NAME¶
Bio::DB::Flat::BDB - Interface for BioHackathon standard BDB-indexed flat file
SYNOPSIS¶
#You should not be using this module directly.
See Bio::DB::Flat.
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/wiki/Mailing_lists - About the mailing lists
Support¶
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.
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:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Lincoln Stein¶
Email - lstein@cshl.org
SEE ALSO¶
Bio::DB::Flat,
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.