diff variant_effect_predictor/Bio/DB/Failover.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/Failover.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,162 @@
+# POD documentation - main docs before the code
+
+# $Id: Failover.pm,v 1.5.2.1 2003/06/25 13:44:18 heikki Exp $
+
+
+=head1 NAME
+
+Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which wraps a priority 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 originally wrote this class.
+
+=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 email
+or the web:
+
+    [e-mail]                   
+    http://bugzilla.bioperl.org/           
+
+=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 vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::DB::RandomAccessI;
+@ISA = qw(Bio::Root::Root Bio::DB::RandomAccessI );
+
+sub new {
+    my ($class,@args) = @_;
+
+    my $self = $class->SUPER::new(@args);
+
+    $self->{'_database'} = [];
+    return $self;
+}
+
+=head2 add_database
+
+ Title   : add_database
+ Usage   : add_database(%db)
+ Function: Adds a database to the 
+ Returns : count of number of databases
+ Args    : hash of db resource name to Bio::DB::SeqI object
+
+=cut
+
+sub add_database {
+    my ($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);
+    }    
+}
+
+
+=head2 get_Seq_by_id
+
+ Title   : get_Seq_by_id
+ Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
+ Function: Gets a Bio::Seq object by its name
+ Returns : a Bio::Seq object
+ Args    : the id (as a string) of a sequence
+ Throws  : "id does not exist" exception
+
+
+=cut
+
+sub get_Seq_by_id {
+    my ($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);
+	};
+	if( defined $seq ) {
+	    return $seq;
+	}
+    }
+
+    return undef;
+}
+
+=head2 get_Seq_by_acc
+
+ Title   : get_Seq_by_acc
+ Usage   : $seq = $db->get_Seq_by_acc('X77802');
+ Function: Gets a Bio::Seq object by accession number
+ Returns : A Bio::Seq object
+ Args    : accession number (as a string)
+ Throws  : "acc does not exist" exception
+
+
+=cut
+
+sub get_Seq_by_acc {
+    my ($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);
+	};
+	if( defined $seq ) {
+	    return $seq;
+	}
+    }
+    return undef;
+}
+
+
+## End of Package
+
+1;
+
+__END__
+