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Summary

Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which
wraps a prioritized list of DBs

Package variables

Inherit

Bio::DB::RandomAccessI Bio::Root::Root

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);

Description

This module provides fail over access to a set of Bio::DB::RandomAccessI
objects.

Methods

Methods description

 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

 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

 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

 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

Methods code

sub new {

    my ($class,@args) = @_;

    my $self = $class->SUPER::new(@args);

    $self->{'_database'} = [];
    return $self;

}

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'}};

}

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;

}

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;

}

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__

}

General documentation

Ewan Birney <birney@ebi.ac.uk> originally wrote this class.

Please direct usage questions or support issues to the mailing list:
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.

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://redmine.open-bio.org/projects/bioperl/

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