Package org.biojavax

Class SimpleRichAnnotation

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.SimpleRichAnnotation

All Implemented Interfaces:

Annotation, Changeable, RichAnnotation

public class SimpleRichAnnotation
extends AbstractChangeable
implements RichAnnotation

Simple annotation wrapper. All non-Note annotations get a rank of zero.

Since:

1.5

Author:

Richard Holland, George Waldon - adapted note change firing

Field Summary

Fields inherited from interface org.biojava.bio.Annotation

PROPERTY

Fields inherited from interface org.biojavax.RichAnnotation

EMPTY_ANNOTATION

Constructor Summary

Constructors

Constructor	Description
SimpleRichAnnotation()	Creates a new, empty instance of SimpleRichAnnotation

Method Summary

Modifier and Type	Method	Description
void	addNote(Note note)	Adds a note to this annotation.
Map	asMap()	Return a map that contains the same key/values as this Annotation.
void	clear()	Removes all notes from this annotation object.
boolean	contains(Note note)	Returns true if the given note exists in this annotation.
boolean	containsProperty(Object key)	Deprecated.
Note	getNote(Note note)	Uses the term and rank to lookup a note in this annotation.
Set<Note>	getNoteSet()	Returns an immutable set of all notes in this annotation.
Note[]	getProperties(Object key)	Deprecated.
Object	getProperty(Object key)	Deprecated.
Set	keys()	Get a set of key objects.
void	removeNote(Note note)	Removes a note from this annotation.
void	removeProperty(Object key)	Deprecated.
void	setNoteSet(Set<Note> notes)	Clears the notes from this annotation and replaces them with those from the given set.
void	setProperty(Object key, Object value)	Deprecated.
String	toString()	Form: list of "[note]" values separated by commas

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, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

SimpleRichAnnotation

public SimpleRichAnnotation()

Creates a new, empty instance of SimpleRichAnnotation

Method Detail

clear

public void clear()
           throws ChangeVetoException

Removes all notes from this annotation object.

Specified by:

clear in interface RichAnnotation

Throws:

ChangeVetoException - if it couldn't do it.

asMap

public 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. The map is a copy of the internal structure. It is a map of ComparableTerms to Strings corresponding to the Term and Value of the Notes in the annotation.

Specified by:

asMap in interface Annotation

Returns:

a Map

addNote

public void addNote(Note note)
             throws ChangeVetoException

Adds a note to this annotation. Must not be null. If the note is already in the annotation, nothing happens. In case the note was already here, a call to ChangeEvent.getPrevious() in the firePostChangeEvent method will return a copy of the original note.

Specified by:

addNote in interface RichAnnotation

Parameters:

note - note to add

Throws:

ChangeVetoException - if it doesn't like this.

contains

public boolean contains(Note note)

Returns true if the given note exists in this annotation. The lookup is done using the term and rank of the note.

Specified by:

contains in interface RichAnnotation

Parameters:

note - note to lookup

Returns:

true if it is in this annotation, false if not.

containsProperty

public boolean containsProperty(Object key)

Deprecated.

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

getNote

public Note getNote(Note note)
             throws NoSuchElementException

Uses the term and rank to lookup a note in this annotation.

Specified by:

getNote in interface RichAnnotation

Parameters:

note - note to lookup, using term and rank.

Returns:

the matching note.

Throws:

NoSuchElementException - if it couldn't be found.

getProperty

public Object getProperty(Object key)
                   throws NoSuchElementException

Deprecated.

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. Strictly it will return the first Note which matches the key (or a Term made with a String key)..

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

See Also:

getProperties(Object key)

getProperties

public Note[] getProperties(Object key)

Deprecated.

Find all the Notes with any rank that match the key. Strictly it will return all Notes which match the key (or a Term made with a String key)..

Specified by:

getProperties in interface RichAnnotation

Parameters:

key - either a String identifier of a term from the default ontology or a ComparableTerm

Returns:

an array of matching Notes in order of rank or an empty array if there are no matches. No implementation should ever return null!

See Also:

Note, ComparableTerm

keys

public Set keys()

Get a set of key objects.

Specified by:

keys in interface Annotation

Returns:

a Set of key objects

removeNote

public void removeNote(Note note)
                throws ChangeVetoException

Removes a note from this annotation. Must not be null. If the note wasn't in the annotation, nothing happens. In case the note is not found, a call to ChangeEvent.getPrevious() in the firePostChangeEvent method will return null.

Specified by:

removeNote in interface RichAnnotation

Parameters:

note - note to remove

Throws:

ChangeVetoException - if it doesn't like this.

removeProperty

public void removeProperty(Object key)
                    throws NoSuchElementException,
                           ChangeVetoException

Deprecated.

Delete a property. Normal raw access to the property. For cleverer access, use methods in AnnotationType. Strictly it will remove the first Note which matches the key (or a Term made with a String key)..

Specified by:

removeProperty in interface Annotation

Parameters:

key - the key object

Throws:

NoSuchElementException - if the property doesn't exist

ChangeVetoException - if the change is vetoed

setProperty

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

Deprecated.

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:

IllegalArgumentException - if the property key is not legal

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

getNoteSet

public Set<Note> getNoteSet()

Returns an immutable set of all notes in this annotation. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

getNoteSet in interface RichAnnotation

Returns:

a set of notes.

See Also:

Note

setNoteSet

public void setNoteSet(Set<Note> notes)
                throws ChangeVetoException

Clears the notes from this annotation and replaces them with those from the given set. The set cannot be null. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

setNoteSet in interface RichAnnotation

Parameters:

notes - a set of Note objects to use from now on.

Throws:

ChangeVetoException - if it doesn't like any of them.

See Also:

Note

toString

public String toString()

Form: list of "[note]" values separated by commas

Overrides:

toString in class Object