org.biojava.bio

Interface Annotation

All Superinterfaces:

Changeable

All Known Subinterfaces:

RichAnnotation

All Known Implementing Classes:

AbstractAnnotation, AnnotationChanger, AnnotationRenamer, BeanAsAnnotation, EmptyRichAnnotation, MergeAnnotation, OverlayAnnotation, ReferenceAnnotation, SimpleAnnotation, SimpleRichAnnotation, SmallAnnotation

public interface Annotation
extends Changeable

Arbitrary annotation associated with one or more objects.

Biological information often does not fit design patterns very well, and can be a jumble of facts and relationships. Annotation objects provide a standard way for you to store this mess as a property of an object.

Annotations may contain keys that have Annotations as values. In this way, annotations can be shared among multiple Annotatable objects, and you can represent semi-structured data.

It is perfectly possible to wrap up almost any tree-like or flat data structure as Annotation.

Other than when using the constructor, you should be able to interact with nearly all Annotation implementations via this API.

Since:

1.0

Author:

Matthew Pocock, Thomas Down

See Also:

RichAnnotation

Field Summary

Fields

Modifier and Type	Field and Description
static Annotation	EMPTY_ANNOTATION A really useful empty and immutable annotation object.
static ChangeType	PROPERTY This type symbolizes that one or more properties have changed.

Method Summary

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.
Object	getProperty(Object key) Retrieve the value of a property by key.
Set	keys() Get a set of key objects.
void	removeProperty(Object key) Delete a property.
void	setProperty(Object key, Object value) Set the value of a property.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

PROPERTY

static final ChangeType PROPERTY

This type symbolizes that one or more properties have changed.

EMPTY_ANNOTATION

static final Annotation EMPTY_ANNOTATION

A really useful empty and immutable annotation object.

Be careful when stooring Annotation arguments to constructors. It is possible that you have been passed EMPTY_ANNOTATION but that code later on will access this object believing it to be mutable. For example, the SeqIO factory code clones some Annotations passed in on Feature.Template instances Use this instead of null when you really don't want an object or an implementation to have annotation even though it should implement Annotatable.

Method Detail

getProperty

Object getProperty(Object key)
            throws NoSuchElementException

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.

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

void setProperty(Object key,
                 Object value)
          throws IllegalArgumentException,
                 ChangeVetoException

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.

Parameters:

key - the key object

value - the new value for this key

Throws:

IllegalArgumentException - if the property key is not legal

ChangeVetoException - if this annotation object can't be changed, or if the change was vetoed.

removeProperty

void removeProperty(Object key)
             throws NoSuchElementException,
                    ChangeVetoException

Delete a property. Normal raw access to the property. For cleverer access, use methods in AnnotationType.

Parameters:

key - the key object

Throws:

NoSuchElementException - if the property doesn't exist

ChangeVetoException - if the change is vetoed

Since:

1.3

containsProperty

boolean containsProperty(Object key)

Returns whether there the property is defined. Normal raw access to the property. For cleverer access, use methods in AnnotationType.

Parameters:

key - the key Object to search for

Returns:

true if this Annotation knows about the key, false otherwise

keys

Set keys()

Get a set of key objects.

Returns:

a Set of key objects

asMap

Map asMap()

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.

Returns:

a Map