org.biojava.bio.program.unigene

Class SQLUnigeneFactory

java.lang.Object

org.biojava.bio.program.unigene.SQLUnigeneFactory

All Implemented Interfaces:

UnigeneFactory

public class SQLUnigeneFactory
extends Object
implements UnigeneFactory

An implementatoin of UnigeneFactory that manages it's data in an SQL database.

This class is for developers and power-users. Usually you will not use this class directly, but rather use UnigeneTools.loadDatabase() with a jdbc URL.

This class will store unigene data in a relational database with a schema defined by the resource src/org/biojava/bio/program/unigene/createUnigene.sql and currently only realy supports mysql. To import data to a newly created database, repeatedly call addCluster() on the UnigeneDB you get back.

Author:

Matthew Pocock

Constructor Summary

Constructors

Constructor and Description
SQLUnigeneFactory()

Method Summary

Modifier and Type	Method and Description
boolean	canAccept(URL dbURL) Accepts all URLs that are of the jdbc protocol.
UnigeneDB	createUnigene(URL dbURL)
UnigeneDB	loadUnigene(URL dbURL)

Methods inherited from class java.lang.Object

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

Constructor Detail

SQLUnigeneFactory

public SQLUnigeneFactory()

Method Detail

canAccept

public boolean canAccept(URL dbURL)

Accepts all URLs that are of the jdbc protocol.

Specified by:

canAccept in interface UnigeneFactory

loadUnigene

public UnigeneDB loadUnigene(URL dbURL)
                      throws BioException

Specified by:

loadUnigene in interface UnigeneFactory

Throws:

BioException

createUnigene

public UnigeneDB createUnigene(URL dbURL)
                        throws BioException

Specified by:

createUnigene in interface UnigeneFactory

Throws:

BioException