Raw content of Bio::DB::RandomAccessI
<![CDATA[# POD documentation - main docs before the code
#
# $Id: RandomAccessI.pm,v 1.12 2002/10/22 07:38:29 lapp Exp $
#
=head1 NAME
Bio::DB::RandomAccessI - Abstract interface for a sequence database
=head1 SYNOPSIS
#
# get a database object somehow using a concrete class
#
$seq = $db->get_Seq_by_id('ROA1_HUMAN');
#
# $seq is a Bio::Seq object
#
=head1 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::RandomAccessI class defines what methods a generic database class
should have. At the moment it is just the ability to make Bio::Seq objects
from a name (id) or a accession number.
=head1 CONTACT
Ewan Birney originally wrote this class.
=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 email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::RandomAccessI;
use vars qw(@ISA);
use strict;
use Bio::Root::RootI;
use Bio::Root::Root;
@ISA = qw(Bio::Root::Root);
=head2 get_Seq_by_id
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object or undef if not found
Args : the id (as a string) of a sequence,
=cut
sub get_Seq_by_id{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
$seq = $db->get_Seq_by_acc(Locus => 'X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object or undef if not found
Args : accession number (as a string), or a two
element list consisting of namespace=>accession
Throws : "more than one sequences correspond to this accession"
if the accession maps to multiple primary ids and
method is called in a scalar context
NOTE: The two-element form allows you to choose the namespace for the
accession number.
=cut
sub get_Seq_by_acc{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 get_Seq_by_version
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by sequence version
Returns : A Bio::Seq object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
=cut
sub get_Seq_by_version{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
## End of Package
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