Raw content of Bio::DB::GFF::Adaptor::dbi::mysqlace
<![CDATA[package Bio::DB::GFF::Adaptor::dbi::mysqlace;
=head1 NAME
Bio::DB::GFF::Adaptor::dbi::mysqlace -- Unholy union between mysql GFF database and acedb database
=head1 SYNOPSIS
Pending
See L<Bio::DB::GFF> and L<Bio::DB::GFF::Adaptor::dbi::mysql>
=head1 SEE ALSO
L<Bio::DB::GFF>, L<bioperl>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
Copyright (c) 2002 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
use strict;
use Bio::DB::GFF::Adaptor::dbi::mysql;
use Bio::DB::GFF::Adaptor::ace;
use Bio::DB::GFF::Util::Rearrange; # for rearrange()
use vars '@ISA';
@ISA = qw(Bio::DB::GFF::Adaptor::dbi::mysql Bio::DB::GFF::Adaptor::ace);
# Create a new Bio::DB::GFF::Adaptor::dbi object
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
my ($dna_db,$acedb) = rearrange([[qw(DNADB DNA FASTA FASTA_DIR)],'ACEDB'],@_);
if ($dna_db) {
if (!ref($dna_db)) {
require Bio::DB::Fasta;
my $fasta_dir = $dna_db;
$dna_db = Bio::DB::Fasta->new($fasta_dir);
$dna_db or $class->throw("new(): Failed to create new Bio::DB::Fasta from files in $fasta_dir");
} else {
$dna_db->isa('Bio::DB::Fasta') or $class->throw("new(): $dna_db is not a Bio::DB::Fasta object");
}
$self->dna_db($dna_db);
}
if ($acedb) {
$acedb->isa('Ace') or $class->throw("$acedb is not an acedb accessor object");
$self->acedb($acedb);
}
$self;
}
=head2 freshen_ace
Title : freshen
Usage : $flag = Bio::DB::GFF->freshen_ace;
Function: Refresh internal acedb handle
Returns : flag if correctly freshened
Args : none
Status : Public
ACeDB has an annoying way of timing out, leaving dangling database
handles. This method will invoke the ACeDB reopen() method, which
causes dangling handles to be refreshed. It has no effect if you are
not using ACeDB to create ACeDB objects.
=cut
#########################
# Moved from mysqlopt.pm
#########################
sub make_object {
my $self = shift;
my ($class,$name,$start,$stop) = @_;
if (my $db = $self->acedb) {
# for Notes we just return a text, no database associated
return $class->new(Text=>$name) if $class eq 'Note';
# for homols, we create the indicated Protein or Sequence object
# then generate a bogus Homology object (for future compatability??)
if ($start ne '') {
require Ace::Sequence::Homol;
return Ace::Sequence::Homol->new_homol($class,$name,$db,$start,$stop);
}
# General case:
my $obj = $db->class->new($class=>$name,$self->acedb);
return $obj if defined $obj;
# Last resort, return a Text
return $class->new(Text=>$name);
}
return $self->SUPER::make_object($class,$name,$start,$stop);
}
sub get_dna {
my $self = shift;
my ($ref,$start,$stop,$class) = @_;
my $dna_db = $self->dna_db or return $self->SUPER::get_dna(@_);
return $dna_db->seq($ref,$start,$stop,$class);
}
1;
]]>