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## org.biojava.bio
Class MergeAnnotation

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.MergeAnnotation

All Implemented Interfaces:
  Serializable, Annotation, Changeable

    public class MergeAnnotation

extends AbstractChangeable
implements Annotation, Serializable

Merged view onto a list of underlying Annotation objects. Currently immutable (but reflects changes to underlying objects). Annotations near the beginning of the list will have properties that take precedence. It is possible to get the ordering of the annotations, or to change it by removing and re-adding methods. This Annotation implementation is immutable.

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
`protected class` | `MergeAnnotation.PropertyForwarder` Listener used to forward changes for any of the underlying annotations to listeners on this annotation.

Field Summary
`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
`MergeAnnotation()`

Method Summary
`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

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