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

  my ($delete,$db,$key,$id) = @_;
  if ($delete) {
    tied(%$db)->del_dup($key,$id);
  } else {
    $db->{$key} = $id;
  }
}

# these methods return pointers to....
# the database that stores serialized objects
sub db {
  my $self = shift;
  my $d = $self->setting('db');
  $self->setting(db=>shift) if @_;
  $d;
}

sub parentage_db {
  my $self = shift;
  my $d = $self->setting('parentage_db');
  $self->setting(parentage_db=>shift) if @_;
  $d;
}

# the Bio::DB::Fasta object
sub dna_db {
  my $self = shift;
  my $d = $self->setting('dna_db');
  $self->setting(dna_db=>shift) if @_;
  $d;
}

# the specialized notes database
sub notes_db {
  my $self = shift;
  my $d = $self->setting('notes_db');
  $self->setting(notes_db=>shift) if @_;
  $d;
}

# the is_indexed_db 
sub is_indexed_db {
  my $self = shift;
  my $d = $self->setting('is_indexed_db');
  $self->setting(is_indexed_db=>shift) if @_;
  $d;
}

# The indicated index berkeley db
sub index_db {
  my $self = shift;
  my $index_name = shift;
  my $d = $self->setting($index_name);
  $self->setting($index_name=>shift) if @_;
  $d;
}


sub _mtime {
  my $file = shift;
  my @stat = stat($file);
  return $stat[9];
}

# return names of all the indexes
sub _index_files {
  return qw(names types locations attributes is_indexed);
}

# the directory in which we store our indexes
sub directory {
  my $self = shift;
  my $d = $self->setting('directory');
  $self->setting(directory=>shift) if @_;
  $d;
}

# flag indicating that we are a temporary database
sub temporary {
  my $self = shift;
  my $d = $self->setting('temporary');
  $self->setting(temporary=>shift) if @_;
  $d;
}

sub _permissions {
  my $self = shift;
  my $d = $self->setting('permissions') or return;
  if (@_) {
    my ($write,$create) = @_;
    $self->setting(permissions=>[$write,$create]);
  }
  @$d;
}

# file name utilities...
sub _qualify {
  my $self = shift;
  my $file = shift;
  return $self->directory .'/' . $file;
}

sub _features_path {
  shift->_qualify('features.bdb');
}

sub _parentage_path {
  shift->_qualify('parentage.bdb');
}

sub _type_path {
  shift->_qualify('types.idx');
}

sub _location_path {
  shift->_qualify('locations.idx');
}

sub _attribute_path {
  shift->_qualify('attributes.idx');
}