lib/Bio/DB/GFF/Aggregator/orf.pm

   1 =head1 NAME
   2
   3 Bio::DB::GFF::Aggregator::orf -- An aggregator for orf regions
   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 => ['orf','clone'],
  13                                  );
  14
  15  ---------------------------
  16  Aggregator method: orf
  17  Main method:       -none-
  18  Sub methods:       ORF
  19  ---------------------------
  20
  21 =head1 DESCRIPTION
  22
  23 Bio::DB::GFF::Aggregator::orf was written to work with the "cds"
  24 glyph.  GFF files.  It aggregates raw "ORF" features into "coding"
  25 features. This is basically identical to the "coding" aggregator,
  26 except that it looks for features of type "ORF" rather than "cds".
  27
  28 =cut
  29
  30 package Bio::DB::GFF::Aggregator::orf;
  31
  32 use strict;
  33 use Bio::DB::GFF::Aggregator;
  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 "orf"
  43  Args    : none
  44  Status  : Public
  45
  46 =cut
  47
  48 sub method { 'orf' }
  49
  50 # sub require_whole_object { 1; }
  51
  52 =head2 part_names
  53
  54  Title   : part_names
  55  Usage   : $aggregator->part_names
  56  Function: return the methods for the sub-parts
  57  Returns : the list "CDS"
  58  Args    : none
  59  Status  : Public
  60
  61 =cut
  62
  63 sub part_names {
  64   return qw(ORF);
  65 }
  66
  67 1;
  68 __END__
  69
  70 =head1 BUGS
  71
  72 None reported.
  73
  74
  75 =head1 SEE ALSO
  76
  77 L<Bio::DB::GFF>, L<Bio::DB::GFF::coding>,
  78 L<Bio::DB::GFF::Aggregator>, L<Bio::Graphics::Glyph::cds>
  79
  80
  81 =head1 AUTHOR
  82
  83 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
  84
  85 Copyright (c) 2001 Cold Spring Harbor Laboratory.
  86
  87 This library is free software; you can redistribute it and/or modify
  88 it under the same terms as Perl itself.
  89
  90 =cut
  91