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

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

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