org.biojava.bio.taxa

Class WeakTaxonFactory

java.lang.Object

org.biojava.bio.taxa.WeakTaxonFactory

All Implemented Interfaces:

TaxonFactory

Deprecated.

replaced by classes in org.biojavax.bio.taxa

public class WeakTaxonFactory
extends Object
implements TaxonFactory

An implementation of TaxonFactory that builds a weak in-memory Taxon tree.

This implementation holds only weak references to the Taxon instances it knows about. This means that WeakTaxonFactory may not be appropriate for situations where you wish to browse the taxon tree. It does, however, mean that massive taxa can be represented, by effectively reflecting the currently useful rooted sub-tree in memory.

Author:

Matthew Pocock

Field Summary

Fields

Modifier and Type	Field and Description
static WeakTaxonFactory	GLOBAL Deprecated. The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.

Constructor Summary

Constructors

Constructor and Description
WeakTaxonFactory(String name) Deprecated.

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 taxon) 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

GLOBAL

public static final WeakTaxonFactory GLOBAL

Deprecated.

The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.

Constructor Detail

WeakTaxonFactory

public WeakTaxonFactory(String name)

Deprecated.

Method Detail

getRoot

public Taxon getRoot()

Deprecated.

Description copied from interface: TaxonFactory

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

Specified by:

getRoot in interface TaxonFactory

Returns:

the 'root' Taxon

getName

public String getName()

Deprecated.

Description copied from interface: TaxonFactory

Name for this TaxonFactory.

Specified by:

getName in interface TaxonFactory

Returns:

the name of this TaxonFactory

importTaxon

public Taxon importTaxon(Taxon taxon)

Deprecated.

Description copied from interface: TaxonFactory

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.

Specified by:

importTaxon in interface TaxonFactory

Parameters:

taxon - the Taxon to copy

Returns:

a new Taxon

createTaxon

public Taxon createTaxon(String scientificName,
                String commonName)

Deprecated.

Description copied from interface: TaxonFactory

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

Specified by:

createTaxon in interface TaxonFactory

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

public Taxon addChild(Taxon parent,
             Taxon child)

Deprecated.

Description copied from interface: TaxonFactory

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.

Specified by:

addChild in interface TaxonFactory

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

removeChild

public Taxon removeChild(Taxon parent,
                Taxon child)

Deprecated.

Description copied from interface: TaxonFactory

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.

Specified by:

removeChild in interface TaxonFactory

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

search

public Taxon search(Object id)

Deprecated.

Description copied from interface: TaxonFactory

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.

Specified by:

search in interface TaxonFactory

Parameters:

id - the Object identifying a Taxon

Returns:

the Taxon matching the ID, or null if none match