Bio::DB Failover
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Summary
Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which
wraps a prioritized list of DBs
Package variables
No package variables defined.
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
new
No description
Code
add_databaseDescriptionCode
get_Seq_by_idDescriptionCode
get_Seq_by_accDescriptionCode
get_Seq_by_versionDescriptionCode
Methods description
add_databasecode    nextTop
 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
get_Seq_by_idcodeprevnextTop
 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
get_Seq_by_acccodeprevnextTop
 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
get_Seq_by_versioncodeprevnextTop
 Title   : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_acc('X77802.2');
Function: Gets a Bio::Seq object by versioned accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
Methods code
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;

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

    $self->{'_database'} = [];
    return $self;
}
add_databasedescriptionprevnextTop
sub add_database {
	my ($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 @{$self->{'_database'}};
}
get_Seq_by_iddescriptionprevnextTop
sub get_Seq_by_id {
	my ($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;
}
get_Seq_by_accdescriptionprevnextTop
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;
}
get_Seq_by_versiondescriptionprevnextTop
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
CONTACTTop
Ewan Birney <birney@ebi.ac.uk> originally wrote this class.
Support Top
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.
Reporting BugsTop
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/
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _