Package org.biojava.bio

Class OverlayAnnotation

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.OverlayAnnotation
All Implemented Interfaces:
Serializable, Annotation, Changeable
public class OverlayAnnotation extends AbstractChangeable implements Annotation, 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.
Since:
1.1 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.
Author:
Thomas Down, Matthew Pocock, Greg Cox
See Also:

  • Constructor Details

    • 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 Details

    • getChangeSupport

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

      Your implementation of this method should have the following structure: 

       ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
      It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.
      Overrides:
      getChangeSupport in class AbstractChangeable

    • getOverlay

      protected Map getOverlay()
      Get the map used for the overlay. Modifying this modifies the Annotation.
      Returns:
      the overlay Map

    • setProperty

      public void setProperty(Object key, 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.

      Normal raw access to the property. For cleverer access, use methods in AnnotationType.
      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(Object key) throws ChangeVetoException
      Description copied from interface: Annotation
      Delete a property. Normal raw access to the property. For cleverer access, use methods in AnnotationType.
      Specified by:
      removeProperty in interface Annotation
      Parameters:
      key - the key object
      Throws:
      ChangeVetoException - if the change is vetoed

    • getProperty

      public Object getProperty(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.

      Normal raw access to the property. For cleverer access, use methods in AnnotationType.
      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(Object key)
      Description copied from interface: Annotation
      Returns whether there the property is defined. Normal raw access to the property. For cleverer access, use methods in AnnotationType.
      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 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:
      the keys as a Set

    • asMap

      public 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 view of this Annotation as an immutable Map