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.