Sendu Bala
and 1 contributors

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>

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