org.biojava.bio.taxa

Class AbstractTaxon

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.taxa.AbstractTaxon

All Implemented Interfaces:

Annotatable, Taxon, Changeable

Direct Known Subclasses:

SimpleTaxon, WeakTaxon

Deprecated.

replaced by classes in org.biojavax.bio.taxa

public abstract class AbstractTaxon
extends AbstractChangeable
implements Taxon

An abstract implementation of Taxon.

It is left up to the impementor to provide methods for accessing the parent and children. All other state is provided for here. A common pattern would be to route any Taxon.getParent() call back via a method on the TaxonFactory used to generate this instance.

Since:

1.3

Author:

Matthew Pocock, Keith James

Nested Class Summary

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

Annotatable.AnnotationForwarder

Field Summary

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

Modifier	Constructor and Description
protected	AbstractTaxon() Deprecated.
protected	AbstractTaxon(String scientificName, String commonName) Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o) Deprecated. Two taxa are equal if they have equivalent children, common and scientific names.
Annotation	getAnnotation() Deprecated. Should return the associated annotation object.
protected ChangeSupport	getChangeSupport(ChangeType ct) Deprecated. Called to retrieve the ChangeSupport for this object.
String	getCommonName() Deprecated. The common name of the Taxon.
String	getScientificName() Deprecated. The scientific name of this taxon.
int	hashCode() Deprecated. The hash-code of a Taxon is equal to the hash-code of it's scientific name.
void	setCommonName(String commonName) Deprecated. Set the new common name of this Taxon.
void	setScientificName(String scientificName) Deprecated. Change the scientific name of this species.
String	toString() Deprecated.

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.bio.taxa.Taxon

getChildren, getParent

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

AbstractTaxon

protected AbstractTaxon()

Deprecated.

AbstractTaxon

protected AbstractTaxon(String scientificName,
             String commonName)

Deprecated.

Method Detail

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Deprecated.

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class AbstractChangeable

getCommonName

public String getCommonName()

Deprecated.

Description copied from interface: Taxon

The common name of the Taxon.

This is the normal name used in common speech, such as 'human'.

Specified by:

getCommonName in interface Taxon

Returns:

a String representing this Taxon's common name

setCommonName

public void setCommonName(String commonName)
                   throws ChangeVetoException

Deprecated.

Description copied from interface: Taxon

Set the new common name of this Taxon.

Specified by:

setCommonName in interface Taxon

Parameters:

commonName - the new common name

Throws:

ChangeVetoException - if the name can't be changed at this time

getScientificName

public String getScientificName()

Deprecated.

Description copied from interface: Taxon

The scientific name of this taxon.

This will be the portion of the scientific classification pertaining to just this node within the classifictaion. It will be something like 'homo sapiens' or 'archaeal group 2', rather than the full classification list.

Specified by:

getScientificName in interface Taxon

setScientificName

public void setScientificName(String scientificName)
                       throws ChangeVetoException

Deprecated.

Description copied from interface: Taxon

Change the scientific name of this species.

Specified by:

setScientificName in interface Taxon

Parameters:

scientificName - the new scientific name

Throws:

ChangeVetoException - if the scientific name can't be changed at this time

getAnnotation

public Annotation getAnnotation()

Deprecated.

Description copied from interface: Annotatable

Should return the associated annotation object.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

equals

public boolean equals(Object o)

Deprecated.

Description copied from interface: Taxon

Two taxa are equal if they have equivalent children, common and scientific names.

Two different implementations of Taxon should be able to appropriately trans-class equality. The parent of a Taxon is not considered in testing equality as this potentially leads to combinatorial problems checking whole taxa hierachies against one another.

Specified by:

equals in interface Taxon

Overrides:

equals in class Object

Parameters:

o - the object to check

Returns:

true if o is a Taxon instance and has the same properties as this

toString

public String toString()

Deprecated.

Overrides:

toString in class Object

hashCode

public int hashCode()

Deprecated.

Description copied from interface: Taxon

The hash-code of a Taxon is equal to the hash-code of it's scientific name.

Specified by:

hashCode in interface Taxon

Overrides:

hashCode in class Object