org.biojava.bio.seq.projection
Class ProjectedStrandedFeature

java.lang.Object
  extended byorg.biojava.bio.seq.projection.ProjectedFeature
      extended byorg.biojava.bio.seq.projection.ProjectedStrandedFeature
All Implemented Interfaces:
Annotatable, Changeable, Feature, FeatureHolder, Projection, StrandedFeature

public class ProjectedStrandedFeature
extends ProjectedFeature
implements StrandedFeature

Internal class used by ProjectedFeatureHolder to wrap StrandedFeatures.

Since:
1.1
Author:
Thomas Down, Matthew Pocock

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand, StrandedFeature.Template
 
Nested classes inherited from class org.biojava.bio.seq.Feature
Feature.ByLocationComparator
 
Nested classes inherited from class org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
 
Nested classes inherited from class org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
 
Fields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, UNKNOWN
 
Fields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, TYPE
 
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
ProjectedStrandedFeature(StrandedFeature f, ProjectionContext ctx)
           
 
Method Summary
 StrandedFeature.Strand getStrand()
          Retrieve the strand that this feature lies upon.
 SymbolList getSymbols()
          Return a list of symbols that are contained in this feature.
 Feature.Template makeTemplate()
          Create a new Template that could be used to generate a feature identical to this one.
 java.lang.String toString()
           
 
Methods inherited from class org.biojava.bio.seq.projection.ProjectedFeature
addChangeListener, addChangeListener, containsFeature, countFeatures, createFeature, equals, features, filter, filter, getAnnotation, getLocation, getParent, getProjectedFeatures, getProjectionContext, getSchema, getSequence, getSource, getType, getViewedFeature, hashCode, isUnchanging, removeChangeListener, removeChangeListener, removeFeature, setLocation, setSource, setType
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.biojava.bio.seq.Feature
features, getLocation, getParent, getSequence, getSource, getType, setLocation, setSource, setType
 
Methods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
 

Constructor Detail

ProjectedStrandedFeature

public ProjectedStrandedFeature(StrandedFeature f,
                                ProjectionContext ctx)
Method Detail

getStrand

public StrandedFeature.Strand getStrand()
Description copied from interface: StrandedFeature
Retrieve the strand that this feature lies upon.

This will be one of StrandedFeature.POSITIVE or NEGATIVE.

Specified by:
getStrand in interface StrandedFeature
Returns:
one of the Strand constants

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 ProjectedFeature

toString

public java.lang.String toString()

getSymbols

public SymbolList getSymbols()
Description copied from interface: StrandedFeature
Return a list of symbols that are contained in this feature.

The symbols may not be contiguous in the original sequence, but they will be concatenated together in the resulting SymbolList.

The order of the Symbols within the resulting symbol list will be according to the concept of ordering within the location object.

If the feature is on the negative strand then the SymbolList will be reverse-complemented as appropriate.

Specified by:
getSymbols in interface StrandedFeature
Overrides:
getSymbols in class ProjectedFeature