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
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 interface org.biojava.bio.seq.Feature |
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, setLocation, setSource, setSourceTerm, setType, setTypeTerm |
SimpleRemoteFeature
public SimpleRemoteFeature(Sequence sourceSeq,
FeatureHolder parent,
RemoteFeature.Template template)
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)