Bio::DB::Registry - Access to the Open Bio Database Access registry scheme use Bio::DB::Registry(); $registry = new Bio::DB::Registry(); @available_services = $registry->services; $db = $registry->get_database('embl'); # $db is a Bio::DB::SeqI implementing class $seq = $db->get_Seq_by_acc("J02231"); 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 net. The Registry object will attempt to store these settings in ${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). Ewan Birney originally wrote this class.

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ 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 it downloads 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 : Function: To find all the seqdatabase.ini files Returns : list of seqdatabase.ini paths Args : $home