org.biojava.bio.seq.impl
Class SimpleStrandedFeature

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
All Implemented Interfaces:
Serializable, Annotatable, Feature, FeatureHolder, RealizingFeatureHolder, StrandedFeature, Changeable
Direct Known Subclasses:
SimpleFramedFeature, SimpleHomologyFeature, SimpleRemoteFeature, SimpleRestrictionSite, SimpleSimilarityPairFeature

public class SimpleStrandedFeature
extends SimpleFeature
implements StrandedFeature

A no-frills implementation of StrandedFeature.

Author:
Matthew Pocock, Thomas Down
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand, StrandedFeature.Template
 
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
SimpleStrandedFeature(Sequence sourceSeq, FeatureHolder parent, StrandedFeature.Template template)
           
 
Method Summary
protected  void fillTemplate(StrandedFeature.Template ft)
           
 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.
 void setStrand(StrandedFeature.Strand strand)
          Set the strand that this feature lies upon.
 String 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.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

SimpleStrandedFeature

public SimpleStrandedFeature(Sequence sourceSeq,
                             FeatureHolder parent,
                             StrandedFeature.Template template)
                      throws IllegalArgumentException
Throws:
IllegalArgumentException
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

getSymbols

public SymbolList getSymbols()
Description copied from interface: Feature
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 location is modified then this does not modify any SymbolList produced by earlier invocations of this method.

Specified by:
getSymbols in interface Feature
Specified by:
getSymbols in interface StrandedFeature
Overrides:
getSymbols in class SimpleFeature
Returns:
a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent

setStrand

public void setStrand(StrandedFeature.Strand strand)
               throws ChangeVetoException
Description copied from interface: StrandedFeature
Set the strand that this feature lies upon.

This will be one of StrandedFeature.POSITIVE or NEGATIVE.

Specified by:
setStrand in interface StrandedFeature
Parameters:
strand - a Strand.
Throws:
ChangeVetoException - if the strand may not be changed.

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 SimpleFeature
Returns:
a new Template that would make a feature like this one

fillTemplate

protected void fillTemplate(StrandedFeature.Template ft)

toString

public String toString()
Overrides:
toString in class SimpleFeature