org.biojava.bio
Interface Annotation

All Known Implementing Classes:
AceAnnotation, Annotation.EmptyAnnotation, OverlayAnnotation, SimpleAnnotation

public interface Annotation

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.

Author:
Matthew Pocock

Inner Class Summary
static class Annotation.EmptyAnnotation
          The empty and immutable implementation.
 
Field Summary
static Annotation EMPTY_ANNOTATION
          A realy useful empty and immutable annotation object.
 
Method Summary
 java.util.Map asMap()
          Retern a map that contains the same key/values as this Annotation.
 java.lang.Object getProperty(java.lang.Object key)
          Retrieve the value of a property by key.
 java.util.Set keys()
          Get a set of key objects.
 void setProperty(java.lang.Object key, java.lang.Object value)
          Set the value of a property.
 

Field Detail

EMPTY_ANNOTATION

public static final Annotation EMPTY_ANNOTATION
A realy useful empty and immutable annotation object.

Use this instead of null when you realy don't want an object or an implementation to have annotation even though it should implement Annotatable.

Method Detail

getProperty

public java.lang.Object getProperty(java.lang.Object key)
                             throws java.util.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.

Parameters:
key - the key of the property to retrieve
Returns:
the object associated with that key
Throws:
java.util.NoSuchElementException - if there is no property with the key

setProperty

public void setProperty(java.lang.Object key,
                        java.lang.Object value)
                 throws java.lang.IllegalArgumentException,
                        java.lang.UnsupportedOperationException
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.

Parameters:
key - the key object
value - the new value for this key
Throws:
java.lang.IllegalArgumentException - if the property key cannot be changed.
java.lang.UnsupportedOperationException - if this annotation object is immutable.

keys

public java.util.Set keys()
Get a set of key objects.
Returns:
a Set of key objects

asMap

public java.util.Map asMap()
Retern 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