org.biojava.nbio.ontology.utils

Class SmallAnnotation

java.lang.Object

org.biojava.nbio.ontology.utils.AbstractAnnotation

org.biojava.nbio.ontology.utils.SmallAnnotation

All Implemented Interfaces:

Serializable, Annotation

public class SmallAnnotation
extends AbstractAnnotation

Annotation that is optimized for memory usage. Access time is linear, so SmallAnnotations are not recommended when the number of entries is large. However, they are fine for small numbers of keys.

Since:

1.2 A minimal-memory alternative to SimpleAnnotation When creating a large number of small Annotation instances, it is worth instantiating SmallAnnotation. Small is anything up to at least 30 properties but will vary with the JavaVM and underlying platform.

Author:

Thomas Down, Matthew Pocock

See Also:

Serialized Form

Field Summary

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

EMPTY_ANNOTATION

Constructor Summary

Constructors

Constructor and Description
SmallAnnotation() Return a new SmallAnnotation optimised for small sets of properties.
SmallAnnotation(Annotation ann) Return a new SmallAnnotation that copies all values from another annoation.
SmallAnnotation(Map map) Return a new SmallAnnotation that copies all values from a Map.

Method Summary

Modifier and Type	Method and Description
protected Map	getProperties() Implement this to return the Map delegate.
protected boolean	propertiesAllocated() A convenience method to see if we have allocated the properties Map.

Methods inherited from class org.biojava.nbio.ontology.utils.AbstractAnnotation

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

Methods inherited from class java.lang.Object

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

Constructor Detail

SmallAnnotation

public SmallAnnotation()

Return a new SmallAnnotation optimised for small sets of properties.

SmallAnnotation

public SmallAnnotation(Annotation ann)

Return a new SmallAnnotation that copies all values from another annoation.

Parameters:

ann - the Annoation to copy all values from

Throws:

NullPointerException - if ann is null

SmallAnnotation

public SmallAnnotation(Map map)

Return a new SmallAnnotation that copies all values from a Map.

Parameters:

map - the Map to copy values from

Method Detail

getProperties

protected final Map getProperties()

Description copied from class: AbstractAnnotation

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.

Specified by:

getProperties in class AbstractAnnotation

Returns:

a Map containing all properties

propertiesAllocated

protected final boolean propertiesAllocated()

Description copied from class: AbstractAnnotation

A convenience method to see if we have allocated the properties Map. This is required for the implementation of an Annotation that extends AbstractAnnotation.

Specified by:

propertiesAllocated in class AbstractAnnotation

Returns:

true if the properties have been allocated, false otherwise