Package org.biojavax

Class SimpleRichAnnotation

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojavax.SimpleRichAnnotation
All Implemented Interfaces:
Annotation, Changeable, 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
  • Constructor Details

    • SimpleRichAnnotation

      Creates a new, empty instance of SimpleRichAnnotation
  • Method Details

    • 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

      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

      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:
    • 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

      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

      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:
    • 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:
    • toString

      public String toString()
      Form: list of "[note]" values separated by commas
      Overrides:
      toString in class Object