————#
#
# BioPerl module for FAST::Bio::DB::SeqI.pm
#
# 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
FAST::Bio::DB::SeqI - Abstract Interface for Sequence databases
=head1 SYNOPSIS
# get a FAST::Bio::DB::SeqI somehow
$seq = $seqdb->get_Seq_by_id('some-id');
$seq = $seqdb->get_Seq_by_acc('some-accession-number');
@ids = $seqdb->get_all_ids();
$stream = $seqdb->get_PrimarySeq_stream();
while((my $seq = $stream->next_seq()) {
# $seq is a PrimarySeqI compliant object
}
=head1 DESCRIPTION
Abstract interface for a sequence database
=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:
=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
FAST::Bio::DB::SeqI;
use
strict;
=head1 Methods inherieted from FAST::Bio::DB::RandomAccessI
=head2 get_Seq_by_id
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a FAST::Bio::Seq object by its name
Returns : a FAST::Bio::Seq object
Args : the id (as a string) of a sequence
Throws : "id does not exist" exception
=cut
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a FAST::Bio::Seq object by accession number
Returns : A FAST::Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
=cut
=head1 Methods [that were] specific for FAST::Bio::DB::SeqI
=head2 get_PrimarySeq_stream
Title : get_PrimarySeq_stream
Usage : $stream = get_PrimarySeq_stream
Function: Makes a FAST::Bio::SeqIO compliant object
which provides a single method, next_seq
Returns : FAST::Bio::SeqIO
Args : none
=cut
sub
get_PrimarySeq_stream{
my
(
$self
,
@args
) =
@_
;
$self
->throw(
"Object did not provide a PrimarySeq stream object"
);
}
=head2 get_all_primary_ids
Title : get_all_ids
Usage : @ids = $seqdb->get_all_primary_ids()
Function: gives an array of all the primary_ids of the
sequence objects in the database. These
maybe ids (display style) or accession numbers
or something else completely different - they
*are not* meaningful outside of this database
implementation.
Example :
Returns : an array of strings
Args : none
=cut
sub
get_all_primary_ids{
my
(
$self
,
@args
) =
@_
;
$self
->throw(
"Object did not provide a get_all_ids method"
);
}
=head2 get_Seq_by_primary_id
Title : get_Seq_by_primary_id
Usage : $seq = $db->get_Seq_by_primary_id($primary_id_string);
Function: Gets a FAST::Bio::Seq object by the primary id. The primary
id in these cases has to come from $db->get_all_primary_ids.
There is no other way to get (or guess) the primary_ids
in a database.
The other possibility is to get FAST::Bio::PrimarySeqI objects
via the get_PrimarySeq_stream and the primary_id field
on these objects are specified as the ids to use here.
Returns : A FAST::Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
=cut
sub
get_Seq_by_primary_id {
my
(
$self
,
@args
) =
@_
;
$self
->throw(
"Abstract database call of get_Seq_by_primary_id. Your database has not implemented this method!"
);
}
1;