Raw content of Bio::DB::Failover
<![CDATA[# POD documentation - main docs before the code
# $Id: Failover.pm,v 1.5.2.1 2003/06/25 13:44:18 heikki Exp $
=head1 NAME
Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs
=head1 SYNOPSIS
$failover = Bio::DB::Failover->new();
$failover->add_database($db);
# fail over Bio::DB::RandomAccessI.pm
# this will check each database in priority, returning when
# the first one succeeds
$seq = $failover->get_Seq_by_id($id);
=head1 DESCRIPTION
This module provides fail over access to a set of Bio::DB::RandomAccessI objects
=head1 CONTACT
Ewan Birney originally wrote this class.
=head2 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/
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::Failover;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::DB::RandomAccessI;
@ISA = qw(Bio::Root::Root Bio::DB::RandomAccessI );
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_database'} = [];
return $self;
}
=head2 add_database
Title : add_database
Usage : add_database(%db)
Function: Adds a database to the
Returns : count of number of databases
Args : hash of db resource name to Bio::DB::SeqI object
=cut
sub add_database {
my ($self,@db) = @_;
foreach my $db ( @db ) {
if( !ref $db || !$db->isa('Bio::DB::RandomAccessI') ) {
$self->throw("Database objects $db is a not a Bio::DB::RandomAccessI");
next;
}
push(@{$self->{'_database'}},$db);
}
}
=head2 get_Seq_by_id
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object
Args : the id (as a string) of a sequence
Throws : "id does not exist" exception
=cut
sub get_Seq_by_id {
my ($self,$id) = @_;
if( !defined $id ) {
$self->throw("no id is given!");
}
foreach my $db ( @{$self->{'_database'}} ) {
my $seq;
eval {
$seq = $db->get_Seq_by_id($id);
};
if( defined $seq ) {
return $seq;
}
}
return undef;
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
=cut
sub get_Seq_by_acc {
my ($self,$id) = @_;
if( !defined $id ) {
$self->throw("no id is given!");
}
foreach my $db ( @{$self->{'_database'}} ) {
my $seq;
eval {
$seq = $db->get_Seq_by_acc($id);
};
if( defined $seq ) {
return $seq;
}
}
return undef;
}
## End of Package
1;
__END__
]]>