region, RemoteFeature.Resolver, RemoteFeature.TemplateNested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand, StrandedFeature.Template -
Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATIONFields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERMFields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMAFields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN -
Constructor Summary
ConstructorsConstructorDescriptionSimpleRemoteFeature(Sequence sourceSeq, FeatureHolder parent, RemoteFeature.Template template) -
Method Summary
Modifier and TypeMethodDescriptionprotected voidRetrieve 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.Create a new Template that could be used to generate a feature identical to this one.Methods inherited from class org.biojava.bio.seq.impl.SimpleStrandedFeature
fillTemplate, getStrand, getSymbols, setStrand, toStringMethods inherited from class org.biojava.bio.seq.impl.SimpleFeature
containsFeature, countFeatures, createFeature, equals, featureHolderAllocated, features, fillTemplate, filter, filter, getAnnotation, getChangeSupport, getFeatureHolder, getLocation, getParent, getSchema, getSequence, getSource, getSourceTerm, getType, getTypeTerm, hashCode, realizeFeature, removeFeature, setLocation, setSource, setSourceTerm, setType, setTypeTermMethods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListenerMethods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, waitMethods inherited from interface org.biojava.bio.Annotatable
getAnnotationMethods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerMethods inherited from interface org.biojava.bio.seq.Feature
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, setLocation, setSource, setSourceTerm, setType, setTypeTermMethods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeatureMethods inherited from interface org.biojava.bio.seq.StrandedFeature
getStrand, getSymbols, setStrand
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Constructor Details
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SimpleRemoteFeature
public SimpleRemoteFeature(Sequence sourceSeq, FeatureHolder parent, RemoteFeature.Template template)
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Method Details
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getRegions
Description copied from interface:RemoteFeatureRetrieve the list of Regions that locate this feature both localy and remotely. Local Regions have a null sequence ID.- Specified by:
getRegionsin interfaceRemoteFeature- Returns:
- an immutable List of Regions
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getResolver
- Specified by:
getResolverin interfaceRemoteFeature
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getRemoteFeature
Description copied from interface:RemoteFeatureRetrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.This method should be equivalent to calling
getResolver().resolve(this).- Specified by:
getRemoteFeaturein interfaceRemoteFeature- Returns:
- the Feature on another Sequence that this is projected onto
- Throws:
BioException- if for any reason the remote Feature could not be constructed
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makeTemplate
Description copied from interface:FeatureCreate a new Template that could be used to generate a feature identical to this one. The fields of the template can be edited without changing the feature.- Specified by:
makeTemplatein interfaceFeature- Overrides:
makeTemplatein classSimpleStrandedFeature- Returns:
- a new Template that would make a feature like this one
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fillTemplate
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