org.biojavax

Interface RichAnnotation

All Superinterfaces:

Annotation, Changeable

All Known Implementing Classes:

EmptyRichAnnotation, SimpleRichAnnotation

public interface RichAnnotation
extends Annotation

An annotation collection which stores annotations as Note objects.

Since:

1.5

Author:

Richard Holland, Mark Schreiber

See Also:

Note, RichAnnotatable

Field Summary

Fields

Modifier and Type	Field and Description
static RichAnnotation	EMPTY_ANNOTATION

Fields inherited from interface org.biojava.bio.Annotation

PROPERTY

Method Summary

Modifier and Type	Method and Description
void	addNote(Note note) Adds a note to 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.
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) Find all the Notes with any rank that match the key.
void	removeNote(Note note) Removes a note from this annotation.
void	setNoteSet(Set<Note> notes) Clears the notes from this annotation and replaces them with those from the given set.

Methods inherited from interface org.biojava.bio.Annotation

asMap, containsProperty, getProperty, keys, removeProperty, setProperty

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

EMPTY_ANNOTATION

static final RichAnnotation EMPTY_ANNOTATION

Method Detail

clear

void clear()
    throws ChangeVetoException

Removes all notes from this annotation object.

Throws:

ChangeVetoException - if it couldn't do it.

addNote

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.

Parameters:

note - note to add

Throws:

ChangeVetoException - if it doesn't like this.

removeNote

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.

Parameters:

note - note to remove

Throws:

ChangeVetoException - if it doesn't like this.

getNote

Note getNote(Note note)
      throws NoSuchElementException

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

Parameters:

note - note to lookup, using term and rank.

Returns:

the matching note.

Throws:

ChangeVetoException - if it doesn't like this.

NoSuchElementException - if it couldn't be found.

contains

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.

Parameters:

note - note to lookup

Returns:

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

getNoteSet

Set<Note> getNoteSet()

Returns an immutable set of all notes in this annotation.

Returns:

a set of notes.

See Also:

Note

setNoteSet

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.

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

getProperties

Note[] getProperties(Object key)

Find all the Notes with any rank that match the key.

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