Ewan Birney

NAME

Bio::DB::Flat::BDB - Interface for BioHackathon standard BDB-indexed flat file

SYNOPSIS

You should not be using this module directly

DESCRIPTION

This object provides the basic mechanism to associate positions in files with primary and secondary name spaces. Unlike Bio::Index::Abstract (see Bio::Index::Abstract), this is specialized to work with the BerkeleyDB-indexed "common" flat file format worked out at the 2002 BioHackathon.

This object is the guts to the mechanism, which will be used by the specific objects inheriting from it.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org             - General discussion
  http://bioperl.org/MailList.shtml - About the mailing lists

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Lincoln Stein

Email - lstein@cshl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore).

get_PrimarySeq_stream

 Title   : get_PrimarySeq_stream
 Usage   : $stream = get_PrimarySeq_stream
 Function: Makes a Bio::DB::SeqStreamI compliant object
           which provides a single method, next_primary_seq
 Returns : Bio::DB::SeqStreamI
 Args    : none

get_all_primary_ids

 Title   : get_all_primary_ids
 Usage   : @ids = $seqdb->get_all_primary_ids()
 Function: gives an array of all the primary_ids of the
           sequence objects in the database.
 Example :
 Returns : an array of strings
 Args    : none

To Be Implemented in Subclasses

The following methods MUST be implemented by subclasses.

May Be Overridden in Subclasses

The following methods MAY be overridden by subclasses.