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# $Id: RichSeqI.pm,v 1.14.4.1 2006/10/02 23:10:27 sendu Exp $
#
# BioPerl module for Bio::Seq::RichSeqI
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
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=head1 NAME
Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases
=head1 SYNOPSIS
    @secondary   = $richseq->get_secondary_accessions;
    $division    = $richseq->division;
    $mol         = $richseq->molecule;
    @dates       = $richseq->get_dates;
    $seq_version = $richseq->seq_version;
    $pid         = $richseq->pid;
    @keywords    = $richseq->get_keywords;
=head1 DESCRIPTION
This interface extends the Bio::SeqI interface to give additional functionality
to sequences with richer data sources, in particular from database sequences 
(EMBL, GenBank and Swissprot).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
 to one of the Bioperl mailing lists.
Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Seq::RichSeqI;
use strict;
use base qw(Bio::SeqI);
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=head2 get_secondary_accessions
 Title   : get_secondary_accessions
 Usage   : 
 Function: Get the secondary accessions for a sequence.
           An implementation that allows modification of this array
           property should provide the methods add_secondary_accession
           and remove_secondary_accessions, with obvious purpose.
 Example :
 Returns : an array of strings
 Args    : none
=cut
sub get_secondary_accessions{
   my ($self,@args) = @_;
   $self->throw("hit get_secondary_accessions in interface definition - error");
}
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=head2 division
 Title   : division
 Usage   :
 Function: Get (and set, depending on the implementation) the divison for
           a sequence.
           Examples from GenBank are PLN (plants), PRI (primates), etc.
 Example :
 Returns : a string
 Args    :
=cut
sub division{
   my ($self,@args) = @_;
   $self->throw("hit division in interface definition - error");
}
HideShow 16 lines of Pod
=head2 molecule
 Title   : molecule
 Usage   :
 Function: Get (and set, depending on the implementation) the molecule
           type for the sequence.
           This is not necessarily the same as Bio::PrimarySeqI::alphabet(),
           because it is databank-specific.
 Example :
 Returns : a string
 Args    :
=cut
sub molecule{
   my ($self,@args) = @_;
   $self->throw("hit molecule in interface definition - error");
}
HideShow 13 lines of Pod
=head2 pid
 Title   : pid
 Usage   :
 Function: Get (and set, depending on the implementation) the PID property
           for the sequence.
 Example :
 Returns : a string
 Args    :
=cut
sub pid {
   my ($self,@args) = @_;
   $self->throw("hit pid in interface definition - error");
}
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=head2 get_dates
 Title   : get_dates
 Usage   :
 Function: Get (and set, depending on the implementation) the dates the
           databank entry specified for the sequence
           An implementation that allows modification of this array
           property should provide the methods add_date and
           remove_dates, with obvious purpose.
 Example :
 Returns : an array of strings
 Args    :
=cut
sub get_dates{
   my ($self,@args) = @_;
   $self->throw("hit get_dates in interface definition - error");
}
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=head2 seq_version
 Title   : seq_version
 Usage   :
 Function: Get (and set, depending on the implementation) the version string
           of the sequence.
 Example :
 Returns : a string
 Args    :
=cut
sub seq_version{
   my ($self,@args) = @_;
   $self->throw("hit seq_version in interface definition - error");
}
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=head2 get_keywords
 Title   : get_keywords
 Usage   : $obj->get_keywords()
 Function: Get the keywords for this sequence object.
           An implementation that allows modification of this array
           property should provide the methods add_keyword and
           remove_keywords, with obvious purpose.
 Returns : an array of strings
 Args    : 
=cut
sub get_keywords {
   my ($self) = @_;
   $self->throw("hit keywords in interface definition - error");
}
1;