Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD

## 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
`static RichAnnotation` | `EMPTY_ANNOTATION`

Fields inherited from interface org.biojava.bio.Annotation
`PROPERTY`

Method Summary
`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` | `getNoteSet()` Returns an immutable set of all notes in this annotation.
`Note[]` | `getProperties(Object key)` Find all the `Note`s with any rank that match the key.
`void` | `removeNote(Note note)` Removes a note from this annotation.
`void` | `setNoteSet(Set 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 getNoteSet()

  Returns an immutable set of all notes in this annotation.

  Returns:
    a set of notes.
  See Also:
    `Note`

### setNoteSet

    void setNoteSet(Set 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 `Note`s with any rank that match the key.

  Parameters:
    `key` - either a `String` identifier of a term from the default onltology 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`

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD