Summary

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

Package variables

Included modules

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 
 Returns : count of number of databases
 Args    : hash of db resource name to Bio::DB::SeqI object

 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

 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

Methods code

sub new {

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

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

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

}

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);
    }

}

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;

}

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 = $db->get_Seq_by_acc($db);
	};
	if( defined $seq ) {
	    return $seq;
	}
    }
    return undef;

}

General documentation

Ewan Birney 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 email
or the web:

    bioperl-bugs@bio.perl.org                   
    http://bio.perl.org/bioperl-bugs/

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