NAME

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

SYNOPSIS

    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");

DESCRIPTION

This module provides access to the Open Bio Database Access scheme, which provides a cross language and cross platform specification of how to get to 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 ';'.

CONTACT

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/

APPENDIX

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

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