| Bio::DB::Flat::BDB(3pm) | User Contributed Perl Documentation | Bio::DB::Flat::BDB(3pm) |
Bio::DB::Flat::BDB - Interface for BioHackathon standard BDB-indexed flat file
#You should not be using this module directly.
See Bio::DB::Flat.
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.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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:
https://github.com/bioperl/bioperl-live/issues
Email - lstein@cshl.org
Bio::DB::Flat,
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.
| 2021-08-15 | perl v5.32.1 |