org.biojava.bio.seq.impl
Class SimpleHomologyFeature

java.lang.Object
  extended byorg.biojava.utils.AbstractChangeable
      extended byorg.biojava.bio.seq.impl.SimpleFeature
          extended byorg.biojava.bio.seq.impl.SimpleStrandedFeature
              extended byorg.biojava.bio.seq.impl.SimpleHomologyFeature
All Implemented Interfaces:
Annotatable, Changeable, Feature, FeatureHolder, HomologyFeature, RealizingFeatureHolder, java.io.Serializable, StrandedFeature

public class SimpleHomologyFeature
extends SimpleStrandedFeature
implements HomologyFeature

Author:
Matthew Pocock, Keith James
See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.seq.homol.HomologyFeature
HomologyFeature.Template
 
Nested classes inherited from class org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand
 
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
SimpleHomologyFeature(Sequence sourceSeq, FeatureHolder parent, HomologyFeature.Template template)
           
 
Method Summary
protected  void fillTemplate(HomologyFeature.Template ft)
           
 Homology getHomology()
           
 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.impl.SimpleStrandedFeature
fillTemplate, getStrand, getSymbols
 
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, getType, hashCode, realizeFeature, removeFeature, setLocation, setSource, setType
 
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, 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
 
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

SimpleHomologyFeature

public SimpleHomologyFeature(Sequence sourceSeq,
                             FeatureHolder parent,
                             HomologyFeature.Template template)
                      throws java.lang.IllegalArgumentException,
                             IllegalAlphabetException
Method Detail

getHomology

public Homology getHomology()
Specified by:
getHomology in interface HomologyFeature

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

fillTemplate

protected void fillTemplate(HomologyFeature.Template ft)

toString

public java.lang.String toString()
Overrides:
toString in class SimpleStrandedFeature