org.biojava.bio
Class OverlayAnnotation

java.lang.Object
  extended byorg.biojava.utils.AbstractChangeable
      extended byorg.biojava.bio.OverlayAnnotation
All Implemented Interfaces:
Annotation, Changeable, java.io.Serializable

public class OverlayAnnotation
extends AbstractChangeable
implements Annotation, java.io.Serializable

Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation. When getProperty is called, we first check for a value stored in the overlay. If this fails, the underlying Annotation is checked. Values passed to setProperty are always stored within the overlay.

Author:
Thomas Down, Matthew Pocock, Greg Cox
See Also:
Serialized Form
For advanced users:
In the case where you wish to wrap an underlying Annotation in a view that will allow it to be edited without altering the original object, but also reflect changes in the original object.

Nested Class Summary
protected  class OverlayAnnotation.PropertyForwarder
           
 
Field Summary
 
Fields inherited from interface org.biojava.bio.Annotation
EMPTY_ANNOTATION, PROPERTY
 
Constructor Summary
OverlayAnnotation(Annotation par)
          Construct an annotation which can overlay new key-value pairs onto an underlying annotation.
 
Method Summary
 java.util.Map asMap()
          Return a Map view onto this annotation.
 boolean containsProperty(java.lang.Object key)
          Returns whether there the property is defined.
protected  ChangeSupport getChangeSupport(ChangeType changeType)
          Called to retrieve the ChangeSupport for this object
protected  java.util.Map getOverlay()
           
 java.lang.Object getProperty(java.lang.Object key)
           Retrieve the value of a property by key.
 java.util.Set keys()
          Return a Set containing all key objects visible in this annotation.
 void removeProperty(java.lang.Object key)
          Delete a property
 void setProperty(java.lang.Object key, java.lang.Object value)
           Set the value of a property.
 
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

Constructor Detail

OverlayAnnotation

public OverlayAnnotation(Annotation par)
Construct an annotation which can overlay new key-value pairs onto an underlying annotation.

Parameters:
par - The `parent' annotation, on which new key-value pairs can be layered.
Method Detail

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType changeType)
Description copied from class: AbstractChangeable
Called to retrieve the ChangeSupport for this object

Overrides:
getChangeSupport in class AbstractChangeable

getOverlay

protected java.util.Map getOverlay()

setProperty

public void setProperty(java.lang.Object key,
                        java.lang.Object value)
                 throws ChangeVetoException
Description copied from interface: Annotation

Set the value of a property.

This method throws an exception if either properties can not be added to this object, or that this particular property is immutable or illegal within the implementation.

Specified by:
setProperty in interface Annotation
Parameters:
key - the key object
value - the new value for this key
Throws:
ChangeVetoException - if this annotation object can't be changed, or if the change was vetoed

removeProperty

public void removeProperty(java.lang.Object key)
                    throws ChangeVetoException
Description copied from interface: Annotation
Delete a property

Specified by:
removeProperty in interface Annotation
Parameters:
key - the key object
Throws:
ChangeVetoException - if the change is vetoed

getProperty

public java.lang.Object getProperty(java.lang.Object key)
Description copied from interface: Annotation

Retrieve the value of a property by key.

Unlike the Map collections, it will complain if the key does not exist. It will only return null if the key is defined and has value null.

Specified by:
getProperty in interface Annotation
Parameters:
key - the key of the property to retrieve
Returns:
the object associated with that key

containsProperty

public boolean containsProperty(java.lang.Object key)
Description copied from interface: Annotation
Returns whether there the property is defined.

Specified by:
containsProperty in interface Annotation
Parameters:
key - the key Object to search for
Returns:
true if this Annotation knows about the key, false otherwise

keys

public java.util.Set keys()
Return a Set containing all key objects visible in this annotation. The Set is unmodifiable, but will dynamically reflect changes made to the annotation.

Specified by:
keys in interface Annotation
Returns:
a Set of key objects

asMap

public java.util.Map asMap()
Return a Map view onto this annotation. The returned Map is unmodifiable, but will dynamically reflect any changes made to this annotation.

Specified by:
asMap in interface Annotation
Returns:
a Map