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## 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:
  Serializable, Annotatable, Feature, FeatureHolder, HomologyFeature, RealizingFeatureHolder, StrandedFeature, Changeable

    public class SimpleHomologyFeature

extends SimpleStrandedFeature
implements HomologyFeature

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

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.seq.homol.HomologyFeature
`HomologyFeature.Template`

Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
`StrandedFeature.Strand`

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
`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.
`String` | `toString()`

Methods inherited from class org.biojava.bio.seq.impl.SimpleStrandedFeature
`fillTemplate, getStrand, getSymbols, setStrand`

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.StrandedFeature
`getStrand, getSymbols, setStrand`

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.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from interface org.biojava.bio.Annotatable
`getAnnotation`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Constructor Detail

### SimpleHomologyFeature

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

Throws:
  `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 String toString()

  Overrides:
    `toString` in class `SimpleStrandedFeature`

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