org.biojava.bio.seq.impl
Class SimpleRemoteFeature

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.seq.impl.SimpleFeature
          extended by org.biojava.bio.seq.impl.SimpleStrandedFeature
              extended by 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
static class SimpleRemoteFeature.DBResolver
           
 
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
 
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.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
 
Fields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN
 
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.Annotatable
ANNOTATION
 
Constructor Summary
SimpleRemoteFeature(Sequence sourceSeq, FeatureHolder parent, RemoteFeature.Template template)
           
 
Method Summary
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.seq.StrandedFeature
getStrand, getSymbols, setStrand
 
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.Annotatable
getAnnotation
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

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)


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