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:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SimpleRemoteFeature.DBResolver

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, 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

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

Constructor Summary

Constructors

Constructor	Description
SimpleRemoteFeature(Sequence sourceSeq, FeatureHolder parent, RemoteFeature.Template template)

Method Summary

Modifier and Type	Method	Description
protected void	fillTemplate(RemoteFeature.Template rt)
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()
Feature.Template	makeTemplate()	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

Constructor Detail

SimpleRemoteFeature

public SimpleRemoteFeature(Sequence sourceSeq,
                           FeatureHolder parent,
                           RemoteFeature.Template template)

Method Detail

getRegions

public List 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 interface RemoteFeature

Returns:

an immutable List of Regions

getResolver

public RemoteFeature.Resolver getResolver()

Specified by:

getResolver in interface RemoteFeature

getRemoteFeature

public Feature getRemoteFeature()
                         throws BioException

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 interface RemoteFeature

Returns:

the Feature on another Sequence that this is projected onto

Throws:

BioException - if for any reason the remote Feature could not be constructed

makeTemplate

public Feature.Template 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 interface Feature

Overrides:

makeTemplate in class SimpleStrandedFeature

Returns:

a new Template that would make a feature like this one

fillTemplate

protected void fillTemplate(RemoteFeature.Template rt)