SimpleHomology (biojava-legacy 1.9.7 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

Modifier and Type

Method

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 Details
- SimpleHomology
  
  public SimpleHomology()
  
  Creates a new empty SimpleHomology containing no Alignment and no FeatureHolder.
Method Details
- 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