Bio::DB::SeqFeature::* move namespace into its own distribution.
[bioperl-live.git] / lib / Bio / DB / GFF / Aggregator / coding.pm
blob0e9e367bf9de969c4884d9b32c4cd7d880efdfe4
1 =head1 NAME
3 Bio::DB::GFF::Aggregator::coding -- The Coding Region Aggregator
5 =head1 SYNOPSIS
7 use Bio::DB::GFF;
9 # Open the sequence database
10 my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
11 -dsn => 'dbi:mysql:elegans42',
12 -aggregator => ['coding'],
15 ------------------------------------------------------------------------
16 Aggregator method: coding
17 Main method: mRNA
18 Sub methods: CDS
19 ------------------------------------------------------------------------
21 =head1 DESCRIPTION
23 Bio::DB::GFF::Aggregator::coding aggregates "CDS" features into a
24 feature called "coding" and was written to be compatible with the
25 Sequence Ontology canonical gene. The CDS features are expected to
26 belong to a parent of type "mRNA," but the aggregator will work even
27 if this isn't the case.
29 =cut
31 package Bio::DB::GFF::Aggregator::coding;
33 use strict;
35 use base qw(Bio::DB::GFF::Aggregator);
37 =head2 method
39 Title : method
40 Usage : $aggregator->method
41 Function: return the method for the composite object
42 Returns : the string "coding"
43 Args : none
44 Status : Public
46 =cut
48 sub method { 'coding' }
50 =head2 part_names
52 Title : part_names
53 Usage : $aggregator->part_names
54 Function: return the methods for the sub-parts
55 Returns : the list (CDS cds)
56 Args : none
57 Status : Public
59 =cut
61 sub part_names {
62 return qw(CDS cds);
65 =head2 main_name
67 Title : main_name
68 Usage : $aggregator->main_name
69 Function: return the method for the main component
70 Returns : the string "mRNA"
71 Args : none
72 Status : Public
74 =cut
76 sub main_name {
77 return 'mRNA';
81 __END__
83 =head1 BUGS
85 None reported.
88 =head1 SEE ALSO
90 L<Bio::DB::GFF>, L<Bio::DB::GFF::Aggregator>
92 =head1 AUTHOR
94 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
96 Copyright (c) 2001 Cold Spring Harbor Laboratory.
98 This library is free software; you can redistribute it and/or modify
99 it under the same terms as Perl itself.
101 =cut