org.biojava.bio

Class AbstractAnnotation

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.AbstractAnnotation

All Implemented Interfaces:

Serializable, Annotation, Changeable

Direct Known Subclasses:

AnnotationChanger, AnnotationRenamer, BeanAsAnnotation, ReferenceAnnotation, SimpleAnnotation, SmallAnnotation

public abstract class AbstractAnnotation
extends AbstractChangeable
implements Annotation, Serializable

A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map. Where possible implementations This class is only intended as a way to implement Annotation. If you are not trying to do that, then don't read on. If you are reading the documentation for an Annotation implementation that extends this, then don't read on. There is nothing to see here. If you are still reading this, then you must be trying to implement Annotation. To do that, extend this class and implement getProperties() and propertiesAllocated(). Where possible implementations should be backed with a LinkedHashMap or similar so properties are iterated in the order they were added.

Since:

1.0

Author:

Matthew Pocock, Greg Cox

See Also:

Serialized Form

Field Summary

Fields inherited from interface org.biojava.bio.Annotation

EMPTY_ANNOTATION, PROPERTY

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractAnnotation() Protected no-args constructor intended for sub-classes.
protected	AbstractAnnotation(Annotation ann) Copy-constructor.
	AbstractAnnotation(Map annMap) Create a new Annotation by copying the key-value pairs from a map.

Method Summary

Methods

Modifier and Type	Method and Description
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.
boolean	equals(Object o)
protected abstract Map	getProperties() Implement this to return the Map delegate.
Object	getProperty(Object key) Retrieve the value of a property by key.
int	hashCode()
Set	keys() Get a set of key objects.
protected abstract boolean	propertiesAllocated() A convenience method to see if we have allocated the properties Map.
void	removeProperty(Object key) Delete a property.
void	setProperty(Object key, Object value) Set the value of a property.
String	toString()

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

AbstractAnnotation

protected AbstractAnnotation()

Protected no-args constructor intended for sub-classes. This class is abstract and can not be directly instantiated.

AbstractAnnotation

protected AbstractAnnotation(Annotation ann)

Copy-constructor.

This does a shallow copy of the annotation. The result is an annotation with the same properties and values, but which is independant of the original annotation.

Parameters:

ann - the Annotation to copy

AbstractAnnotation

public AbstractAnnotation(Map annMap)

Create a new Annotation by copying the key-value pairs from a map. The resulting Annotation is independant of the map.

Parameters:

annMap - the Map to copy from.

Method Detail

getProperties

protected abstract Map getProperties()

Implement this to return the Map delegate. Modifying this return value will modify the properties associated with this annotation. From code in the 1.2 version of AbstractAnnotation This is required for the implementation of an Annotation that extends AbstractAnnotation. Where possible implementations should be backed with a LinkedHashMap or similar so properties are iterated in the order they were added.

Returns:

a Map containing all properties

propertiesAllocated

protected abstract boolean propertiesAllocated()

A convenience method to see if we have allocated the properties Map. This is required for the implementation of an Annotation that extends AbstractAnnotation.

Returns:

true if the properties have been allocated, false otherwise

getProperty

public Object getProperty(Object key)
                   throws NoSuchElementException

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

Throws:

NoSuchElementException - if there is no property with the key

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,
                           NoSuchElementException

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

NoSuchElementException - if the property doesn't exist

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

toString

public String toString()

Overrides:

toString in class Object

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

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object