Bio::EnsEMBL
DBLoader
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Summary
Bio::EnsEMBL::DBLoader - Run time database loader
Package variables
No package variables defined.
Synopsis
$db =
Bio::EnsEMBL::DBLoader->new( "Bio::EnsEMBL::DBSQL::DBAdaptor/"
. "host=localhost;"
. "dbname=homo_sapiens_core_19_34a;"
. "user=ensro;" );
# $db is a database object
$db = Bio::EnsEMBL::DBLoader->standard();
# equivalent to
# Bio::EnsEMBL::DBLoader->new( $ENV{'ENSEMBL_DATABASE'} );
Description
This system provides a run-time loading of the database for ensembl,
allowing two things
a) Only "using" the database module which is required for a
particular implementation
b) Providing a simple string method to indicate where the database
is, allowing per sites defaults and other things as such
The string is parsed as follows:
Before the / is the Perl database object to load, after are the
parameters to pass to that database. The parameters are series of
key=values separated by semi-colons. These are passed as a hash to the
new method of the database object
Methods
Methods description
Arg [1] : string $string
An Ensembl database locator string.
Example : Bio::EnsEMBL::DBSQL::DBLoader->new("Bio::EnsEMBL::DBSQL::DBAdaptor/host=localhost;dbname=homo_sapiens_core_19_34a;user=ensro;"
Description: Connects to an Ensembl database using the module specified in
the locator string.
Returntype : The module specified in the load string is returned.
Exceptions : thrown if the specified module cannot be instantiated or the
locator string cannot be parsed
Caller : ?
Status : Stable |
Methods code
sub _load_module
{ my ($modulein) = @_;
my ($module,$load,$m);
$module = "_<$modulein.pm";
$load = "$modulein.pm";
$load =~ s/::/\//g;
return 1 if $main::{$module};
eval {
require $load;
};
if( $@ ) {
print STDERR <<END;
$load: cannot be found
Exception $@
END
;
return;
}
return 1;
}
1;} | sub new
{ my ($class,$string) = @_;
my ($module,%hash);
$string =~ /(\S+?)\/([\S+\s*]+)/ || die "Could not parse [$string] as a ensembl database locator. Needs database_module/params";
$module = $1;
my $param = $2;
&_load_module($module);
my @param = split(/;/,$param);
foreach my $keyvalue ( @param ) {
$keyvalue =~ /(\S+?)=([\S*\s*]*)/ || do { warn("In loading $keyvalue, could not split into keyvalue for loading $module. Ignoring"); next; };
my $key = $1;
my $value = $2;
$hash{"-$key"} = $value;
}
my @kv = %hash;
return "$module"->new(%hash);} | General documentation
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html