Reference

Bio::DB::Failover(3pm)

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

NAME

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

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.

CONTACT

Ewan Birney <[email protected]> originally wrote this class.

Support

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

[email protected]

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 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 the web:

  https://github.com/bioperl/bioperl-live/issues

APPENDIX

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

add_database

 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_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  : "no id" exception

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  : "no id" exception

get_Seq_by_version

 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

History