Package org.biojava.directory

Interface RegistryConfiguration

  • All Known Implementing Classes:
    RegistryConfiguration.Composite, RegistryConfiguration.Impl
    public interface RegistryConfiguration

    The BioDirectory Registry is a simple system for specifying where to find services which provide sequence databases. A client should look at the following places in order to find this file:

      $HOME/.bioinformatics/seqdatabase.ini
  /etc/bioinformatics/seqdatabase.ini
  http://www.open-bio.org/registry/seqdatabase.ini

    The file is a simple stanza format

      [database-name]
  tag=value
  tag=value

  [database-name]
  tag=value
  tag=value

    where each stanza starts with the declaration of the database being in square brackets and following that one line tag=value tag value formats.

    Database-name stanzas can be repeated, in which case the client should try each service in turn (starting at the first one).

    The options under each stanza must have two non-optional tag=value lines being

      protocol=<protocol-type>
  location=<location-string>

    'protocol' currently can be one of

    • flat
    • biofetch
    • biosql

    'location' is a string specific to the protocol. Any number of additional tag values are allowed in the stanza which should be passed to the appropiate constructor of the protocol to interpret. Some protocols might insist on other mandatory tags.

    Version:
    $Revision$
    Author:
    Brian Gilman, Keith James, Matthew Pocock

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Interface Description
      static class  RegistryConfiguration.Composite
      A RegistryConfiguration that allows you to treat other configurations as providing important or default configuration information.
      static class  RegistryConfiguration.Impl
      A simple implementation of RegistryConfiguration backed by a Map.