Package org.biojava.nbio.ontology.utils

Interface Annotation

All Known Implementing Classes:
AbstractAnnotation, SmallAnnotation
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.

Other than when using the constructor, you should be able to interact with nearly all Annotation implementations via this API.
Since:
1.0
Author:
Matthew Pocock, Thomas Down
See Also:
  • org.biojavax.RichAnnotation

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final Annotation
    EMPTY_ANNOTATION
    A really useful empty and immutable annotation object.

  • Method Summary

    Modifier and Type
    Method
    Description
    Map
    asMap()
    Return a map that contains the same key/values as this Annotation.
    boolean
    containsProperty(Object key)
    Returns whether there the property is defined.
    Object
    getProperty(Object key)
    Retrieve the value of a property by key.
    Set
    keys()
    Get a set of key objects.
    void
    removeProperty(Object key)
    Delete a property.
    void
    setProperty(Object key, Object value)
    Set the value of a property.

  • Field Details

    • EMPTY_ANNOTATION

      static final Annotation EMPTY_ANNOTATION

      A really useful empty and immutable annotation object.

      Be careful when stooring Annotation arguments to constructors. It is possible that you have been passed EMPTY_ANNOTATION but that code later on will access this object believing it to be mutable. For example, the SeqIO factory code clones some Annotations passed in on Feature.Template instances Use this instead of null when you really don't want an object or an implementation to have annotation even though it should implement Annotatable.

  • Method Details

    • getProperty

      Object getProperty(Object key) throws 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.

      Normal raw access to the property. For cleverer access, use methods in AnnotationType.
      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

    • setProperty

      void setProperty(Object key, Object value) throws IllegalArgumentException

      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.
      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.

    • removeProperty

      void removeProperty(Object key) throws NoSuchElementException
      Delete a property. Normal raw access to the property. For cleverer access, use methods in AnnotationType.
      Parameters:
      key - the key object
      Throws:
      NoSuchElementException - if the property doesn't exist
      ChangeVetoException - if the change is vetoed
      Since:
      1.3

    • containsProperty

      boolean containsProperty(Object key)
      Returns whether there the property is defined. Normal raw access to the property. For cleverer access, use methods in AnnotationType.
      Parameters:
      key - the key Object to search for
      Returns:
      true if this Annotation knows about the key, false otherwise

    • keys

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

    • asMap

      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.

      Returns:
      a Map