branch-1-6/Bio/DB/GFF/Adaptor/ace.pm

   1 package Bio::DB::GFF::Adaptor::ace;
   2
   3 =head1 NAME
   4
   5 Bio::DB::GFF::Adaptor::ace -- ace interface (for multiple inheritance)
   6
   7 =head1 SYNOPSIS
   8
   9 Pending
  10
  11 See L<Bio::DB::GFF> and L<Bio::DB::GFF::Adaptor::dbi::mysql>
  12
  13 =head1 SEE ALSO
  14
  15 L<Bio::DB::GFF>, L<bioperl>
  16
  17 =head1 AUTHOR
  18
  19 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
  20
  21 Copyright (c) 2002 Cold Spring Harbor Laboratory.
  22
  23 This library is free software; you can redistribute it and/or modify
  24 it under the same terms as Perl itself.
  25
  26 =cut
  27
  28 use strict;
  29 use Ace;
  30 use Bio::DB::GFF::Util::Rearrange; # for rearrange()
  31
  32 sub dna_db      {
  33   my $self = shift;
  34   my $d = $self->{dna_db};
  35   $self->{dna_db} = shift if @_;
  36   $d;
  37 }
  38 sub acedb      {
  39   my $self = shift;
  40   my $d = $self->{acedb};
  41   $self->{acedb} = shift if @_;
  42   $d;
  43 }
  44
  45 =head2 freshen_ace
  46
  47  Title   : freshen
  48  Usage   : $flag = Bio::DB::GFF->freshen_ace;
  49  Function: Refresh internal acedb handle
  50  Returns : flag if correctly freshened
  51  Args    : none
  52  Status  : Public
  53
  54 ACeDB has an annoying way of timing out, leaving dangling database
  55 handles.  This method will invoke the ACeDB reopen() method, which
  56 causes dangling handles to be refreshed.  It has no effect if you are
  57 not using ACeDB to create ACeDB objects.
  58
  59 =cut
  60
  61 sub freshen_ace {
  62   my $acedb = shift->acedb or return;
  63   $acedb->reopen();
  64 }
  65
  66 1;