SimpleHomology (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojava.utils.AbstractChangeable
- - org.biojava.bio.seq.homol.SimpleHomology

All Implemented Interfaces:

Homology, Changeable
```
public class SimpleHomology
extends AbstractChangeable
implements Homology
```
A no-frills implementation of Homology.

Since:

1.2

Author:

Matthew Pocock, Keith James

Field Summary
- Fields inherited from interface org.biojava.bio.seq.homol.Homology
  ALIGNMENT

Constructor Summary

Constructors
Constructor Description

SimpleHomology()
Creates a new empty SimpleHomology containing no Alignment and no FeatureHolder.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Alignment`	`getAlignment()`	`getAlignment` returns the alignment, which uses the `HomologyFeature`s as keys.
`FeatureHolder`	`getFeatures()`	`getFeatures` returns the constituent `HomologyFeature`s which are also used as the keys in the alignment.
`void`	`setAlignment(Alignment alignment)`	`setAlignment` sets the alignment which describes the homology.
`String`	`toString()`

Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - SimpleHomology
```
public SimpleHomology()
```
    Creates a new empty SimpleHomology containing no Alignment and no FeatureHolder.
- Method Detail
  - getFeatures
```
public FeatureHolder getFeatures()
```
    getFeatures returns the constituent HomologyFeatures which are also used as the keys in the alignment.
    
    Specified by:
    
    getFeatures in interface Homology
    
    Returns:
    
    a FeatureHolder.
  - getAlignment
```
public Alignment getAlignment()
```
    getAlignment returns the alignment, which uses the HomologyFeatures as keys.
    
    Specified by:
    
    getAlignment in interface Homology
    
    Returns:
    
    an Alignment.
  - setAlignment
```
public void setAlignment(Alignment alignment)
                  throws BioException,
                         ChangeVetoException
```
    setAlignment sets the alignment which describes the homology. The alignment, should use the HomologyFeatures as keys. A suitable FeatureHolder is automatically created.
    
    Parameters:
    
    alignment - an Alignment.
    
    Throws:
    
    BioException - if an error occurs.
    
    ChangeVetoException - if the SimpleHomology is locked.
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object