Ewan Birney


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


You should not be using this module directly


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.


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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:


AUTHOR - Lincoln Stein

Email - lstein@cshl.org


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


 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


 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.