org.biojava.bio
Class MergeAnnotation

java.lang.Object
  |
  +--org.biojava.utils.AbstractChangeable
        |
        +--org.biojava.bio.MergeAnnotation

All Implemented Interfaces:

Annotation, Changeable, java.io.Serializable

public class MergeAnnotation

extends AbstractChangeable

implements Annotation, java.io.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. This Annotation implementation is immutable.

Since:

1.2

Author:

Thomas Down, Matthew Pocock, Greg Cox

See Also:

Serialized Form

For developers:

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.

Nested Class Summary

protected class

MergeAnnotation.PropertyForwarder

Field Summary

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 the list to be merged.
java.util.Map	asMap() Return a Map view onto this annotation.
boolean	containsProperty(java.lang.Object key) Returns whether there the property is defined.
protected ChangeSupport	getChangeSupport(ChangeType changeType) Called to retrieve the ChangeSupport for this object
java.lang.Object	getProperty(java.lang.Object key) Retrieve the value of a property by key.
java.util.Set	keys() Return a Set containing all key objects visible in this annotation.
void	removeProperty(java.lang.Object key) Delete a property
void	setProperty(java.lang.Object key, java.lang.Object value) Set the value of a property.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, 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

Constructor Detail

MergeAnnotation

public MergeAnnotation()

Method Detail

addAnnotation

public void addAnnotation(Annotation ann)
                   throws ChangeVetoException

Add a new Annotation to the list to be merged.

Parameters:

ann - the Annotation to add

ChangeVetoException

For advanced users:

Use this to alter the Annotations being merged

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType changeType)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object

Overrides:

getChangeSupport in class AbstractChangeable

setProperty

public void setProperty(java.lang.Object key,
                        java.lang.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.

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(java.lang.Object key)
                    throws ChangeVetoException

Description copied from interface: Annotation

Delete a property

Specified by:

removeProperty in interface Annotation

Parameters:

key - the key object

Throws:

ChangeVetoException - if the change is vetoed

getProperty

public java.lang.Object getProperty(java.lang.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.

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(java.lang.Object key)

Description copied from interface: Annotation

Returns whether there the property is defined.

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 java.util.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:

a Set of key objects

asMap

public java.util.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 Map