Bio::DB::InMemoryCache.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

   $cachedb = 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 Bio::Seq object
   #
 
 

DESCRIPTION

This is a memory cache system which saves the objects returned by 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:
   http://bugzilla.open-bio.org/
 
 

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 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
 
 

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
 
 

get_Seq_by_version

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