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

   1 =head1 NAME
   2
   3 Bio::DB::GFF::Aggregator::match -- Match 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 => ['match'],
  13                                  );
  14
  15  -------------------------------------------------
  16  Aggregator method: match
  17  Main method:       match
  18  Sub methods:       similarity HSP
  19  -------------------------------------------------
  20
  21 =head1 DESCRIPTION
  22
  23 This aggregator is used for Sequence Ontology-compatible gapped
  24 alignments, in which there is a single top-level alignment called
  25 "match" and a series of subalignments called either "similarity" or
  26 "HSP".
  27
  28 Also see the "alignment" aggregator.
  29
  30 =cut
  31
  32 package Bio::DB::GFF::Aggregator::match;
  33
  34 use strict;
  35
  36 use base qw(Bio::DB::GFF::Aggregator);
  37
  38 =head2 method
  39
  40  Title   : method
  41  Usage   : $aggregator->method
  42  Function: return the method for the composite object
  43  Returns : the string "match"
  44  Args    : none
  45  Status  : Public
  46
  47 =cut
  48
  49 sub method { 'match' }
  50
  51 =head2 part_names
  52
  53  Title   : part_names
  54  Usage   : $aggregator->part_names
  55  Function: return the methods for the sub-parts
  56  Returns : the list "similarity", "HSP"
  57  Args    : none
  58  Status  : Public
  59
  60 =cut
  61
  62 sub part_names {
  63   return qw(similarity HSP);
  64 }
  65
  66 =head2 main_name
  67
  68  Title   : main_name
  69  Usage   : $aggregator->main_name
  70  Function: return the method for the main component
  71  Returns : the string "match"
  72  Args    : none
  73  Status  : Public
  74
  75 =cut
  76
  77 sub main_name {
  78   return 'match';
  79 }
  80
  81 sub require_whole_object {1}
  82
  83 1;
  84 __END__
  85
  86 =head1 BUGS
  87
  88 None reported.
  89
  90
  91 =head1 SEE ALSO
  92
  93 L<Bio::DB::GFF>, L<Bio::DB::GFF::Aggregator>
  94
  95 =head1 AUTHOR
  96
  97 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
  98
  99 Copyright (c) 2001 Cold Spring Harbor Laboratory.
 100
 101 This library is free software; you can redistribute it and/or modify
 102 it under the same terms as Perl itself.
 103
 104 =cut
 105