branch-1-6/Bio/DB/GFF/Aggregator/coding.pm

   1 =head1 NAME
   2
   3 Bio::DB::GFF::Aggregator::coding -- The Coding Region Aggregator
   4
   5 =head1 SYNOPSIS
   6
   7   use Bio::DB::GFF;
   8
   9   # Open the sequence database
  10   my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
  11                                    -dsn     => 'dbi:mysql:elegans42',
  12                                    -aggregator => ['coding'],
  13                                  );
  14
  15  ------------------------------------------------------------------------
  16  Aggregator method: coding
  17  Main method:       mRNA
  18  Sub methods:       CDS
  19  ------------------------------------------------------------------------
  20
  21 =head1 DESCRIPTION
  22
  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.
  28
  29 =cut
  30
  31 package Bio::DB::GFF::Aggregator::coding;
  32
  33 use strict;
  34
  35 use base qw(Bio::DB::GFF::Aggregator);
  36
  37 =head2 method
  38
  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
  45
  46 =cut
  47
  48 sub method { 'coding' }
  49
  50 =head2 part_names
  51
  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
  58
  59 =cut
  60
  61 sub part_names {
  62   return qw(CDS cds);
  63 }
  64
  65 =head2 main_name
  66
  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
  73
  74 =cut
  75
  76 sub main_name {
  77   return 'mRNA';
  78 }
  79
  80 1;
  81 __END__
  82
  83 =head1 BUGS
  84
  85 None reported.
  86
  87
  88 =head1 SEE ALSO
  89
  90 L<Bio::DB::GFF>, L<Bio::DB::GFF::Aggregator>
  91
  92 =head1 AUTHOR
  93
  94 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
  95
  96 Copyright (c) 2001 Cold Spring Harbor Laboratory.
  97
  98 This library is free software; you can redistribute it and/or modify
  99 it under the same terms as Perl itself.
 100
 101 =cut
 102