org.biojava.bio.program.unigene

Class FlatFileUnigeneFactory

java.lang.Object

org.biojava.bio.program.unigene.FlatFileUnigeneFactory

All Implemented Interfaces:

UnigeneFactory

public class FlatFileUnigeneFactory
extends Object
implements UnigeneFactory

A UnigeneFactory that will use flat-file indexing of the unigene ascii-art files.

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

This will create all the index files necisary to look up records in a timely manner. It requires read/write access to the unigene directory. No files will be deleted during this opperation. The indexing strategy used is compattible with the OBDA flat-file indexing spec and uses the package org.biojava.bio.program.indexdb and parsers that are compattible with the tag-value API.

Author:

Matthew Pocock

Constructor Summary

Constructors

Constructor and Description
FlatFileUnigeneFactory()

Method Summary

Methods

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

Methods inherited from class java.lang.Object

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

Constructor Detail

FlatFileUnigeneFactory

public FlatFileUnigeneFactory()

Method Detail

canAccept

public boolean canAccept(URL unigeneLoc)

Accepts all URLs that are of the file protocol.

Specified by:

canAccept in interface UnigeneFactory

loadUnigene

public UnigeneDB loadUnigene(URL unigeneLoc)
                      throws BioException

Specified by:

loadUnigene in interface UnigeneFactory

Throws:

BioException

createUnigene

public UnigeneDB createUnigene(URL unigeneLoc)
                        throws BioException

Specified by:

createUnigene in interface UnigeneFactory

Throws:

BioException