NAME

FAST::Bio::DB::InMemoryCache - Abstract interface for a sequence database

SYNOPSIS

$cachedb = FAST::Bio::DB::InMemoryCache->new( -seqdb => $real_db,
                                        -number => 1000);
#
# get a database object somehow using a concrete class
#

$seq = $cachedb->get_Seq_by_id('ROA1_HUMAN');

#
# $seq is a FAST::Bio::Seq object
#

DESCRIPTION

This is a memory cache system which saves the objects returned by FAST::Bio::DB::RandomAccessI in memory to a hard limit of sequences.

CONTACT

Ewan Birney <birney@ebi.ac.uk>

Support

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 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://redmine.open-bio.org/projects/bioperl/

APPENDIX

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

get_Seq_by_id

Title   : get_Seq_by_id
Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a FAST::Bio::Seq object by its name
Returns : a FAST::Bio::Seq object
Args    : the id (as a string) of a sequence
Throws  : "id does not exist" exception

get_Seq_by_acc

Title   : get_Seq_by_acc
Usage   : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a FAST::Bio::Seq object by accession number
Returns : A FAST::Bio::Seq object
Args    : accession number (as a string)
Throws  : "acc does not exist" exception

get_Seq_by_version

Title   : get_Seq_by_version
Usage   : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a FAST::Bio::Seq object by sequence version
Returns : A FAST::Bio::Seq object
Args    : accession.version (as a string)
Throws  : "acc.version does not exist" exception