view variant_effect_predictor/Bio/DB/RandomAccessI.pm @ 0:1f6dce3d34e0

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# 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:

    [e-mail]                   
    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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