Package org.biojava.bio

Class AbstractAnnotation

  • All Implemented Interfaces:
    Serializable, Annotation, Changeable
    Direct Known Subclasses:
    AnnotationChanger, AnnotationRenamer, BeanAsAnnotation, ReferenceAnnotation, SimpleAnnotation, SmallAnnotation
    public abstract class AbstractAnnotation
extends AbstractChangeable
implements Annotation, Serializable
    A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map. Where possible implementations This class is only intended as a way to implement Annotation. If you are not trying to do that, then don't read on. If you are reading the documentation for an Annotation implementation that extends this, then don't read on. There is nothing to see here. If you are still reading this, then you must be trying to implement Annotation. To do that, extend this class and implement getProperties() and propertiesAllocated(). Where possible implementations should be backed with a LinkedHashMap or similar so properties are iterated in the order they were added.
    Since:
    1.0
    Author:
    Matthew Pocock, Greg Cox
    See Also:
    Serialized Form

    • Constructor Detail

      • AbstractAnnotation

        protected AbstractAnnotation()
        Protected no-args constructor intended for sub-classes. This class is abstract and can not be directly instantiated.

      • AbstractAnnotation

        protected AbstractAnnotation​(Annotation ann)
        Copy-constructor.

        This does a shallow copy of the annotation. The result is an annotation with the same properties and values, but which is independant of the original annotation.

        Parameters:
        ann - the Annotation to copy

      • AbstractAnnotation

        public AbstractAnnotation​(Map annMap)
        Create a new Annotation by copying the key-value pairs from a map. The resulting Annotation is independant of the map.
        Parameters:
        annMap - the Map to copy from.

    • Method Detail

      • getProperties

        protected abstract Map getProperties()
        Implement this to return the Map delegate. Modifying this return value will modify the properties associated with this annotation. From code in the 1.2 version of AbstractAnnotation This is required for the implementation of an Annotation that extends AbstractAnnotation. Where possible implementations should be backed with a LinkedHashMap or similar so properties are iterated in the order they were added.
        Returns:
        a Map containing all properties

      • propertiesAllocated

        protected abstract boolean propertiesAllocated()
        A convenience method to see if we have allocated the properties Map. This is required for the implementation of an Annotation that extends AbstractAnnotation.
        Returns:
        true if the properties have been allocated, false otherwise

      • getProperty

        public Object getProperty​(Object key)
                   throws NoSuchElementException
        Description copied from interface: Annotation

        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.
        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

      • setProperty

        public void setProperty​(Object key,
                        Object value)
                 throws ChangeVetoException
        Description copied from interface: Annotation

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

      • containsProperty

        public boolean containsProperty​(Object key)
        Description copied from interface: Annotation
        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

      • keys

        public Set keys()
        Description copied from interface: Annotation
        Get a set of key objects.
        Specified by:
        keys in interface Annotation
        Returns:
        a Set of key objects

      • asMap

        public Map asMap()
        Description copied from interface: Annotation
        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.

        Specified by:
        asMap in interface Annotation
        Returns:
        a Map