NAME

       Bio::DB::Registry - Access to the Open Bio Database Access registry scheme

SYNOPSIS

           use Bio::DB::Registry();

           $registry = Bio::DB::Registry->new();

           @available_services = $registry->services;

           $db = $registry->get_database('embl');
           # $db is a Bio::DB::SeqI implementing class

           $seq = $db->get_Seq_by_acc("J02231");

DESCRIPTION

       This module provides access to the Open Bio Database Access (OBDA) scheme, which provides
       a single cross-language and cross-platform specification of how to get to databases. These
       databases may be accessible through the Web, they may be BioSQL databases, or they may be
       local, indexed flatfile databases.

       If the user or system administrator has not installed the default init file,
       seqdatabase.ini, in /etc/bioinformatics or ${HOME}/.bioinformatics then creating the first
       Registry object copies the default settings from the www.open-bio.org. The Registry object
       will attempt to store these settings in a new file,
       ${HOME}/.bioinformatics/seqdatabase.ini.

       Users can specify one or more custom locations for the init file by setting
       $OBDA_SEARCH_PATH to those directories, where multiple directories should be separated by
       ';'.

       Please see the OBDA Access HOWTO for more information
       (<http://bioperl.org/howtos/OBDA_HOWTO.html>).

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   _load_registry
        Title   : _load_registry
        Usage   :
        Function: Looks for seqdatabase.ini files in the expected locations and
                  in the directories specified by $OBDA_SEARCH_PATH. If no files
                  are found download a default file from www.open-bio.org
        Returns : nothing
        Args    : none

   get_database
        Title   : get_database
        Usage   : my $db = $registry->get_database($dbname);
        Function: Retrieve a Database object which implements Bio::DB::SeqI interface
        Returns : Bio::DB::SeqI object
        Args    : string describing the name of the database

   services
        Title   : services
        Usage   : my @available = $registry->services();
        Function: returns list of possible services
        Returns : list of strings
        Args    : none

   _get_ini_files
        Title   : _get_ini_files
        Usage   : my @files = $self->_get_ini_files
        Function: To find all the seqdatabase.ini files
        Returns : list of seqdatabase.ini paths
        Args    : None

   _make_private_registry
        Title   : _make_private_registry
        Usage   :
        Function: Make private registry in file in $HOME
        Returns : Path to private registry file
        Args    : None