All Implemented Interfaces:

Serializable, Annotation, Changeable

public class MergeAnnotation
extends AbstractChangeable
implements Annotation, Serializable 

Since:

1.2 Use these when you have a list of Annotation instances that need to be viewed as one. For example, if you have annotation for a feature from a local database, in-memory objects and a web-page, you could build three Annotation instances and merge them using a MergeAnnotation.

Author:

Thomas Down, Matthew Pocock, Greg Cox, Francois Pepin

See Also:

Serialized Form

• Nested Class Summary

  Nested Classes

  Modifier and Type	Class and Description
  protected class	MergeAnnotation.PropertyForwarder Listener used to forward changes for any of the underlying annotations to listeners on this annotation.

• Field Summary

  Fields

  Modifier and Type	Field and Description
  static ChangeType	ANNOTATION_ADD ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
  static ChangeType	ANNOTATION_CHANGED ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
  static ChangeType	ANNOTATION_REMOVE ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.

  • Fields inherited from interface org.biojava.bio.Annotation

    EMPTY_ANNOTATION, PROPERTY

• Constructor Summary

  Constructors

  Constructor and Description
  MergeAnnotation ()

• Method Summary

  All Methods

  Modifier and Type	Method and Description
  void	addAnnotation (Annotation ann) Add a new Annotation to to the end of the list to be merged.
  Map	asMap () Return a map that contains the same key/values as this Annotation.
  boolean	containsProperty (Object key) Returns whether there the property is defined.
  List	getAnnotations () Gets an unmodifiable view of the list of Annotations that are part of the MergeAnnotation.
  protected ChangeSupport	getChangeSupport (ChangeType changeType) Called to retrieve the ChangeSupport for this object.
  Object	getProperty (Object key) Retrieve the value of a property by key.
  Set	keys () Get a set of key objects.
  void	removeAnnotation (Annotation ann) Remove an Annotation from the list.
  void	removeProperty (Object key) Delete a property.
  void	setProperty (Object key, Object value) Set the value of a property.

  • Methods inherited from class org.biojava.utils.AbstractChangeable

    addChangeListener, addChangeListener, generateChangeSupport, hasListeners, 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

• Field Detail

  • ANNOTATION_CHANGED

    public static final ChangeType ANNOTATION_CHANGED 

    ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.

  • ANNOTATION_ADD

    public static final ChangeType ANNOTATION_ADD 

    ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.

  • ANNOTATION_REMOVE

    public static final ChangeType ANNOTATION_REMOVE 

    ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.

• Constructor Detail

  • MergeAnnotation

    public MergeAnnotation()

• Method Detail

  • addAnnotation

    public void addAnnotation(Annotation ann)
     throws ChangeVetoException 

    Add a new Annotation to to the end of the list to be merged. Use this to alter the Annotations being merged

    Parameters:

    ann - the Annotation to add

    Throws:

    ChangeVetoException - if the annotation could not be added

  • getAnnotations

    public List getAnnotations()

    Gets an unmodifiable view of the list of Annotations that are part of the MergeAnnotation. Lower indices Annotation have precedence if 2 Annotations share the same property.

    Returns:

    an unmodifiable List of the Annotations that form this MergeAnnotation.

  • removeAnnotation

    public void removeAnnotation(Annotation ann)
     throws ChangeVetoException 

    Remove an Annotation from the list. This can be used to change the ordering of the Annotations by re-adding it later.

    Parameters:

    ann - an Annotation to be removed.

    Throws:

    ChangeVetoException - if an error occurs

  • 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

  • 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()

    Description copied from interface: Annotation
    Get a set of key objects.

    Specified by:

    keys in interface Annotation

    Returns:

    a Set of key objects

  • asMap

    public Map asMap()

    Description copied from interface: Annotation
    Return a map that contains the same key/values as this Annotation.

    If the annotation changes, the map may not reflect this. The Map may be unmodifiable.

    Specified by:

    asMap in interface Annotation

    Returns:

    a Map