Package org.biojava.bio

Class 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:
    Serialized Form

    • 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.

        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.

      • 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