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.AnnotationForwarder
Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature
Feature.ByLocationComparator, Feature.Template
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
Nested classes/interfaces inherited from interface org.biojava.bio.seq.RemoteFeature
RemoteFeature.Region, RemoteFeature.Resolver, RemoteFeature.Template
Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand, StrandedFeature.Template
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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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Constructor Summary
ConstructorsConstructorDescriptionSimpleRemoteFeature
(Sequence sourceSeq, FeatureHolder parent, RemoteFeature.Template template) -
Method Summary
Modifier and TypeMethodDescriptionprotected void
Retrieve 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, toString
Methods 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, setTypeTerm
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
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, 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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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:RemoteFeature
Retrieve the list of Regions that locate this feature both localy and remotely. Local Regions have a null sequence ID.- Specified by:
getRegions
in interfaceRemoteFeature
- Returns:
- an immutable List of Regions
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getResolver
- Specified by:
getResolver
in interfaceRemoteFeature
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getRemoteFeature
Description copied from interface:RemoteFeature
Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.This method should be equivalent to calling
getResolver().resolve(this)
.- Specified by:
getRemoteFeature
in 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:Feature
Create 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:
makeTemplate
in interfaceFeature
- Overrides:
makeTemplate
in classSimpleStrandedFeature
- Returns:
- a new Template that would make a feature like this one
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fillTemplate
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