Package org.biojava.directory

Open Bio Sequence Database Access (OBDA) registry support.

Interface Summary

Interface	Description
RegistryConfiguration	The BioDirectory Registry is a simple system for specifying where to find services which provide sequence databases.
SequenceDBProvider	Interfaces for named resources that can provide sequences via a database given some configuration information as defined by the OBDA standard.

Class Summary

Class	Description
OBDARegistryParser	This class encapsulates all the parsing of the OBDA registry configuration file.
Registry	Registry is a factory which gets implementations of the BioJava SequenceDBLite interface.
RegistryConfiguration.Composite	A RegistryConfiguration that allows you to treat other configurations as providing important or default configuration information.
RegistryConfiguration.Impl	A simple implementation of RegistryConfiguration backed by a Map.
SystemRegistry	A registry that loads up the standard biodirectory files.

Exception Summary

Exception	Description
ProviderNotFoundException	ProviderNotFoundException is thrown when a sequence database provider can not be located.
RegistryException	A RegistryException thrown when the registry cannot find an implementation of a requested SequenceDB.