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lib/Bio/DB/SeqFeature/Store/Loader.pm  view on Meta::CPAN

sub msg {
  my $self = shift;
  my @msg  = @_;
  return unless $self->verbose;
  print STDERR @msg;
}

=item loaded_ids

 my $ids    = $loader->loaded_ids;
 my $id_cnt = @$ids;

After performing a load, this returns an array ref containing all the
feature primary ids that were created during the load.

=cut

sub loaded_ids {
    my $self = shift;
    my @ids  = values %{$self->{load_data}{Local2GlobalID}}
                     if $self->{load_data};
    return \@ids;
}

=item local_ids

 my $ids    = $self->local_ids;
 my $id_cnt = @$ids;

After performing a load, this returns an array ref containing all the
load file IDs that were contained within the file just loaded.

=cut

sub local_ids {
    my $self = shift;
    my @ids  = keys %{$self->{load_data}{Local2GlobalID}}
                   if $self->{load_data};
    return \@ids;
}

=item time

 my $time = $loader->time

This method returns the current time in seconds, using Time::HiRes if available.

=cut

sub time {
  return Time::HiRes::time() if Time::HiRes->can('time');
  return time();
}

=item unescape

 my $unescaped = GFF3Loader::unescape($escaped)

This is an internal utility.  It is the same as CGI::Util::unescape,
but doesn't change pluses into spaces and ignores unicode escapes.

=cut

sub unescape {
    my $self = shift;
    my $todecode = shift;
    $todecode =~ s/%([0-9a-fA-F]{2})/chr hex($1)/ge;
    return $todecode;
}

sub DESTROY {
    my $self = shift;
    # Close filehandles, so temporal files can be properly deleted
    my $store = $self->store;
    if (   $store->isa('Bio::DB::SeqFeature::Store::memory')
	or $store->isa('Bio::DB::SeqFeature::Store::berkeleydb3')
	) {
      $store->private_fasta_file->close;

      if ($store->{fasta_db} && !$self->{no_close_fasta}) {
	while (my ($file, $fh) = each %{ $store->{fasta_db}->{fhcache} }) {
	  $fh->close;
	}
	$store->{fasta_db}->_close_index($store->{fasta_db}->{offsets});
      }
    }
    elsif ($store->isa('Bio::DB::SeqFeature::Store::DBI::SQLite')) {
      if (%DBI::installed_drh) {
	DBI->disconnect_all;
	%DBI::installed_drh = ();
      }
      undef $store->{dbh};
    }

    if (my $ld = $self->{temp_load}) {
	unlink $ld;
    }
}

1;
__END__

=back

=head1 BUGS

This is an early version, so there are certainly some bugs. Please
use the BioPerl bug tracking system to report bugs.

=head1 SEE ALSO

L<bioperl>,
L<Bio::DB::SeqFeature::Store>,
L<Bio::DB::SeqFeature::Segment>,
L<Bio::DB::SeqFeature::NormalizedFeature>,
L<Bio::DB::SeqFeature::Store::GFF3Loader>,
L<Bio::DB::SeqFeature::Store::DBI::mysql>,
L<Bio::DB::SeqFeature::Store::berkeleydb>

=head1 AUTHOR