#
# BioPerl module for Bio::Seq::RichSeqI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# 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 - 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 = $richseq->get_keywords;
=head1 DESCRIPTION
This interface extends the L<Bio::SeqI> interface to give additional
functionality to sequences with richer data sources, in particular from database
sequences (EMBL, GenBank and Swissprot). For a general implementation, please
see the documentation for L<Bio::Seq::RichSeq>.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Seq::RichSeqI;
use strict;
use base qw(Bio::SeqI);
=head2 get_secondary_accessions
Title : get_secondary_accessions
Usage :
Function: Get the secondary accessions for a sequence.
An implementation that allows modification of this array
property should provide the methods add_secondary_accession
and remove_secondary_accessions, with obvious purpose.
Example :
Returns : an array of strings
Args : none
=cut
sub get_secondary_accessions{
my ($self,@args) = @_;
$self->throw("hit get_secondary_accessions in interface definition - error");
}
=head2 division
Title : division
Usage :
Function: Get (and set, depending on the implementation) the divison for
a sequence.
Examples from GenBank are PLN (plants), PRI (primates), etc.
Example :
Returns : a string
Args :
=cut
sub division{
my ($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) = @_;
$self->throw("hit pid in interface definition - error");
}
=head2 get_dates
Title : get_dates
Usage :
Function: Get (and set, depending on the implementation) the dates the
databank entry specified for the sequence
An implementation that allows modification of this array
property should provide the methods add_date and
remove_dates, with obvious purpose.
Example :
Returns : an array of strings
Args :
=cut
sub get_dates{
my ($self,@args) = @_;
$self->throw("hit get_dates in interface definition - error");
}
=head2 seq_version
Title : seq_version
Usage :
Function: Get (and set, depending on the implementation) the version string
of the sequence.
Example :
Returns : a string
Args :
Note : this differs from Bio::PrimarySeq version() in that this explicitly
refers to the sequence record version one would find in a typical
sequence file. It is up to the implementation whether this is set
separately or falls back to the more generic Bio::Seq::version()
=cut
sub seq_version{
my ($self,@args) = @_;
$self->throw("hit seq_version in interface definition - error");
}
=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;