AbstractAnnotation (biojava 5.0.0 API)

java.lang.Object
- org.biojava.nbio.ontology.utils.AbstractAnnotation

All Implemented Interfaces:

Serializable, Annotation

Direct Known Subclasses:

SmallAnnotation
```
public abstract class AbstractAnnotation
extends Object
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

Field Summary
- Fields inherited from interface org.biojava.nbio.ontology.utils.Annotation
  EMPTY_ANNOTATION

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`AbstractAnnotation()` Protected no-args constructor intended for sub-classes.
`protected`	`AbstractAnnotation(Annotation ann)` Copy-constructor.
	`AbstractAnnotation(Map annMap)` Create a new Annotation by copying the key-value pairs from a map.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and 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.
`boolean`	`equals(Object o)`
`protected abstract Map`	`getProperties()` Implement this to return the Map delegate.
`Object`	`getProperty(Object key)` Retrieve the value of a property by key.
`int`	`hashCode()`
`Set`	`keys()` Get a set of key objects.
`protected abstract boolean`	`propertiesAllocated()` A convenience method to see if we have allocated the properties Map.
`void`	`removeProperty(Object key)` Delete a property.
`void`	`setProperty(Object key, Object value)` Set the value of a property.
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- 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)
```
    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
  - removeProperty
```
public void removeProperty(Object key)
                    throws NoSuchElementException
```
    Description copied from interface: Annotation
    
    Delete a property. Normal raw access to the property. For cleverer access, use methods in AnnotationType.
    
    Specified by:
    
    removeProperty in interface Annotation
    
    Parameters:
    
    key - the key object
    
    Throws:
    
    NoSuchElementException - if the property doesn't exist
  - 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
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - 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
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object

Class AbstractAnnotation

Field Summary

Fields inherited from interface org.biojava.nbio.ontology.utils.Annotation

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AbstractAnnotation

AbstractAnnotation

AbstractAnnotation

Method Detail

getProperties

propertiesAllocated

getProperty

setProperty

removeProperty

containsProperty

keys

toString

asMap

hashCode

equals