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# $Id: 15549 2009-02-21 00:48:48Z maj $
# BioPerl module for Bio::DB::LocationI
# Please direct questions and support issues to <>
# Cared for by Chris Fields <cjfields at bioperl dot org>
# Copyright Chris Fields
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::LocationI - A RandomAccessI-like abstract interface for
retrieving location data from a sequence database and returning
Bio::LocationI objects
# get a database object somehow using a concrete class
$loc = $db->get_Location_by_id('123456');
# $loc is a Bio::LocationI object
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::LocationI class defines methods used to retrieve location data
from a sequence. This is returned in the form of Bio::LocationI objects,
which can include:
At the moment it is just the ability to make Bio::LocationI objects
from a name or unique id (id), an accession number (acc), and so on.
=head1 CONTACT
Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this class
is based.
=head2 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. - General discussion - About the mailing lists
=head2 Support
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.
=head2 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.
=head1 AUTHOR
Email cjfields at bioperl dot org
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
# Let the code begin...
package Bio::DB::LocationI;
use strict;
use Bio::Root::RootI;
use base qw(Bio::Root::Root);
=head2 get_Location_by_id
Title : get_Location_by_id
Usage : $loc = $db->get_Location_by_id('123456')
Function: Gets a Bio::LocationI-implementing object by its name (id)
Returns : a Bio::LocationI object or undef if not found
Args : the id (as a string) of a sequence
sub get_Location_by_id{
my ($self,@args) = @_;
=head2 get_Location_by_acc
Title : get_Location_by_acc
Usage : $loc = $db->get_Location_by_acc('X77802');
Function: Gets a Bio::LocationI object by accession number
Returns : A Bio::LocationI object or undef if not found
Args : accession number (as a string)
Throws : "more than one sequences correspond to this accession"
if the accession maps to multiple primary ids and
method is called in a scalar context
sub get_Location_by_acc{
my ($self,@args) = @_;
=head2 get_Location_by_version
Title : get_Location_by_version
Usage : $loc = $db->get_Location_by_version('X77802.1');
Function: Gets a Bio::LocationI object by sequence version
Returns : A Bio::LocationI object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
sub get_Location_by_version{
my ($self,@args) = @_;
## End of Package