# POD documentation - main docs before the code
=head1 NAME
Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which
wraps a prioritized 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 E<lt>birney@ebi.ac.ukE<gt> originally wrote this class.
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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 the
web:
https://github.com/bioperl/bioperl-live/issues
=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 strict;
use base qw(Bio::Root::Root Bio::DB::RandomAccessI);
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_database'} = [];
return $self;
}
=head2 add_database
Title : add_database
Usage : add_database(%db)
Function: Adds a database to the Failover object
Returns : Count of number of databases
Args : Array of db resources
Throws : Not a RandomAccessI exception
=cut
sub add_database {
my ($self,@db) = @_;
for my $db ( @db ) {
if ( !ref $db || !$db->isa('Bio::DB::RandomAccessI') ) {
$self->throw("Database object $db is a not a Bio::DB::RandomAccessI");
next;
}
push(@{$self->{'_database'}},$db);
}
scalar @{$self->{'_database'}};
}
=head2 get_Seq_by_id
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object
Args : the id (as a string) of a sequence
Throws : "no id" exception
=cut
sub get_Seq_by_id {
my ($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);
};
$self->warn($@) if $@;
if ( defined $seq ) {
return $seq;
} else {
$self->warn("No sequence retrieved by database " . ref($db));
}
}
return;
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "no id" exception
=cut
sub get_Seq_by_acc {
my ($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);
};
$self->warn($@) if $@;
if ( defined $seq ) {
return $seq;
} else {
$self->warn("No sequence retrieved by database " . ref($db));
}
}
return;
}
=head2 get_Seq_by_version
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_acc('X77802.2');
Function: Gets a Bio::Seq object by versioned accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
=cut
sub get_Seq_by_version {
my ($self,$id) = @_;
if( !defined $id ) {
$self->throw("no acc is given!");
}
foreach my $db ( @{$self->{'_database'}} ) {
my $seq;
eval {
$seq = $db->get_Seq_by_version($id);
};
$self->warn($@) if $@;
if ( defined $seq ) {
return $seq;
} else {
$self->warn("No sequence retrieved by database " . ref($db));
}
}
return;
}
## End of Package
1;
__END__