Raw content of Bio::DB::UpdateableSeqI
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# $Id: UpdateableSeqI.pm,v 1.6 2002/12/01 00:05:19 jason Exp $
#
# BioPerl module for Bio::DB::UpdateableSeqI
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
#
# _history
# June 18, 2000 - module begun
#
# POD Doc - main docs before code
=head1 NAME
Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences.
=head1 SYNOPSIS
# get a Bio::DB::UpdateableSeqI somehow
eval {
my ( @updatedseqs, @newseqs, @deadseqs);
my $seq = $db->get_Seq_by_id('ROA1_HUMAN');
$seq->desc('a new description');
push @updatedseqs, $seq;
$db->write_seq(\@updatedseqs, \@newseqs, \@deadseqs);
};
if( $@ ) {
print STDERR "an error when trying to write seq : $@\n";
}
=head1 DESCRIPTION
This module seeks to provide a simple method for pushing sequence changes
back to a Sequence Database - which can be an SQL compliant database, a file
based database, AceDB, etc.
=head1 AUTHOR
Jason Stajich E<lt>jason@bioperl.orgE<gt>
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
#Lets start some code
package Bio::DB::UpdateableSeqI;
use strict;
use vars qw( @ISA );
use Bio::DB::SeqI;
@ISA = qw(Bio::DB::SeqI);
=head2 write_seq
Title : write_seq
Usage : write_seq(\@updatedseqs, \@addedseqs, \@deadseqs)
Function: updates sequences in first array,
adds sequences in the second array,
and removes sequences in the third array.
Example :
Returns :
Args : arrays of sequence objects that must be obtained from
Bio::DB::UpdateableSeqI.
=cut
sub write_seq {
my ($self) = @_;
$self->throw("Abstract database call of write_seq. Your database has not implemented this method!");
}
=head2 _add_seq
Title : _add_seq
Usage : _add_seq($seq)
Function: Adds a new sequence
Example :
Returns : will throw an exception if
sequences accession number already exists
Args : a new seq object - should have an accession number
=cut
sub _add_seq {
my ($self ) = @_;
$self->throw("Abstract database call of _add_seq. Your database has not implemented this method!");
}
=head2 _remove_seq
Title : _remove_seq
Usage : _remove_seq($seq)
Function: Removes an existing sequence
Example :
Returns : will throw an exception if
sequence does not exists for the primary_id
Args : a seq object that was retrieved from Bio::DB::UpdateableSeqI
=cut
sub _remove_seq {
my ($self) = @_;
$self->throw("Abstract database call of _remove_seq. Your database has not implemented this method!");
}
=head2 _update_seq
Title : _update_seq
Usage : _update_seq($seq)
Function: Updates a sequence
Example :
Returns : will throw an exception if
sequence is out of sync from expected val.
Args : a seq object that was retrieved from Bio::DB::UpdateableSeqI
=cut
sub _update_seq {
my ($self) = @_;
$self->throw("Abstract database call of _update_seq. Your database has not implemented this method!");
}
=head1 Methods inherieted from 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 Bio::Seq object by its name
Returns : a 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 Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
=cut
=head1 Methods inheirited from Bio::DB::SeqI
=head2 get_PrimarySeq_stream
Title : get_PrimarySeq_stream
Usage : $stream = get_PrimarySeq_stream
Function: Makes a Bio::DB::SeqStreamI compliant object
which provides a single method, next_primary_seq
Returns : Bio::DB::SeqStreamI
Args : none
=cut
=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
=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 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 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 Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
=cut
1;
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