org.biojava.bio.taxa

Interface Taxon

All Superinterfaces:

Annotatable, Changeable

All Known Implementing Classes:

AbstractTaxon, SimpleTaxon, WeakTaxon

Deprecated.

replaced by classes in org.biojavax.bio.taxa

public interface Taxon
extends Annotatable

A taxon within a classification.

Taxa may be 'leaf' nodes specifying species, or 'internal' nodes specifying kingdoms and the like.

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
static ChangeType	CHANGE_COMMON_NAME Deprecated. Change type to indicate that the common name of this Taxon is changing.
static ChangeType	CHANGE_SCIENTIFIC_NAME Deprecated. Change type to indicate that the scientific name of this Taxon is changing.

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

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.
Set	getChildren() Deprecated. The children of this Taxon.
String	getCommonName() Deprecated. The common name of the Taxon.
Taxon	getParent() Deprecated. The parent of this 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.

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

CHANGE_COMMON_NAME

static final ChangeType CHANGE_COMMON_NAME

Deprecated.

Change type to indicate that the common name of this Taxon is changing.

CHANGE_SCIENTIFIC_NAME

static final ChangeType CHANGE_SCIENTIFIC_NAME

Deprecated.

Change type to indicate that the scientific name of this Taxon is changing.

Method Detail

getCommonName

String getCommonName()

Deprecated.

The common name of the Taxon.

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

Returns:

a String representing this Taxon's common name

setCommonName

void setCommonName(String commonName)
                   throws ChangeVetoException

Deprecated.

Set the new common name of this Taxon.

Parameters:

commonName - the new common name

Throws:

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

getScientificName

String getScientificName()

Deprecated.

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.

setScientificName

void setScientificName(String scientificName)
                       throws ChangeVetoException

Deprecated.

Change the scientific name of this species.

Parameters:

scientificName - the new scientific name

Throws:

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

getParent

Taxon getParent()

Deprecated.

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

Set getChildren()

Deprecated.

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

equals

boolean equals(Object o)

Deprecated.

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.

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

hashCode

int hashCode()

Deprecated.

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

Overrides:

hashCode in class Object