Manual Reference Pages - BIO::DB::FLAT::BDB (3)
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.
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.
firstname.lastname@example.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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 - email@example.com
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.
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.
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