org.biojava.bio.seq.impl
Class SimpleHomologyFeature

java.lang.Object
  |
  +--org.biojava.utils.AbstractChangeable
        |
        +--org.biojava.bio.seq.impl.SimpleFeature
              |
              +--org.biojava.bio.seq.impl.SimpleStrandedFeature
                    |
                    +--org.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, StrandedFeature.Template

Nested classes inherited from class org.biojava.bio.seq.Feature

Feature.ByLocationComparator, Feature.Template

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

Returns:

a new Template that would make a feature like this one

fillTemplate

protected void fillTemplate(HomologyFeature.Template ft)

toString

public java.lang.String toString()

Overrides:

toString in class SimpleStrandedFeature