Bio::DB::ReferenceI(3)User Contributed Perl DocumentatioBio::DB::ReferenceI(3)NAMEBio::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.
CONTACT
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.
http://bugzilla.open-bio.org/
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
perl v5.14.1 2011-07-22 Bio::DB::ReferenceI(3)