org.biojava.bio.taxa

Class WeakTaxon

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.taxa.AbstractTaxon

org.biojava.bio.taxa.WeakTaxon

All Implemented Interfaces:

Annotatable, Taxon, Changeable

Deprecated.

replaced by classes in org.biojavax.bio.taxa

public class WeakTaxon
extends AbstractTaxon

An implementation of Taxon that keeps only weak references to children, but full references to parents.

This may be suitable for deriving memory-savy implementations of TaxonFactory.

To manipulate the children set, use the getChildrenRaw and setChildrenRaw methods. These 'box' the actual weak reference, but recognize null to mean that there are no children currently known. A code-fragment may wish to do something like this:

 Set children = weakTaxon.getChildrenRaw();
 if(children == null) {
   children = new HashSet();
   weakTaxon.setChildrenRaw(children);
 }
 // do stuff to update child set e.g. add children 
 

Author:

Matthew Pocock

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field and Description
protected Taxon	parent Deprecated.

Fields inherited from interface org.biojava.bio.taxa.Taxon

CHANGE_COMMON_NAME, CHANGE_SCIENTIFIC_NAME

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Constructor and Description
WeakTaxon() Deprecated.
WeakTaxon(String scientificName, String commonName) Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
Set	getChildren() Deprecated. The children of this Taxon.
Set	getChildrenRaw() Deprecated.
Taxon	getParent() Deprecated. The parent of this Taxon.
void	setChildrenRaw(Set children) Deprecated.

Methods inherited from class org.biojava.bio.taxa.AbstractTaxon

equals, getAnnotation, getChangeSupport, getCommonName, getScientificName, hashCode, setCommonName, setScientificName, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, 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

Field Detail

parent

protected Taxon parent

Deprecated.

Constructor Detail

WeakTaxon

public WeakTaxon()

Deprecated.

WeakTaxon

public WeakTaxon(String scientificName,
         String commonName)

Deprecated.

Method Detail

getParent

public Taxon getParent()

Deprecated.

Description copied from interface: Taxon

The parent of this Taxon.

Taxa live within a tree data-structure, so every taxon has a single parent except for the root type. This has the null parent.

Returns:

the parent Taxon, or null if this is the root type.

getChildren

public Set getChildren()

Deprecated.

Description copied from interface: Taxon

The children of this Taxon.

Taxa live within a tree data-structure, so every taxon has zero or more children. In the case of zero children, the empty set is returned.

? read-only ? dynamicaly updated with taxon object ? copy of data ?

Returns:

the Set (possibly empty) of all child Taxa

getChildrenRaw

public Set getChildrenRaw()

Deprecated.

setChildrenRaw

public void setChildrenRaw(Set children)

Deprecated.