Raw content of Bio::Seq::RichSeqI
<![CDATA[# $Id: RichSeqI.pm,v 1.8 2002/10/22 07:38:40 lapp 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
=head1 NAME
Bio::Seq::RichSeqI - RichSeq interface, mainly for database orientated sequences
=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 = $richseq->keywords;
=head1 DESCRIPTION
This interface extends the Bio::SeqI interface to give additional functionality
to sequences with richer data sources, in particular from database sequences
(EMBL, GenBank and Swissprot).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Seq::RichSeqI;
use vars qw(@ISA);
use strict;
use Bio::SeqI;
@ISA = ('Bio::SeqI');
=head2 get_secondary_accessions
Title : get_secondary_accessions
Usage :
Function: Get the secondary accessions for a sequence.
Example :
Returns : an array of strings
Args : none
=cut
sub get_secondary_accessions{
my ($self,@args) = @_;
$self->throw("hit get_secondary_accessions in interface definition - error");
}
=head2 division
Title : division
Usage :
Function: Get (and set, depending on the implementation) the divison for
a sequence.
Examples from GenBank are PLN (plants), PRI (primates), etc.
Example :
Returns : a string
Args :
=cut
sub division{
my ($self,@args) = @_;
$self->throw("hit division in interface definition - error");
}
=head2 molecule
Title : molecule
Usage :
Function: Get (and set, depending on the implementation) the molecule
type for the sequence.
This is not necessarily the same as Bio::PrimarySeqI::alphabet(),
because it is databank-specific.
Example :
Returns : a string
Args :
=cut
sub molecule{
my ($self,@args) = @_;
$self->throw("hit molecule in interface definition - error");
}
=head2 pid
Title : pid
Usage :
Function: Get (and set, depending on the implementation) the PID property
for the sequence.
Example :
Returns : a string
Args :
=cut
sub pid {
my ($self,@args) = @_;
$self->throw("hit pid in interface definition - error");
}
=head2 get_dates
Title : get_dates
Usage :
Function: Get (and set, depending on the implementation) the dates the
databank entry specified for the sequence
Example :
Returns : an array of strings
Args :
=cut
sub get_dates{
my ($self,@args) = @_;
$self->throw("hit get_dates in interface definition - error");
}
=head2 seq_version
Title : seq_version
Usage :
Function: Get (and set, depending on the implementation) the version string
of the sequence.
Example :
Returns : a string
Args :
=cut
sub seq_version{
my ($self,@args) = @_;
$self->throw("hit seq_version in interface definition - error");
}
=head2 keywords
Title : keywords
Usage : $obj->keywords($newval)
Function:
Returns : value of keywords (a string)
Args : newvalue (optional) (a string)
=cut
sub keywords {
my ($self) = @_;
$self->throw("hit keywords in interface definition - error");
}
1;
]]>