Databases documentation.

Databases.pm is the main configuration file which holds the different
parameters (usernames, hosts, passwords, ports, database-names) to
connect to different databases used in the Ensembl-Analysis pipeline.
It imports and sets a number of standard global variables into the
calling package. Without arguments all the standard variables are set,
and with a list, only those variables whose names are provided are set.
The module will die if a variable which doesn\'t appear in its
%Config hash is asked to be set.

 
A common way to get an DBAdaptor in a module is 
 
 print "Loading database : ".  $$DATABASES{REFERENCE_DB}{"-dbname"} . "\n";  

 my $ref_db = new Bio::EnsEMBL::DBSQL::DBAdaptor( %{ $$DATABASES{REFERENCE_DB} }) ;

 
 OR if you write a RunnableDB:  

   use Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild;
   @ISA = qw ( Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild ) 

   my $genes_db = $self->get_dbadaptor("GENEBUILD_DB");

 
 OR for normal scripts :

   use Bio::EnsEMBL::Analysis::Tools::Utilities qw( get_db_adaptor_by_string );
   get_db_adaptor_by_string("GENEBUILD_DB")

  
 
The variables can also be references to arrays or hashes.

Edit %Config to add or alter variables.
All the variables are in capitals, so that they resemble environment
variables.
Databases is a pure ripoff of humConf written by James Gilbert.
humConf is based upon ideas from the standard perl Env environment
module.

sub import {

    my ($callpack) = caller(0); # Name of the calling package
    my $pack = shift; # Need to move package off @_

    # Get list of variables supplied, or else all
    my @vars = @_ ? @_ : keys(%Config);
    return unless @vars;

    # Predeclare global variables in calling package
    eval "package $callpack; use vars qw("
         . join(' ', map { '$'.$_ } @vars) . ")";
    die $@ if $@;


    foreach (@vars) {
	if (defined $Config{ $_ }) {
            no strict 'refs';
	    # Exporter does a similar job to the following
	    # statement, but for function names, not
	    # scalar variables:
	    *{"${callpack}::$_"} =\$ Config{ $_ };
	} else {
	    die "Error: Config: $_ not known\n";
	}
    }
}

1;

}