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;

}

General documentation

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

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:

  http://bugzilla.open-bio.org/

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