comparison variant_effect_predictor/Bio/DB/UpdateableSeqI.pm @ 0:1f6dce3d34e0

Uploaded

0:1f6dce3d34e0

#
# $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 <[e-mail]>
#
# 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>[e-mail]<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:

    [e-mail]                   
    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;