Bio::DB::InMemoryCache(3)

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:

  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 _

  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