Summary

Bio::DB::SeqFeature::Store::bdb - fetch and store objects from a BerkeleyDB

Package variables

Included modules

Inherit

Bio::DB::SeqFeature::Store

Synopsis

No synopsis!

Description

No description!

Methods

Methods description

None available.

Methods code

sub init {

  my $self          = shift;
  my ($directory,
      $is_temporary) = rearrange([['DSN','DIR','DIRECTORY'],
				 ['TMP','TEMP','TEMPORARY']
				 ],@_);
  $directory ||= $is_temporary ? File::Spec->tmpdir : '.';
  $directory = tempdir(__PACKAGE__.'_XXXXXX',TMPDIR=>1,CLEANUP=>1,DIR=>$directory) if $is_temporary;
  -d $directory && -w _ or $self->throw("Can't write into the directory $directory");
  $self->default_settings;
  $self->directory($directory);
  $self->temporary($is_temporary);

  my %h;
  tie (%h,'DB_File',$self->path,O_RDWR|O_CREAT,0666,$DB_HASH) or $self->throw("Couldn't tie: $!");
  $self->db(\%h);
  $h{'.next_id'} ||= 1;

}

sub _store {

  my $self = shift;
  my $indexed = shift;
  my $db   = $self->db;
  my $count = 0;
  for my $obj (@_) {
    my $primary_id = $obj->primary_id;
    $primary_id    = $db->{'.next_id'}++ unless defined $primary_id;
    $db->{$primary_id} = $self->freeze($obj);
    $obj->primary_id($primary_id);
    $count++;
  }
  $count;

}

sub _update {

  my $self = shift;
  my ($object,$primary_id) = @_;
  my $db = $self->db;
  $self->throw("$object is not in database") unless exists $db->{$primary_id};
  $db->{$primary_id} = $self->freeze($object);

}

sub _fetch {

  my $self = shift;
  my $id   = shift;
  my $db = $self->db;
  my $obj = $self->thaw($db->{$id},$id);
  $obj;

}

sub db {

  my $self = shift;
  my $d = $self->setting('db');
  $self->setting(db=>shift) if @_;
  $d;

}

sub directory {

  my $self = shift;
  my $d = $self->setting('directory');
  $self->setting(directory=>shift) if @_;
  $d;

}

sub temporary {

  my $self = shift;
  my $d = $self->setting('temporary');
  $self->setting(temporary=>shift) if @_;
  $d;

}

sub path {

  my $self = shift;
  return $self->directory .'/' . 'feature.bdb';

}

sub DESTROY {

  my $self = shift;
  my $db   = $self->db;
  warn "CLEANING UP";
  untie %$db;
  rmtree($self->directory,0,1) if $self->temporary;

}

General documentation