- AUTHOR - Lincoln Stein
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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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
The following methods MUST be implemented by subclasses.
The following methods MAY be overridden by subclasses.