org.biojava.bio.taxa

Interface TaxonFactory

All Known Implementing Classes:

SimpleTaxonFactory, WeakTaxonFactory

Deprecated.

replaced by classes in org.biojavax.bio.taxa

public interface TaxonFactory

Factory for handling a particular implementation of a Taxon.

Author:

Matthew Pocock

Method Summary

Methods

Modifier and Type	Method and Description
Taxon	addChild(Taxon parent, Taxon child) Deprecated. Add a taxon as a child to a parent.
Taxon	createTaxon(String scientificName, String commonName) Deprecated. Create a new orphan Taxon with a given scientific and common name.
String	getName() Deprecated. Name for this TaxonFactory.
Taxon	getRoot() Deprecated. Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.
Taxon	importTaxon(Taxon source) Deprecated. Import a Taxon and all its children into the implementation provided by this factory.
Taxon	removeChild(Taxon parent, Taxon child) Deprecated. Remove a Taxon as a child to this one.
Taxon	search(Object id) Deprecated. Retrieve a Taxon that matches some ID.

Method Detail

getName

String getName()

Deprecated.

Name for this TaxonFactory.

Returns:

the name of this TaxonFactory

importTaxon

Taxon importTaxon(Taxon source)

Deprecated.

Import a Taxon and all its children into the implementation provided by this factory.

The return value of this method should be .equals() and .hasCode() compatable with the taxon parameter. It may not be implemented by the same underlying implementation.

Parameters:

source - the Taxon to copy

Returns:

a new Taxon

getRoot

Taxon getRoot()

Deprecated.

Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.

Returns:

the 'root' Taxon

search

Taxon search(Object id)

Deprecated.

Retrieve a Taxon that matches some ID.

This method is here out of desperation. It's nasty and should be replaced by some propper querying API. Without having different methods for every TaxonFactory I don't know what to do. All ideas appreciated.

Parameters:

id - the Object identifying a Taxon

Returns:

the Taxon matching the ID, or null if none match

createTaxon

Taxon createTaxon(String scientificName,
                String commonName)

Deprecated.

Create a new orphan Taxon with a given scientific and common name.

Parameters:

scientificName - the scientificName to give the Taxon

commonName - the common name to give the Taxon

Returns:

a new Taxon with no parent and no children

addChild

Taxon addChild(Taxon parent,
             Taxon child)
               throws ChangeVetoException,
                      CircularReferenceException

Deprecated.

Add a taxon as a child to a parent.

The TaxonFactory may chose to add the child directly, or make a new object which is .equals() compatable with child. The actual Taxon instance inserted into the child set is returned by the add method.

Parameters:

parent - the parent Taxon to add the child to

child - the Taxon to add as a child

Returns:

the Taxon object actualy present as the child

Throws:

ChangeVetoException - if for any reason the child can't be added

CircularReferenceException - if child is this Taxon or any of its parents

removeChild

Taxon removeChild(Taxon parent,
                Taxon child)
                  throws ChangeVetoException

Deprecated.

Remove a Taxon as a child to this one.

This Taxon should attempt to remove a child that is .equals() compatable with child. If it is sucessful, it should return the Taxon instance that was removed. If not, it should return null.

Parameters:

parent - the parent Taxon to remove the child from

child - the Taxon to remove as a child

Returns:

the actual Taxon removed, or null if none were removed

Throws:

ChangeVetoException - if for any reason the child can't be removed