org.biojava.bio.seq.homol

Class SimpleHomology

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

Method Summary

Modifier and Type	Method and Description
Alignment	getAlignment() getAlignment returns the alignment, which uses the HomologyFeatures as keys.
FeatureHolder	getFeatures() getFeatures returns the constituent HomologyFeatures 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