org.biojava.bio

Class SimpleAnnotation

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.AbstractAnnotation

org.biojava.bio.SimpleAnnotation

All Implemented Interfaces:

Serializable, Annotation, Changeable

public class SimpleAnnotation
extends AbstractAnnotation

A no-frills implementation of Annotation that is just a wrapper around a LinkedHashMap.

It will allow you to set any property, but will throw exceptions if you try to retrieve a property that is not set. Because of the use of a LinkedHashMap properties are iterated in the order they are entered.

When you need to make a new Annotation instance and will want to populate it with properties, use this class.

Since:

1.0

Author:

Matthew Pocock, Greg Cox, Mark Schreiber

See Also:

SimpleRichAnnotation, Serialized Form

Field Summary

Fields inherited from interface org.biojava.bio.Annotation

EMPTY_ANNOTATION, PROPERTY

Constructor Summary

Constructors

Constructor and Description
SimpleAnnotation() Create a new, empty SimpleAnnotation instance.
SimpleAnnotation(Annotation ann) Create a new SimpleAnnotation by copying the properties from another one.
SimpleAnnotation(Map map) Create a new SimpleAnnotation using the values in a Map.

Method Summary

Modifier and Type	Method and Description
protected Map	getProperties() Get the property value pairs in this annotation
protected boolean	propertiesAllocated() Test to see if any properties have been allocated

Methods inherited from class org.biojava.bio.AbstractAnnotation

asMap, containsProperty, equals, getProperty, hashCode, keys, removeProperty, setProperty, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

SimpleAnnotation

public SimpleAnnotation()

Create a new, empty SimpleAnnotation instance.

SimpleAnnotation

public SimpleAnnotation(Annotation ann)

Create a new SimpleAnnotation by copying the properties from another one. The new Annotation instance will be independant of the original.

Parameters:

ann - the Annotation to copy

SimpleAnnotation

public SimpleAnnotation(Map map)

Create a new SimpleAnnotation using the values in a Map.

Parameters:

map - the Map to copy properties out of

Method Detail

getProperties

protected final Map getProperties()

Get the property value pairs in this annotation

Specified by:

getProperties in class AbstractAnnotation

Returns:

a LinkedHashMap of properties and values

propertiesAllocated

protected final boolean propertiesAllocated()

Test to see if any properties have been allocated

Specified by:

propertiesAllocated in class AbstractAnnotation

Returns:

true if any have (even if they have since been removed), false otherwise