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SENDU / bioperl-1.5.2_004-RCc / Bio / DB / GFF / Aggregator / coding.pm 

            

              
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=head1 NAME
Bio::DB::GFF::Aggregator::coding -- The Coding Region Aggregator
=head1 SYNOPSIS
  use Bio::DB::GFF;
  # Open the sequence database
  my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                   -dsn     => 'dbi:mysql:elegans42',
                                   -aggregator => ['coding'],
                                 );
 ------------------------------------------------------------------------
 Aggregator method: coding
 Main method:       mRNA
 Sub methods:       CDS
 ------------------------------------------------------------------------
=head1 DESCRIPTION
Bio::DB::GFF::Aggregator::coding aggregates "CDS" features into a
feature called "coding" and was written to be compatible with the
Sequence Ontology canonical gene.  The CDS features are expected to
belong to a parent of type "mRNA," but the aggregator will work even
if this isn't the case.
=cut
package Bio::DB::GFF::Aggregator::coding;
use strict;
use base qw(Bio::DB::GFF::Aggregator);
=head2 method
 Title   : method
 Usage   : $aggregator->method
 Function: return the method for the composite object
 Returns : the string "coding"
 Args    : none
 Status  : Public
=cut
sub method { 'coding' }
=head2 part_names
 Title   : part_names
 Usage   : $aggregator->part_names
 Function: return the methods for the sub-parts
 Returns : the list (CDS cds)
 Args    : none
 Status  : Public
=cut
sub part_names {
  return qw(CDS cds);
}
=head2 main_name
 Title   : main_name
 Usage   : $aggregator->main_name
 Function: return the method for the main component
 Returns : the string "mRNA"
 Args    : none
 Status  : Public
=cut
sub main_name {
  return 'mRNA';
}
1;
__END__
=head1 BUGS
None reported.
=head1 SEE ALSO
L<Bio::DB::GFF>, L<Bio::DB::GFF::Aggregator>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut