NAME¶
Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for retrieving
Reference data from a sequence database and returning
Bio::Annotation::Reference objects
SYNOPSIS¶
#
# get a database object somehow using a concrete class
#
$ref = $db->get_Reference_by_id('123456');
#
# $ref is a Bio::Annotation::Reference object
#
DESCRIPTION¶
This is a pure interface class - in other words, all this does is define methods
which other (concrete) classes will actually implement.
The Bio::DB::ReferenceI class defines methods used to retrieve reference data
from a sequence. This is returned in the form of Bio::Annotation::Reference
objects.
At the moment it is just the ability to make Bio::Annotation::Reference objects
from a name or unique id (id), an accession number (acc), and so on.
Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this class is
based.
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@lists.open-bio.org - General discussion
http://www.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 the web.
https://github.com/bioperl/bioperl-live/issues
AUTHOR¶
Email cjfields at bioperl dot org
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
get_Reference_by_id¶
Title : get_Reference_by_id
Usage : $ref = $db->get_Reference_by_id('123456')
Function: Gets a Bio::Annotation::Reference-implementing object by its name (id)
Returns : a Bio::Annotation::Reference object or undef if not found
Args : the id (as a string) of a sequence
get_Reference_by_acc¶
Title : get_Reference_by_acc
Usage : $ref = $db->get_Reference_by_acc('X77802');
Function: Gets a Bio::Annotation::Reference object by accession number
Returns : A Bio::Annotation::Reference object or undef if not found
Args : accession number (as a string)
Throws : "more than one sequences correspond to this accession"
if the accession maps to multiple primary ids and
method is called in a scalar context
get_Reference_by_version¶
Title : get_Reference_by_version
Usage : $ref = $db->get_Reference_by_version('X77802.1');
Function: Gets a Bio::Annotation::Reference object by sequence version
Returns : A Bio::Annotation::Reference object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception